From 02b65aac0c64142c2ea67972b1234386baa4aa07 Mon Sep 17 00:00:00 2001 From: Jeremy Date: Wed, 13 Nov 2024 14:53:48 -0800 Subject: [PATCH 01/17] Added pre-split script to remove problematic drugs --- .../broad_sanger/05a_remove_problem_drugs.py | 43 +++++++++++++++++++ ...e_datasets.py => 05b_separate_datasets.py} | 1 - build/broad_sanger/build_misc.sh | 8 +++- build/docker/Dockerfile.broad_sanger_omics | 3 +- 4 files changed, 51 insertions(+), 4 deletions(-) create mode 100644 build/broad_sanger/05a_remove_problem_drugs.py rename build/broad_sanger/{05_separate_datasets.py => 05b_separate_datasets.py} (99%) diff --git a/build/broad_sanger/05a_remove_problem_drugs.py b/build/broad_sanger/05a_remove_problem_drugs.py new file mode 100644 index 00000000..a240fc14 --- /dev/null +++ b/build/broad_sanger/05a_remove_problem_drugs.py @@ -0,0 +1,43 @@ +import gc +import polars as pl + + + +def main(): + + # Remove Problematic Drugs before Splitting Data + + # Load the datasets + all_drugs = pl.read_csv("broad_sanger_drugs.tsv", separator="\t") + all_experiments = pl.read_csv("broad_sanger_experiments.tsv", separator="\t") + + # Define the brd_list with lowercase entries for case-insensitive matching + brd_list = [ + 'brd-k03911514', + 'brd-k07442505', + 'brd-k13185470', + 'brd-k16130065', + 'brd-k20514654', + 'brd-k27188169', + 'brd-k55473186', + 'yl54', + 'brd-k58730230', + 'brd-k79669418', + 'brd-k99584050'] + + # Identify rows in all_drugs that match brd_list entries (case insensitive) + removed_drugs = all_drugs.filter(pl.col("chem_name").str.to_lowercase().is_in(brd_list)) + + # Store the improve_drug_id IDs of removed entries + improve_drug_id = removed_drugs["improve_drug_id"].to_list() + + # Remove these rows from all_drugs and all_experiments + all_drugs = all_drugs.filter(~pl.col("improve_drug_id").is_in(improve_drug_id)) + all_experiments = all_experiments.filter(~pl.col("improve_drug_id").is_in(improve_drug_id)) + + all_drugs.write_csv("broad_sanger_drugs.tsv", separator="\t") + all_experiments.write_csv("broad_sanger_experiments.tsv", separator="\t") + + +if __name__ == "__main__": + main() diff --git a/build/broad_sanger/05_separate_datasets.py b/build/broad_sanger/05b_separate_datasets.py similarity index 99% rename from build/broad_sanger/05_separate_datasets.py rename to build/broad_sanger/05b_separate_datasets.py index 9e99adc9..f4d5481d 100644 --- a/build/broad_sanger/05_separate_datasets.py +++ b/build/broad_sanger/05b_separate_datasets.py @@ -4,7 +4,6 @@ def main(): - datasets_to_process = ["CCLE", "CTRPv2", "PRISM", "GDSCv1", "GDSCv2", "FIMM", "gCSI", "NCI60"] omics_datatypes = ["transcriptomics","proteomics", "copy_number","mutations"] # csv samples_datatypes = ["samples"] #csv diff --git a/build/broad_sanger/build_misc.sh b/build/broad_sanger/build_misc.sh index 2fa847f1..d5896e98 100644 --- a/build/broad_sanger/build_misc.sh +++ b/build/broad_sanger/build_misc.sh @@ -4,8 +4,12 @@ set -euo pipefail trap 'echo "Error on or near line $LINENO while executing: $BASH_COMMAND"; exit 1' ERR cp /tmp/broad_sanger* . -echo "Running 05_separate_datasets.py..." -/opt/venv/bin/python 05_separate_datasets.py + +echo "Running 05a_remove_problem_drugs.py..." +/opt/venv/bin/python 05a_remove_problem_drugs.py + +echo "Running 05b_separate_datasets.py..." +/opt/venv/bin/python 05b_separate_datasets.py echo "Removing broad_sanger* files..." rm broad_sanger* diff --git a/build/docker/Dockerfile.broad_sanger_omics b/build/docker/Dockerfile.broad_sanger_omics index 2d4cbde8..43f4a428 100755 --- a/build/docker/Dockerfile.broad_sanger_omics +++ b/build/docker/Dockerfile.broad_sanger_omics @@ -34,7 +34,8 @@ ADD build/broad_sanger/build_samples.sh ./ ADD build/broad_sanger/build_omics.sh ./ ADD build/utils/* ./ ADD build/broad_sanger/build_misc.sh ./ -ADD build/broad_sanger/05_separate_datasets.py ./ +ADD build/broad_sanger/05a_remove_problem_drugs.py ./ +ADD build/broad_sanger/05b_separate_datasets.py ./ ADD build/broad_sanger/requirements.txt . ADD build/broad_sanger/omics_requirements.r . From 163000a2a824dd1359b052be64bdfca3e93cf4b8 Mon Sep 17 00:00:00 2001 From: Jeremy Date: Wed, 20 Nov 2024 15:58:23 -0800 Subject: [PATCH 02/17] SMILES moved to Canonical. IsoSMILES dropped --- build/beatAML/GetBeatAML.py | 125 ++++++++++++++------------- build/broad_sanger/03a-nci60Drugs.py | 6 +- build/mpnst/02_get_drug_data.R | 4 +- build/utils/pubchem_retrieval.py | 8 +- 4 files changed, 74 insertions(+), 69 deletions(-) diff --git a/build/beatAML/GetBeatAML.py b/build/beatAML/GetBeatAML.py index 5afdff8e..5bf94233 100755 --- a/build/beatAML/GetBeatAML.py +++ b/build/beatAML/GetBeatAML.py @@ -9,25 +9,25 @@ import argparse import time -def download_from_github(raw_url, save_path): - """ - Download a file from a raw GitHub URL and save to the specified path. - - Parameters - ---------- - raw_url : str - The raw GitHub URL pointing to the file to be downloaded. - save_path : str - The local path where the downloaded file will be saved. - - Returns - ------- - None - """ - response = requests.get(raw_url) - with open(save_path, 'wb') as f: - f.write(response.content) - return +# def download_from_github(raw_url, save_path): +# """ +# Download a file from a raw GitHub URL and save to the specified path. + +# Parameters +# ---------- +# raw_url : str +# The raw GitHub URL pointing to the file to be downloaded. +# save_path : str +# The local path where the downloaded file will be saved. + +# Returns +# ------- +# None +# """ +# response = requests.get(raw_url) +# with open(save_path, 'wb') as f: +# f.write(response.content) +# return def retrieve_figshare_data(url): """ @@ -178,14 +178,14 @@ def retrieve_drug_info(compound_name): properties = data["PropertyTable"]["Properties"][0] pubchem_id = properties.get('CID',np.nan) canSMILES = properties.get("CanonicalSMILES", np.nan) - isoSMILES = properties.get("IsomericSMILES", np.nan) + # isoSMILES = properties.get("IsomericSMILES", np.nan) InChIKey = properties.get("InChIKey", np.nan) formula = properties.get("MolecularFormula", np.nan) weight = properties.get("MolecularWeight", np.nan) - return pubchem_id, canSMILES, isoSMILES, InChIKey, formula, weight + return pubchem_id, canSMILES, InChIKey, formula, weight else: - return np.nan, np.nan, np.nan, np.nan, np.nan, np.nan + return np.nan, np.nan, np.nan, np.nan, np.nan def update_dataframe_with_pubchem(d_df): @@ -230,14 +230,14 @@ def update_dataframe_with_pubchem(d_df): if row['chem_name'] in data_dict and not all(pd.isna(val) for val in data_dict[row['chem_name']]): values = data_dict[row['chem_name']] else: - values = data_dict.get(row['other_name'], (np.nan, np.nan, np.nan, np.nan, np.nan, np.nan)) + values = data_dict.get(row['other_name'], (np.nan, np.nan, np.nan, np.nan, np.nan)) d_df.at[idx, 'pubchem_id'] = values[0] d_df.at[idx, "canSMILES"] = values[1] - d_df.at[idx, "isoSMILES"] = values[2] - d_df.at[idx, "InChIKey"] = values[3] - d_df.at[idx, "formula"] = values[4] - d_df.at[idx, "weight"] = values[5] + # d_df.at[idx, "isoSMILES"] = values[2] + d_df.at[idx, "InChIKey"] = values[2] + d_df.at[idx, "formula"] = values[3] + d_df.at[idx, "weight"] = values[4] return d_df @@ -250,24 +250,24 @@ def merge_drug_info(d_df,drug_map): d_df : pd.DataFrame Main drug dataframe containing drug-related columns. drug_map : pd.DataFrame - Mapping dataframe containing drug information and the column 'isoSMILES'. + Mapping dataframe containing drug information and the column 'canSMILES'. Returns ------- pd.DataFrame The merged dataframe containing combined drug information. """ - print(d_df['isoSMILES'].dtype, drug_map['isoSMILES'].dtype) - d_df['isoSMILES'] = d_df['isoSMILES'].astype(str) - drug_map['isoSMILES'] = drug_map['isoSMILES'].astype(str) - result_df = d_df.merge(drug_map[['isoSMILES', 'improve_drug_id']], on='isoSMILES', how='left') + # print(d_df['isoSMILES'].dtype, drug_map['isoSMILES'].dtype) + d_df['canSMILES'] = d_df['canSMILES'].astype(str) + drug_map['canSMILES'] = drug_map['canSMILES'].astype(str) + result_df = d_df.merge(drug_map[['canSMILES', 'improve_drug_id']], on='canSMILES', how='left') return result_df def format_drug_map(drug_map_path): """ Format and clean up the drug mapping file. - Reads a drug map file, removes duplicates based on the 'isoSMILES' column, + Reads a drug map file, removes duplicates based on the 'canSMILES' column, and returns the cleaned dataframe. Parameters @@ -282,11 +282,11 @@ def format_drug_map(drug_map_path): """ if drug_map_path: drug_map = pd.read_csv(drug_map_path, sep = "\t") - drug_map = drug_map.drop_duplicates(subset='isoSMILES', keep='first') + drug_map = drug_map.drop_duplicates(subset='canSMILES', keep='first') else: drug_map = pd.DataFrame(columns=[ - 'improve_drug_id', 'chem_name', 'pubchem_id', 'canSMILES', - 'isoSMILES', 'InChIKey', 'formula', 'weight' + 'improve_drug_id', 'chem_name', 'pubchem_id', + 'canSMILES', 'InChIKey', 'formula', 'weight' ]) return drug_map @@ -316,7 +316,7 @@ def format_drug_df(drug_path): def add_improve_id(previous_df, new_df): """ - Add 'improve_drug_id' to the new dataframe based on unique 'isoSMILES' not present in the previous dataframe. + Add 'improve_drug_id' to the new dataframe based on unique 'canSMILES' not present in the previous dataframe. Parameters ---------- @@ -335,16 +335,16 @@ def add_improve_id(previous_df, new_df): max_id = max(id_list) if id_list else 0 else: max_id = 0 - # Identify isoSMILES in the new dataframe that don't exist in the old dataframe - unique_new_smiles = set(new_df['isoSMILES']) - set(previous_df['isoSMILES']) - # Identify rows in the new dataframe with isoSMILES that are unique and where improve_drug_id is NaN - mask = (new_df['isoSMILES'].isin(unique_new_smiles)) & (new_df['improve_drug_id'].isna()) + # Identify canSMILES in the new dataframe that don't exist in the old dataframe + unique_new_smiles = set(new_df['canSMILES']) - set(previous_df['canSMILES']) + # Identify rows in the new dataframe with canSMILES that are unique and where improve_drug_id is NaN + mask = (new_df['canSMILES'].isin(unique_new_smiles)) & (new_df['improve_drug_id'].isna()) id_map = {} for smiles in unique_new_smiles: max_id += 1 id_map[smiles] = f"SMI_{max_id}" - # Apply the mapping to the new dataframe for rows with unique isoSMILES and NaN improve_drug_id - new_df.loc[mask, 'improve_drug_id'] = new_df['isoSMILES'].map(id_map) + # Apply the mapping to the new dataframe for rows with unique canSMILES and NaN improve_drug_id + new_df.loc[mask, 'improve_drug_id'] = new_df['canSMILES'].map(id_map) return new_df @@ -541,7 +541,7 @@ def generate_drug_list(drug_map_path,drug_path): d_res = add_improve_id(drug_map, d_res) #Drug Data #print(d_res) - drug_res = d_res[["improve_drug_id","chem_name","pubchem_id","formula","weight","InChIKey","canSMILES","isoSMILES"]] + drug_res = d_res[["improve_drug_id","chem_name","pubchem_id","formula","weight","InChIKey","canSMILES"]] drug_res = drug_res.drop_duplicates() drug_res.to_csv("/tmp/beataml_drugs.tsv",sep="\t", index=False) @@ -587,7 +587,12 @@ def generate_drug_list(drug_map_path,drug_path): # 'syn32533104', # 'syn32529921', 'syn26642974', - 'syn26427390' + 'syn26427390', + 'syn64126458', + 'syn64126462', + 'syn64126463', + 'syn64126464', + 'syn64126468' ] print("Downloading Files from Synapse") for entity_id in entity_ids: @@ -597,13 +602,13 @@ def generate_drug_list(drug_map_path,drug_path): #gene_url = "https://figshare.com/ndownloader/files/40576109?private_link=525f7777039f4610ef47" #entrez_map_file = retrieve_figshare_data(gene_url) - additional_mapping_url = "https://github.com/biodev/beataml2.0_data/raw/main/beataml_waves1to4_sample_mapping.xlsx" + # additional_mapping_url = "https://github.com/biodev/beataml2.0_data/raw/main/beataml_waves1to4_sample_mapping.xlsx" sample_mapping_file = "beataml_waves1to4_sample_mapping.xlsx" - download_from_github(additional_mapping_url, sample_mapping_file) + # download_from_github(additional_mapping_url, sample_mapping_file) - supplementary_url = 'https://ars.els-cdn.com/content/image/1-s2.0-S1535610822003129-mmc2.xlsx' + # supplementary_url = 'https://ars.els-cdn.com/content/image/1-s2.0-S1535610822003129-mmc2.xlsx' supplimentary_file = '1-s2.0-S1535610822003129-mmc2.xlsx' - download_from_github(supplementary_url, supplimentary_file) + # download_from_github(supplementary_url, supplimentary_file) if args.samples: @@ -619,9 +624,9 @@ def generate_drug_list(drug_map_path,drug_path): else: print("Drug File Provided. Proceeding with build.") original_drug_file = "beataml_wv1to4_raw_inhibitor_v4_dbgap.txt" - original_drug_url = "https://github.com/biodev/beataml2.0_data/raw/main/beataml_wv1to4_raw_inhibitor_v4_dbgap.txt" - download_from_github(original_drug_url, original_drug_file) - generate_drug_list(args.drugFile, original_drug_file) ##this doesn't exist, need to add + # original_drug_url = "https://github.com/biodev/beataml2.0_data/raw/main/beataml_wv1to4_raw_inhibitor_v4_dbgap.txt" + # download_from_github(original_drug_url, original_drug_file) + generate_drug_list(args.drugFile, original_drug_file) if args.omics: if args.genes is None or args.curSamples is None: print('Cannot process omics without sample mapping and gene mapping files') @@ -629,16 +634,16 @@ def generate_drug_list(drug_map_path,drug_path): else: improve_map_file = args.curSamples transcriptomics_file = "beataml_waves1to4_counts_dbgap.txt" #"beataml_waves1to4_norm_exp_dbgap.txt" ##this is the wrong file, these are the normalize values - transcriptomics_url = "https://github.com/biodev/beataml2.0_data/raw/main/beataml_waves1to4_counts_dbgap.txt" #"https://github.com/biodev/beataml2.0_data/raw/main/beataml_waves1to4_norm_exp_dbgap.txt" - download_from_github(transcriptomics_url, transcriptomics_file) + # transcriptomics_url = "https://github.com/biodev/beataml2.0_data/raw/main/beataml_waves1to4_counts_dbgap.txt" #"https://github.com/biodev/beataml2.0_data/raw/main/beataml_waves1to4_norm_exp_dbgap.txt" + # download_from_github(transcriptomics_url, transcriptomics_file) mutations_file = "beataml_wes_wv1to4_mutations_dbgap.txt" - mutations_url = "https://github.com/biodev/beataml2.0_data/raw/main/beataml_wes_wv1to4_mutations_dbgap.txt" - download_from_github(mutations_url, mutations_file) + # mutations_url = "https://github.com/biodev/beataml2.0_data/raw/main/beataml_wes_wv1to4_mutations_dbgap.txt" + # download_from_github(mutations_url, mutations_file) mutation_map_file = "beataml_waves1to4_sample_mapping.xlsx" - mutation_map_url = "https://github.com/biodev/beataml2.0_data/raw/main/beataml_waves1to4_sample_mapping.xlsx" - download_from_github(mutation_map_url, mutation_map_file) + # mutation_map_url = "https://github.com/biodev/beataml2.0_data/raw/main/beataml_waves1to4_sample_mapping.xlsx" + # download_from_github(mutation_map_url, mutation_map_file) # New Transcriptomics Data print("Starting Transcriptomics Data") ##first run conversion tool @@ -680,9 +685,9 @@ def generate_drug_list(drug_map_path,drug_path): imp_samp_map = pd.read_csv(args.curSamples) imp_drug_map = pd.read_csv(args.drugFile,sep='\t') original_drug_file = "beataml_wv1to4_raw_inhibitor_v4_dbgap.txt" - original_drug_url = "https://github.com/biodev/beataml2.0_data/raw/main/beataml_wv1to4_raw_inhibitor_v4_dbgap.txt" + # original_drug_url = "https://github.com/biodev/beataml2.0_data/raw/main/beataml_wv1to4_raw_inhibitor_v4_dbgap.txt" # Generate Raw Drugs File to use in Curve fitting algorithm - download_from_github(original_drug_url, original_drug_file) + # download_from_github(original_drug_url, original_drug_file) # Experiment Data updated_raw_drug_file = "beatAML_drug_raw.tsv" generate_raw_drug_file(original_drug_file,sample_mapping_file, updated_raw_drug_file,supplimentary_file) diff --git a/build/broad_sanger/03a-nci60Drugs.py b/build/broad_sanger/03a-nci60Drugs.py index 28720c90..529c002e 100644 --- a/build/broad_sanger/03a-nci60Drugs.py +++ b/build/broad_sanger/03a-nci60Drugs.py @@ -39,7 +39,7 @@ def main(): opts = parser.parse_args() ###primary DF - df = {'improve_drug_id':[],'chem_name':[],'canSMILES':[],'isoSMILES':[],\ + df = {'improve_drug_id':[],'chem_name':[],'canSMILES':[],\ 'InChIKey':[],'formula':[],'weight':[],'pubchem_id':[]} print('Downloading NSC identifiers for nci60 data') @@ -69,7 +69,7 @@ def main(): upper=[a.upper() for a in smiles['SMILES']] smiles= pl.DataFrame({'NSC':smiles['NSC'],'upper':upper})#smiles.with_columns(upper=upper) ##reduce to smiels only in current drugs - ssmiles = smiles.filter(~pl.col('upper').is_in(curdrugs['isoSMILES'])) + # ssmiles = smiles.filter(~pl.col('upper').is_in(curdrugs['isoSMILES'])) ssmiles = ssmiles.filter(~pl.col('upper').is_in(curdrugs['canSMILES'])) pubchems = pubchems.filter(pl.col('NSC').is_in(ssmiles['NSC'])) arr = set(pubchems['CID']) @@ -102,7 +102,7 @@ def main(): { "improve_drug_id": ["SMI_"+str(a) for a in range(max_imp+1,max_imp+1+smicount,1)], 'canSMILES': [a for a in set(mdf['SMILES'])], - 'isoSMILES': [a for a in set(mdf['SMILES'])], + # 'isoSMILES': [a for a in set(mdf['SMILES'])], 'InChIKey': [None for a in range(smicount)], 'formula': [None for a in range(smicount)], 'weight': [None for a in range(smicount)] diff --git a/build/mpnst/02_get_drug_data.R b/build/mpnst/02_get_drug_data.R index 7c07af9b..e90a31fb 100644 --- a/build/mpnst/02_get_drug_data.R +++ b/build/mpnst/02_get_drug_data.R @@ -103,7 +103,7 @@ if (!is.na(olddrugfiles)) { chem_name = character(), pubchem_id = character(), canSMILES = character(), - isoSMILES = character(), + # isoSMILES = character(), InChIKey = character(), formula = character(), weight = numeric(), @@ -118,7 +118,7 @@ if (!is.na(olddrugfiles)) { chem_name = character(), pubchem_id = character(), canSMILES = character(), - isoSMILES = character(), + # isoSMILES = character(), InChIKey = character(), formula = character(), weight = numeric(), diff --git a/build/utils/pubchem_retrieval.py b/build/utils/pubchem_retrieval.py index e6bdc836..1cf646af 100644 --- a/build/utils/pubchem_retrieval.py +++ b/build/utils/pubchem_retrieval.py @@ -54,12 +54,12 @@ def retrieve_drug_info(compound,ignore_chems,isname=True): if isname: urls = { - "properties": f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{compound}/property/CanonicalSMILES,IsomericSMILES,InChIKey,MolecularFormula,MolecularWeight/JSON", + "properties": f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{compound}/property/CanonicalSMILES,InChIKey,MolecularFormula,MolecularWeight/JSON", "synonyms": f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{compound}/synonyms/JSON" } else: urls = { - "properties": f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/{compound}/property/CanonicalSMILES,IsomericSMILES,InChIKey,MolecularFormula,MolecularWeight/JSON", + "properties": f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/{compound}/property/CanonicalSMILES,InChIKey,MolecularFormula,MolecularWeight/JSON", "synonyms": f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/{compound}/synonyms/JSON" } @@ -188,9 +188,9 @@ def update_dataframe_and_write_tsv(unique_names, output_filename="drugs.tsv",ign mode = 'a' if file_exists else 'w' with open(output_filename, mode) as f: if not file_exists: - f.write("improve_drug_id\tchem_name\tpubchem_id\tcanSMILES\tisoSMILES\tInChIKey\tformula\tweight\n") + f.write("improve_drug_id\tchem_name\tpubchem_id\tcanSMILES\tInChIKey\tformula\tweight\n") for entry in data: - f.write(f"{entry['improve_drug_id']}\t{entry['name']}\t{entry.get('CID', '')}\t{entry['CanonicalSMILES']}\t{entry.get('IsomericSMILES', '')}\t{entry['InChIKey']}\t{entry['MolecularFormula']}\t{entry['MolecularWeight']}\n") + f.write(f"{entry['improve_drug_id']}\t{entry['name']}\t{entry.get('CID', '')}\t{entry['CanonicalSMILES']}\t{entry['InChIKey']}\t{entry['MolecularFormula']}\t{entry['MolecularWeight']}\n") with open(ignore_chems,"a") as ig_f: for entry in data: From 45842dd5a54da23ff4bde3a2bb3e5b973e5d7867 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Wed, 20 Nov 2024 18:04:06 -0800 Subject: [PATCH 03/17] continued updatest to MT dta and pDX data --- build/mpnst/01_mpnst_get_omics.R | 26 +- build/mpnstPDX/01_mpnst_get_omics.R | 18 +- build/mpnstPDX/03_get_drug_response_data.R | 2 +- build/utils/calc_pdx_metrics.py | 382 +++++++++++++++++++++ 4 files changed, 408 insertions(+), 20 deletions(-) create mode 100755 build/utils/calc_pdx_metrics.py diff --git a/build/mpnst/01_mpnst_get_omics.R b/build/mpnst/01_mpnst_get_omics.R index 77a5466d..173ca71e 100755 --- a/build/mpnst/01_mpnst_get_omics.R +++ b/build/mpnst/01_mpnst_get_omics.R @@ -34,6 +34,7 @@ samples_df <- fread(patients)|> pdx_samps<-subset(samples_df,model_type=='patient derived xenograft') tumor_samps<-subset(samples_df,model_type=='tumor') +mt_samps<-subset(samples_df,model_type=='organoid') ##now get the manifest from synapse manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|> @@ -45,14 +46,19 @@ manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|> ##they each get their own sample identifier pdx_data<-manifest|>dplyr::select(common_name,starts_with("PDX"))|> left_join(pdx_samps)|> - dplyr::select(improve_sample_id,RNASeq='PDX_RNASeq',Mutations='PDX_Somatic_Mutations',CopyNumber='PDX_CNV',Proteomics='PDX_Proteomics') + dplyr::select(improve_sample_id,common_name,model_type,RNASeq='PDX_RNASeq',Mutations='PDX_Somatic_Mutations',CopyNumber='PDX_CNV',Proteomics='PDX_Proteomics') tumor_data<- manifest|>dplyr::select(common_name,starts_with("Tumor"))|> left_join(tumor_samps)|> - dplyr::select(improve_sample_id,RNASeq='Tumor_RNASeq',Mutations='Tumor_Somatic_Mutations',CopyNumber='Tumor_CNV')|> + dplyr::select(improve_sample_id,common_name,model_type,RNASeq='Tumor_RNASeq',Mutations='Tumor_Somatic_Mutations',CopyNumber='Tumor_CNV')|> mutate(Proteomics='') ##we dont have tumor proteomics from these samples #print(tumor_data) +mt_data<- manifest|>dplyr::select(common_name,starts_with("PDX"))|> + left_join(mt_samps)|> + dplyr::select(improve_sample_id,common_name,model_type, RNASeq='PDX_RNASeq',Mutations='PDX_Somatic_Mutations',CopyNumber='PDX_CNV',Proteomics='PDX_Proteomics')##we dont have mt data yet, so collecting PDX instead +#print(tumor_data) + combined<-rbind(pdx_data,tumor_data)|>distinct() @@ -61,10 +67,10 @@ genes_df <- fread(genefile) ##added proteomics first -proteomics<-do.call('rbind',lapply(setdiff(combined$Proteomics,c('',NA,"NA")),function(x){ +proteomics<-do.call('rbind',lapply(setdiff(mt_data$Proteomics,c('',NA,"NA")),function(x){ # if(x!=""){ #print(x) - sample<-subset(combined,Proteomics==x) + sample<-subset(mt_data,Proteomics==x) #print(sample) res<-fread(synGet(x)$path)|> #tidyr::separate(Name,into=c('other_id','vers'),sep='\\.')|> @@ -88,10 +94,10 @@ fwrite(proteomics,'/tmp/mpnst_proteomics.csv.gz') #### FIRST WE GET RNASeq Data -rnaseq<-do.call('rbind',lapply(setdiff(combined$RNASeq,c(NA,"NA")),function(x){ +rnaseq<-do.call('rbind',lapply(setdiff(mt_data$RNASeq,c(NA,"NA")),function(x){ # if(x!=""){ #print(x) - sample<-subset(combined,RNASeq==x) + sample<-subset(mt_data,RNASeq==x) #print(sample) res<-fread(synGet(x)$path)|> tidyr::separate(Name,into=c('other_id','vers'),sep='\\.')|> @@ -114,11 +120,11 @@ fwrite(rnaseq,'/tmp/mpnst_transcriptomics.csv.gz') #####NEXT WE DO WES DATA print("Getting WES") -wes<-do.call(rbind,lapply(setdiff(combined$`Mutations`,c(NA,"NA")),function(x){ +wes<-do.call(rbind,lapply(setdiff(mt_data$`Mutations`,c(NA,"NA")),function(x){ x2=x#gsub('"','',gsub("[",'',gsub("]",'',x,fixed=T),fixed=T),fixed=T) print(x) - sample<-subset(combined,Mutations==x) + sample<-subset(mt_data,Mutations==x) print(sample$improve_sample_id) res<-NULL try(res<-fread(synGet(x2)$path)|> @@ -141,11 +147,11 @@ fwrite(wes,'/tmp/mpnst_mutations.csv.gz') print(paste("getting CNV")) ##next let's do CNVs! -cnv<-do.call(rbind,lapply(setdiff(combined$CopyNumber,c(NA,"NA")),function(x){ +cnv<-do.call(rbind,lapply(setdiff(mt_data$CopyNumber,c(NA,"NA")),function(x){ x2=x#gsub('"','',gsub("[",'',gsub("]",'',x,fixed=T),fixed=T),fixed=T) print(x) - sample<-subset(combined,CopyNumber==x) + sample<-subset(mt_data,CopyNumber==x) print(sample$improve_sample_id) res<-fread(synGet(x2)$path) diff --git a/build/mpnstPDX/01_mpnst_get_omics.R b/build/mpnstPDX/01_mpnst_get_omics.R index 7e4fb9ad..776ea41c 100755 --- a/build/mpnstPDX/01_mpnst_get_omics.R +++ b/build/mpnstPDX/01_mpnst_get_omics.R @@ -54,17 +54,17 @@ tumor_data<- manifest|>dplyr::select(common_name,starts_with("Tumor"))|> #print(tumor_data) -combined<-rbind(pdx_data,tumor_data)|>distinct() +pdx_data<-rbind(pdx_data,tumor_data)|>distinct() # gene mapping table genes_df <- fread(genefile) ##added proteomics first -proteomics<-do.call('rbind',lapply(setdiff(combined$Proteomics,c('',NA,"NA")),function(x){ +proteomics<-do.call('rbind',lapply(setdiff(pdx_data$Proteomics,c('',NA,"NA")),function(x){ # if(x!=""){ #print(x) - sample<-subset(combined,Proteomics==x) + sample<-subset(pdx_data,Proteomics==x) #print(sample) res<-fread(synGet(x)$path)|> #tidyr::separate(Name,into=c('other_id','vers'),sep='\\.')|> @@ -88,10 +88,10 @@ fwrite(proteomics,'/tmp/mpnstPDX_proteomics.csv.gz') #### FIRST WE GET RNASeq Data -rnaseq<-do.call('rbind',lapply(setdiff(combined$RNASeq,c(NA,"NA")),function(x){ +rnaseq<-do.call('rbind',lapply(setdiff(pdx_data$RNASeq,c(NA,"NA")),function(x){ # if(x!=""){ #print(x) - sample<-subset(combined,RNASeq==x) + sample<-subset(pdx_data,RNASeq==x) #print(sample) res<-fread(synGet(x)$path)|> tidyr::separate(Name,into=c('other_id','vers'),sep='\\.')|> @@ -114,11 +114,11 @@ fwrite(rnaseq,'/tmp/mpnstPDX_transcriptomics.csv.gz') #####NEXT WE DO WES DATA print("Getting WES") -wes<-do.call(rbind,lapply(setdiff(combined$`Mutations`,c(NA,"NA")),function(x){ +wes<-do.call(rbind,lapply(setdiff(pdx_data$`Mutations`,c(NA,"NA")),function(x){ x2=x#gsub('"','',gsub("[",'',gsub("]",'',x,fixed=T),fixed=T),fixed=T) print(x) - sample<-subset(combined,Mutations==x) + sample<-subset(pdx_data,Mutations==x) print(sample$improve_sample_id) res<-NULL try(res<-fread(synGet(x2)$path)|> @@ -141,11 +141,11 @@ fwrite(wes,'/tmp/mpnstPDX_mutations.csv.gz') print(paste("getting CNV")) ##next let's do CNVs! -cnv<-do.call(rbind,lapply(setdiff(combined$CopyNumber,c(NA,"NA")),function(x){ +cnv<-do.call(rbind,lapply(setdiff(pdx_data$CopyNumber,c(NA,"NA")),function(x){ x2=x#gsub('"','',gsub("[",'',gsub("]",'',x,fixed=T),fixed=T),fixed=T) print(x) - sample<-subset(combined,CopyNumber==x) + sample<-subset(pdx_data,CopyNumber==x) print(sample$improve_sample_id) res<-fread(synGet(x2)$path) diff --git a/build/mpnstPDX/03_get_drug_response_data.R b/build/mpnstPDX/03_get_drug_response_data.R index 1ad073ec..2cc947c5 100644 --- a/build/mpnstPDX/03_get_drug_response_data.R +++ b/build/mpnstPDX/03_get_drug_response_data.R @@ -161,7 +161,7 @@ pdx_data<-rbind(old_data,new_data) fwrite(pdx_data,'/tmp/curve_data.tsv',sep='\t') ##TODO: create new curve fitting script in python -pycmd = '/opt/venv/bin/python fit_pdx_curve.py --input /tmp/curve_data.tsv --output /tmp/experiments' +pycmd = '/opt/venv/bin/python fit_pdx_curve.py --input /tmp/curve_data.tsv --output /tmp/mpnstPDX_experiments.tsv' print('running curve fitting') #system(pycmd) diff --git a/build/utils/calc_pdx_metrics.py b/build/utils/calc_pdx_metrics.py new file mode 100755 index 00000000..584584c1 --- /dev/null +++ b/build/utils/calc_pdx_metrics.py @@ -0,0 +1,382 @@ +''' +python script designed to compute pdx curve metrics from file +''' + + +from argparse import * +import pandas as pd +from tqdm import tqdm +import numpy as np + +import statsmodels.api as sm +from statsmodels.formula.api import mixedlm + + +####mRECIST code +def tumor_volume_change(volume): + """ + Calculate the percent change in tumor volume relative to the initial volume. + + Parameters: + volume (np.ndarray or list): Array of tumor volumes. + + Returns: + np.ndarray: Array of percent changes in tumor volume. + """ + Vini = volume[0] + return np.array([100 * (vt - Vini) / Vini for vt in volume]) + +def avg_response(volume_change): + """ + Calculate the average response for each time point. + + Parameters: + volume_change (np.ndarray or list): Array of volume percent changes. + + Returns: + np.ndarray: Array of average responses. + """ + cumsum = np.cumsum(volume_change) + ar = cumsum / np.arange(1, len(volume_change) + 1) + return ar + +def check_numeric_int_char_zero(u): + """ + Check if the input array is empty and return NA if true. + + Parameters: + u (any): Input value or array. + + Returns: + The input value or None if it is empty. + """ + return None if len(u) == 0 else u + +def get_best_response(time, response, min_time=None): + """ + Determine the best response after a specified minimum time. + + Parameters: + time (np.ndarray or list): Array of time points. + response (np.ndarray or list): Array of response values. + min_time (float or None): Minimum time after which tumor volume will be considered. + + Returns: + dict: Dictionary containing the best response time, value, and index. + """ + rtz = {"time": None, "value": None, "index": None} + + exdf = pd.DataFrame({"time": time, "response": response}) + exdf = exdf.dropna() + exdf.reset_index() + if min_time is not None: + exdf_a = exdf[exdf['time'] >= min_time] + + if exdf.shape[0] == 0: + return rtz + exdf_a.reset_index() + # print(exdf.shape) + min_indx = list(exdf.response).index(min(exdf_a.response)) + + rtz['time'] = check_numeric_int_char_zero([list(exdf.time)[min_indx]]) + rtz['value'] = check_numeric_int_char_zero([list(exdf.response)[min_indx]]) + rtz['index'] = check_numeric_int_char_zero([min_indx]) + return rtz + +def mrecist(time, volume, min_time=10, return_detail=False): + """ + Compute the mRECIST for given volume response. + + Parameters: + time (np.ndarray or list): Array of time points. + volume (np.ndarray or list): Array of tumor volumes. + min_time (float): Minimum time after which tumor volume will be considered. + return_detail (bool): If True, return all intermediate values. + + Returns: + str or dict: mRECIST classification or a dictionary with detailed intermediate values. + """ + if volume[0] == 0: + volume = np.array(volume) + 1 + + exdf = { + "volume_change": None, + "average_response": None, + "best_response": None, + "best_response)time": None, + "best_average_response": None, + "best_average_response_time": None, + "mRECIST": None + } + + exdf["volume_change"] = tumor_volume_change(volume) + exdf["average_response"] = avg_response(exdf["volume_change"]) + nxdf = {'metric':'mRESCIST','value':None} + + df = pd.DataFrame({"time": time, "volume": volume}) + df = df[df['time'] >= min_time] + + if df.shape[0] < 2: + print(f"Warning: insufficient data after time {min_time}") + else: + br = get_best_response(time, exdf["volume_change"], min_time) + exdf["best_response"] = br["value"] + exdf["best_response_time"] = br["time"] + + bar = get_best_response(time, exdf["average_response"], min_time) + exdf["best_average_response"] = bar["value"] + exdf["best_average_response_time"] = bar["time"] + + best_response = exdf["best_response"][0] + best_average_response = exdf["best_average_response"][0] + + mrecist = None + nxdf = {'metric':'mRESCIST','value':mrecist} +# exdf["mRECIST"] = mrecist + + if best_response is not None and best_average_response is not None: + # Order of mRECIST assignment matters + mrecist = "PD" + + if best_response < 35 and best_average_response < 30: + mrecist = "SD" + + if best_response < -50 and best_average_response < -20: + mrecist = "PR" + + if best_response < -95 and best_average_response < -40: + mrecist = "CR" + +# exdf["mRECIST"] = mrecist + nxdf = {'metric':'mRESCIST','value':mrecist} + if not return_detail: + return nxdf + + return nxdf + +###AUC CODE + +def trapz_auc(x, y): + """ + Compute the area under the curve using trapezoidal rule. + + Parameters: + x (np.ndarray): Array of x values. + y (np.ndarray): Array of y values. + + Returns: + float: Area under the curve. + """ + n = np.arange(1, len(x)) + auc = np.dot((x[n] - x[n - 1]), (y[n] + y[n - 1])) / 2 + return auc + +def AUC(time, volume, time_normalize=True): + """ + Calculate the area under the curve (AUC). + + Parameters: + time (np.ndarray): Array of time points recorded for the experiment. + volume (np.ndarray): Array of volumes corresponding to the time points. + time_normalize (bool): If True, AUC value will be divided by max time. + + Returns: + dict: Dictionary containing the AUC value. + """ + auc = trapz_auc(time, volume) + #print(time) + if time_normalize: + auc = auc/np.max(time) + return {"metric": "auc", "value": auc} + +def TGI(contr_volume, treat_volume): + """ + Computes the tumor growth inhibition (TGI) between two time-volume curves. + + Parameters: + contr_volume (np.ndarray or list): Volume vector for control. + treat_volume (np.ndarray or list): Volume vector for treatment. + + Returns: + dict: Dictionary containing the TGI value. + """ + tgi = None + if len(contr_volume) > 0 and len(treat_volume) > 0: + tgi = (contr_volume[-1] - treat_volume[-1]) / (contr_volume[0] - treat_volume[0]) + + # Simulated batch response class object + rtx = { + "metric": "TGI", + "value": tgi + } + return rtx + + +def ABC(contr_time=None, contr_volume=None, treat_time=None, treat_volume=None): + """ + Compute the area between two time-volume curves. + + Parameters: + contr_time (np.ndarray): Array of time points for control. + contr_volume (np.ndarray): Array of control volumes. + treat_time (np.ndarray): Array of time points for treatment. + treat_volume (np.ndarray): Array of treatment volumes. + + Returns: + dict: Dictionary containing the area between curves. + """ + con = {'name': 'auc', 'value': None} + tre = {'name': 'auc', 'value': None} + abc = None + + if contr_time is not None and contr_volume is not None: + if len(contr_time) != len(contr_volume): + raise ValueError("contr.time and contr.volume should have same length") + con = AUC(contr_time, contr_volume) + + if treat_time is not None and treat_volume is not None: + if len(treat_time) != len(treat_volume): + raise ValueError("treat.time and treat.volume should have same length") + tre = AUC(treat_time, treat_volume) + + abc = con['value'] - tre['value'] + return {"metric": "abc", "value": abc}#, "control": con, "treatment": tre} + + +###LMM CODE +def lmm(time, volume, treatment, drug_name): + """ + Compute the linear mixed model (lmm) statistics for a PDX batch. + + Parameters: + data (pd.DataFrame): A DataFrame containing the batch data. Must contain the columns: model_id, volume, time, exp_type. + + Returns: + dict: A dictionary containing the fit object and the specific coefficient value. + """ + + data = pd.DataFrame({'model_id':['model']*len(time),\ + 'volume':volume,\ + 'time':time,\ + 'exp_type':treatment}) + + data = data.dropna() + + ##create data frame from these 4 vectors + required_columns = ["model_id", "volume", "time", "exp_type"] + + if not all(column in data.columns for column in required_columns): + raise ValueError("These columns must be present: 'model_id', 'volume', 'time', 'exp_type'") + + data['log_volume'] = np.log(data['volume']) + + # Define the formula for mixed linear model + formula = 'log_volume ~ time*exp_type' + + # Fit the model + model = mixedlm(formula, data, groups=data['model_id']) + fit = model.fit() + + # Get the coefficient for the interaction term 'time:exp_type' + #interaction_term = 'time:exp_type' +# if interaction_term in fit.params: +# time_coef_value = fit.params['time'] + #print(fit.params) + i_coef_value = fit.params['time:exp_type[T.'+drug_name+']'] + # else: + # coef_value = None # Handle the case when the interaction term is not present + + # Create a dictionary to store the fit object and the specific coefficient value + result = { + 'fit': fit, + 'interaction_coef_value': i_coef_value + } + + return {'metric': 'lmm','value': i_coef_value} + +def main(): + parser=ArgumentParser() + ###read in file with model id, volume, time, condition + parser.add_argument('curvefile') + parser.add_argument('--drugfile') + + args = parser.parse_args() + + tab = pd.read_csv(args.curvefile,sep='\t') + drugs = pd.read_csv(args.drugfile,sep='\t') + + singles, combos = get_drug_stats(tab) + + ##join with drug ids + + ##stats.to_csv('pdx_exp.tsv',sep='\t',index=False) + +def get_drug_stats(df,control='control'): + ##for each experiment, call group + cols = ['experiment','model_id'] + groups = df.groupby(cols) + singleres = [] + combores = [] + + for name,group in tqdm(groups): + #each group contains multiple treatments anda control + drugs = set(group.treatment)-set([control]) + print(name[0]) + print(drugs) + mod = list(set(group.model_id))[0] + # print(set(group.model_id)) + ctl_data = group[group.treatment==control] + ctl_time = np.array(ctl_data.time) + ctl_volume = np.array(ctl_data.volume) + + ctl_auc = AUC(ctl_time,ctl_volume) + for d in drugs: + print(d) + d_data = group[group.treatment==d] + treat_time = np.array(d_data.time) + treat_volume = np.array(d_data.volume) + + #get abc for group + treat_auc = AUC(treat_time,treat_volume) + treat_abc = ABC(ctl_time,ctl_volume,treat_time,treat_volume) + #print(f"AUC: {treat_auc}") + #print(f"ABC: {treat_abc}") + treat_abc.update({'sample':mod,'drug':d}) + if '+' in d: + combores.append(treat_abc) + else: + singleres.append(treat_abc) + #lmm + comb = pd.concat([ctl_data,d_data]) + lmm_res = lmm(comb.time, comb.volume, comb.treatment,d) + lmm_res.update({'sample':mod,'drug':d}) + #print(f"LMM: {lmm_res}") + if '+' in d: + combores.append(lm_res) + else: + singleres.append(lm_res) + + #get tgi for group + tg = TGI(ctl_volume,treat_volume) + tg.update({'sample':mod,'drug':d}) + #print(tg) + if '+' in d: + combores.append(tg) + else: + singleres.append(tg) + + + #get mRECIST for group + mr = mrecist(treat_time,treat_volume) + mr.update({'sample':mod,'drug':d}) + if '+' in d: + combores.append(mr) + else: + singleres.append(mr) + + sing = pd.DataFrame.from_records(singlres) + comb = pd.DataFrame.from_records(combores) + return sing,comb + +if __name__=='__main__': + main() From ea9be4a2425fc66d9a6d13d09f70f3fedce6fb65 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Thu, 21 Nov 2024 11:19:09 -0800 Subject: [PATCH 04/17] added docker and code for PDX data build --- build/docker/Dockerfile.mpnstPDX | 26 ++++++++++++ build/mpnstPDX/02_get_drug_data.R | 2 +- build/mpnstPDX/03_get_drug_response_data.R | 7 ++-- build/mpnstPDX/build_exp.sh | 2 +- build/utils/calc_pdx_metrics.py | 46 +++++++++++++++------- schema/coderdata.yaml | 8 ++-- 6 files changed, 68 insertions(+), 23 deletions(-) create mode 100755 build/docker/Dockerfile.mpnstPDX diff --git a/build/docker/Dockerfile.mpnstPDX b/build/docker/Dockerfile.mpnstPDX new file mode 100755 index 00000000..070d676c --- /dev/null +++ b/build/docker/Dockerfile.mpnstPDX @@ -0,0 +1,26 @@ +FROM r-base:4.3.2 +ENV DEBIAN_FRONTEND=noninteractive +RUN apt-get update --allow-insecure-repositories +#RUN apt-get install -y --allow-unauthenticated build-essential --fix-missing libpq-dev python3-pip python3-setuptools python3-dev python3-venv libcurl4-openssl-dev libxml2-dev +RUN apt-get install -y --allow-unauthenticated build-essential --fix-missing python3-pip python3-setuptools python3-dev python3-venv libcurl4-openssl-dev libxml2-dev + +RUN python3 -m venv /opt/venv +RUN /opt/venv/bin/pip3 install --upgrade pip + + +ENV PYTHONPATH "${PYTHONPATH}:/app" +WORKDIR /app + +ADD build/mpnstPDX/requirements.txt . +ADD build/mpnstPDX/requirements.r . +ADD build/mpnstPDX/* ./ +ADD build/utils/* ./ + +# installing python libraries +RUN /opt/venv/bin/pip3 install -r requirements.txt + +# installing r libraries +RUN Rscript requirements.r + + +VOLUME ["/tmp"] diff --git a/build/mpnstPDX/02_get_drug_data.R b/build/mpnstPDX/02_get_drug_data.R index d888cced..1f6ad47e 100644 --- a/build/mpnstPDX/02_get_drug_data.R +++ b/build/mpnstPDX/02_get_drug_data.R @@ -101,7 +101,7 @@ ignore_file_path <- '/tmp/mpnstpdx_ignore_chems.txt' use_python("/opt/venv/bin/python3", required = TRUE) source_python("pubchem_retrieval.py") -update_dataframe_and_write_tsv(unique_names=alldrugs,output_filename=output_file_path,ignore_chems=ignore_file_path) +update_dataframe_and_write_tsv(unique_names=drugs,output_filename=output_file_path,ignore_chems=ignore_file_path) tab<-read.table(newdrugfile,sep='\t',header=T,quote="",comment.char="") diff --git a/build/mpnstPDX/03_get_drug_response_data.R b/build/mpnstPDX/03_get_drug_response_data.R index 2cc947c5..7f3eabb9 100644 --- a/build/mpnstPDX/03_get_drug_response_data.R +++ b/build/mpnstPDX/03_get_drug_response_data.R @@ -97,6 +97,7 @@ pdx_meta$parentId=unlist(lapply(pdx_meta$id,function(x) synGet(x)$parentId)) oldfolders=c('syn22018363','syn22024460','syn22024428','syn22024429','syn22024437','syn22024438') old_meta<-subset(pdx_meta,parentId%in%oldfolders) + old_data<-do.call(rbind,lapply(unique(old_meta$parentId),function(x){ ids<-subset(old_meta,parentId==x)|> subset(!is.na(id)) @@ -121,7 +122,7 @@ old_data<-do.call(rbind,lapply(unique(old_meta$parentId),function(x){ })) }))|> left_join(unique(select(old_meta,id=parentId,improve_sample_id)))|> - dplyr::select(experiment=id,model_id=improve_sample_id,specimen_id,treatment=chem_name,time=experimental_time_point,volume=assay_value)|>distinct() + dplyr::select(experiment=id,model_id=improve_sample_id,specimen_id,treatment=chem_name,time=experimental_time_point,time_unit=experimental_time_point_unit,volume=assay_value)|>distinct() @@ -150,7 +151,7 @@ new_data<-do.call(rbind,lapply(unique(new_meta$id), function(x){ #print(head(tab)) return(tab)}))|> left_join(pdx_meta)|> - dplyr::select(experiment=id,model_id=improve_sample_id,specimen_id,treatment=chem_name,time=experimental_time_point,volume=assay_value)|>distinct() + dplyr::select(experiment=id,model_id=improve_sample_id,specimen_id,treatment=chem_name,time=experimental_time_point,time_unit=experimental_time_point_unit,volume=assay_value)|>distinct() ##maybe tweak the data frame a bit depending on curve fitting script pdx_data<-rbind(old_data,new_data) @@ -161,7 +162,7 @@ pdx_data<-rbind(old_data,new_data) fwrite(pdx_data,'/tmp/curve_data.tsv',sep='\t') ##TODO: create new curve fitting script in python -pycmd = '/opt/venv/bin/python fit_pdx_curve.py --input /tmp/curve_data.tsv --output /tmp/mpnstPDX_experiments.tsv' +pycmd = '/opt/venv/bin/python calc_pdx_metrics.py --input /tmp/curve_data.tsv --outprefix /tmp/mpnstPDX' print('running curve fitting') #system(pycmd) diff --git a/build/mpnstPDX/build_exp.sh b/build/mpnstPDX/build_exp.sh index cc0b5abc..f11f8616 100644 --- a/build/mpnstPDX/build_exp.sh +++ b/build/mpnstPDX/build_exp.sh @@ -1,2 +1,2 @@ Rscript 03_get_drug_response_data.R $SYNAPSE_AUTH_TOKEN $1 $2 -/opt/venv/bin/python3 compute_metrics.py /tmp/file.tsv --drugfile=/tmp/mpnstpdx_drugs.tsv +/opt/venv/bin/python3 compute_metrics.py /tmp/curve_data.tsv --drugfile=/tmp/mpnstpdx_drugs.tsv --outprefix=/tmp/mpnstpdx diff --git a/build/utils/calc_pdx_metrics.py b/build/utils/calc_pdx_metrics.py index 584584c1..c1a32d26 100755 --- a/build/utils/calc_pdx_metrics.py +++ b/build/utils/calc_pdx_metrics.py @@ -187,9 +187,9 @@ def AUC(time, volume, time_normalize=True): #print(time) if time_normalize: auc = auc/np.max(time) - return {"metric": "auc", "value": auc} + return {"metric": "auc", "value": auc, 'time':np.max(time)} -def TGI(contr_volume, treat_volume): +def TGI(contr_volume, treat_volume,time): """ Computes the tumor growth inhibition (TGI) between two time-volume curves. @@ -207,7 +207,8 @@ def TGI(contr_volume, treat_volume): # Simulated batch response class object rtx = { "metric": "TGI", - "value": tgi + "value": tgi, + 'time': np.max(time) } return rtx @@ -240,7 +241,7 @@ def ABC(contr_time=None, contr_volume=None, treat_time=None, treat_volume=None): tre = AUC(treat_time, treat_volume) abc = con['value'] - tre['value'] - return {"metric": "abc", "value": abc}#, "control": con, "treatment": tre} + return {"metric": "abc", "value": abc,'time':np.max(treat_time)}#, "control": con, "treatment": tre} ###LMM CODE @@ -292,13 +293,14 @@ def lmm(time, volume, treatment, drug_name): 'interaction_coef_value': i_coef_value } - return {'metric': 'lmm','value': i_coef_value} + return {'metric': 'lmm','value': i_coef_value,'time':np.max(time)} def main(): parser=ArgumentParser() ###read in file with model id, volume, time, condition parser.add_argument('curvefile') parser.add_argument('--drugfile') + parser.add_argument('--outprefix',default='/tmp/') args = parser.parse_args() @@ -308,8 +310,24 @@ def main(): singles, combos = get_drug_stats(tab) ##join with drug ids + expsing = singles.rename({'drug':'chem_name','metric':'drug_combination_metric','value':'drug_combination_value','sample':'improve_sample_id'},axis=1).merge(drugs,on='chem_name',how='left')[['improve_drug_id','improve_sample_id','drug_combination_metric','drug_combination_value']] + expsing = expsing.dropna() + + combos[['drug1','drug2']]=combos.drug.str.split('+',expand=True) + combos = combos.rename({'metric':'drug_combination_metric','value':'drug_combination_value','sample':'improve_sample_id'},axis=1).dropna() + + expcomb = combos.rename({'drug1':'chem_name'},axis=1).merge(drugs,on='chem_name',how='left').rename({'improve_drug_id':'improve_drug_1'},axis=1)[['improve_drug_1','drug2','improve_sample_id','drug_combination_metric','drug_combination_value']] + expcomb = expcomb.rename({'drug2':'chem_name'},axis=1).merge(drugs,on='chem_name',how='left').rename({'improve_drug_id':'improve_drug_2'},axis=1)[['improve_drug_1','improve_drug_2','improve_sample_id','drug_combination_metric','drug_combination_value']] + + expcomb[['source']]='Synapse' + expcomb[['study']]='MPNST PDX in vivo' + + expsing[['source']]='Synapse' + expsing[['study']]='MPNST PDX in vivo' + expsing.to_csv(args.outprefix+'_experiments.csv',index=False) + expcomb.to_csv(args.outprefix+'_combinations.csv',index=False) - ##stats.to_csv('pdx_exp.tsv',sep='\t',index=False) + def get_drug_stats(df,control='control'): ##for each experiment, call group @@ -341,7 +359,7 @@ def get_drug_stats(df,control='control'): treat_abc = ABC(ctl_time,ctl_volume,treat_time,treat_volume) #print(f"AUC: {treat_auc}") #print(f"ABC: {treat_abc}") - treat_abc.update({'sample':mod,'drug':d}) + treat_abc.update({'sample':mod,'drug':d,'time_unit':'days'}) if '+' in d: combores.append(treat_abc) else: @@ -349,16 +367,16 @@ def get_drug_stats(df,control='control'): #lmm comb = pd.concat([ctl_data,d_data]) lmm_res = lmm(comb.time, comb.volume, comb.treatment,d) - lmm_res.update({'sample':mod,'drug':d}) + lmm_res.update({'sample':mod,'drug':d,'time_unit':'days'}) #print(f"LMM: {lmm_res}") if '+' in d: - combores.append(lm_res) + combores.append(lmm_res) else: - singleres.append(lm_res) + singleres.append(lmm_res) #get tgi for group - tg = TGI(ctl_volume,treat_volume) - tg.update({'sample':mod,'drug':d}) + tg = TGI(ctl_volume,treat_volume,treat_time) + tg.update({'sample':mod,'drug':d,'time_unit':'days'}) #print(tg) if '+' in d: combores.append(tg) @@ -368,13 +386,13 @@ def get_drug_stats(df,control='control'): #get mRECIST for group mr = mrecist(treat_time,treat_volume) - mr.update({'sample':mod,'drug':d}) + mr.update({'sample':mod,'drug':d,'time_unit':'days'}) if '+' in d: combores.append(mr) else: singleres.append(mr) - sing = pd.DataFrame.from_records(singlres) + sing = pd.DataFrame.from_records(singleres) comb = pd.DataFrame.from_records(combores) return sing,comb diff --git a/schema/coderdata.yaml b/schema/coderdata.yaml index 1b5f9916..d04bb071 100755 --- a/schema/coderdata.yaml +++ b/schema/coderdata.yaml @@ -187,13 +187,13 @@ classes: - source - study attributes: - drug_one_id: + drug_drug_2: description: improve_drug_id of first drug - drug_two_id: + improve_drug_2: description: imrrove_drug_id of second drug - combination_metric: + drug_combination_metric: description: metric calculated for synergy, or other metric of two drugs - combination_value: + drug_combination_value: description: value of metric for synergy or combination enums: ResponseMetric: From 51adfeb37264110fb95e4301cf7c6f0c6b335412 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Thu, 21 Nov 2024 14:40:25 -0800 Subject: [PATCH 05/17] Moved over files from main to enable build test --- build.out | 1721 ++++++++++++++++++++++++++++++ build/build_dataset.py | 321 ++++++ build/docker/Dockerfile.mpnst | 44 +- build/docker/Dockerfile.mpnstPDX | 44 +- build/docker/docker-compose.yml | 9 +- build/mpnst/requirements.r | 14 +- build/mpnst/requirements.txt | 2 +- build/mpnstPDX/README.md | 10 +- build/mpnstPDX/build_exp.sh | 2 +- build/mpnstPDX/requirements.r | 17 +- build/mpnstPDX/requirements.txt | 3 +- mpnstpdx_ignore_chems.txt | 130 +++ 12 files changed, 2279 insertions(+), 38 deletions(-) create mode 100644 build.out create mode 100644 build/build_dataset.py create mode 100644 mpnstpdx_ignore_chems.txt diff --git a/build.out b/build.out new file mode 100644 index 00000000..36a601f4 --- /dev/null +++ b/build.out @@ -0,0 +1,1721 @@ +#0 building with "desktop-linux" instance using docker driver + +#1 [internal] load build definition from Dockerfile.mpnstpdx +#1 transferring dockerfile: 1.79kB done +#1 DONE 0.0s + +#2 [internal] load metadata for docker.io/library/r-base:4.3.2 +#2 DONE 0.4s + +#3 [internal] load .dockerignore +#3 transferring context: 116B 0.0s done +#3 DONE 0.0s + +#4 [ 1/15] FROM docker.io/library/r-base:4.3.2@sha256:4bdf68161b2ed65fa6ca8285d1dc445ceb8100e94f503c56f59d2cfc453c7cdd +#4 DONE 0.0s + +#5 [internal] load build context +#5 transferring context: 2.62kB 0.0s done +#5 DONE 0.0s + +#6 [ 2/15] RUN apt-get update && apt-get install -y build-essential wget curl libcurl4-openssl-dev libxml2-dev zlib1g-dev libssl-dev libbz2-dev libreadline-dev libsqlite3-dev libffi-dev +#6 CACHED + +#7 [ 7/15] RUN /opt/venv/bin/pip install --upgrade pip +#7 CACHED + +#8 [ 5/15] RUN echo "/usr/local/lib" >> /etc/ld.so.conf.d/python3.10.conf && ldconfig +#8 CACHED + +#9 [ 8/15] WORKDIR /app +#9 CACHED + +#10 [ 4/15] RUN ln -s /usr/local/bin/python3.10 /usr/bin/python3 && ln -s /usr/local/bin/pip3.10 /usr/bin/pip3 +#10 CACHED + +#11 [ 6/15] RUN python3 -m venv /opt/venv +#11 CACHED + +#12 [ 3/15] RUN wget https://www.python.org/ftp/python/3.10.12/Python-3.10.12.tgz && tar -xf Python-3.10.12.tgz && cd Python-3.10.12 && ./configure --enable-optimizations --enable-shared && make -j$(nproc) && make altinstall && cd .. && rm -rf Python-3.10.12.tgz Python-3.10.12 +#12 CACHED + +#13 [ 9/15] RUN mkdir -p /app/tmp/matplotlib +#13 CACHED + +#14 [10/15] ADD build/mpnstPDX/requirements.txt . +#14 DONE 0.0s + +#15 [11/15] ADD build/mpnstPDX/requirements.r . +#15 DONE 0.0s + +#16 [12/15] ADD build/mpnstPDX/* ./ +#16 DONE 0.0s + +#17 [13/15] ADD build/utils/* ./ +#17 DONE 0.0s + +#18 [14/15] RUN /opt/venv/bin/pip3 install -r requirements.txt +#18 0.470 Collecting pyarrow (from -r requirements.txt (line 1)) +#18 0.536 Downloading pyarrow-18.0.0-cp310-cp310-manylinux_2_28_aarch64.whl.metadata (3.3 kB) +#18 0.647 Collecting pandas (from -r requirements.txt (line 2)) +#18 0.663 Downloading 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--upgrade pip +#18 DONE 19.8s + +#19 [15/15] RUN Rscript requirements.r +#19 0.252 Installing package into ‘/usr/local/lib/R/site-library’ +#19 0.252 (as ‘lib’ is unspecified) +#19 1.128 also installing the dependencies ‘rprojroot’, ‘Rcpp’, ‘RcppTOML’, ‘here’, ‘jsonlite’, ‘png’, ‘rappdirs’, ‘rlang’, ‘withr’ +#19 1.128 +#19 1.129 trying URL 'https://cloud.r-project.org/src/contrib/rprojroot_2.0.4.tar.gz' +#19 1.576 Content type 'application/x-gzip' length 59946 bytes (58 KB) +#19 1.576 ================================================== +#19 1.595 downloaded 58 KB +#19 1.595 +#19 1.599 trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.13-1.tar.gz' +#19 2.063 Content type 'application/x-gzip' length 3435726 bytes (3.3 MB) +#19 2.077 ================================================== +#19 2.183 downloaded 3.3 MB +#19 2.183 +#19 2.185 trying URL 'https://cloud.r-project.org/src/contrib/RcppTOML_0.2.2.tar.gz' +#19 2.792 Content type 'application/x-gzip' length 141195 bytes (137 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'application/x-gzip' length 12288 bytes (12 KB) +#19 5.016 ================================================== +#19 5.016 downloaded 12 KB +#19 5.016 +#19 5.024 trying URL 'https://cloud.r-project.org/src/contrib/rlang_1.1.4.tar.gz' +#19 5.582 Content type 'application/x-gzip' length 767041 bytes (749 KB) +#19 5.582 ================================================== +#19 5.631 downloaded 749 KB +#19 5.631 +#19 5.634 trying URL 'https://cloud.r-project.org/src/contrib/withr_3.0.2.tar.gz' +#19 6.192 Content type 'application/x-gzip' length 103240 bytes (100 KB) +#19 6.192 ================================================== +#19 6.207 downloaded 100 KB +#19 6.207 +#19 6.212 trying URL 'https://cloud.r-project.org/src/contrib/reticulate_1.40.0.tar.gz' +#19 6.789 Content type 'application/x-gzip' length 1640550 bytes (1.6 MB) +#19 6.794 ================================================== +#19 6.856 downloaded 1.6 MB +#19 6.856 +#19 7.024 * installing *source* package ‘rprojroot’ ... +#19 7.025 ** package ‘rprojroot’ successfully unpacked and MD5 sums checked +#19 7.025 ** using staged installation +#19 7.033 ** R +#19 7.036 ** inst +#19 7.037 ** byte-compile and prepare package for lazy loading +#19 7.325 ** help +#19 7.341 *** installing help indices +#19 7.353 *** copying figures +#19 7.353 ** building package indices +#19 7.491 ** installing vignettes +#19 7.494 ** testing if installed package can be loaded from temporary location +#19 7.609 ** testing if installed package can be loaded from final location +#19 7.719 ** testing if installed package keeps a record of temporary installation path +#19 7.719 * DONE (rprojroot) +#19 8.206 * installing *source* package ‘Rcpp’ ... +#19 8.237 ** package ‘Rcpp’ successfully unpacked and MD5 sums checked +#19 8.237 ** using staged installation +#19 8.244 ** libs +#19 8.254 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ +#19 8.255 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c api.cpp -o api.o +#19 9.262 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c attributes.cpp -o attributes.o +#19 15.62 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c barrier.cpp -o barrier.o +#19 15.73 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c date.cpp -o date.o +#19 16.79 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c module.cpp -o module.o +#19 19.45 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rcpp_init.cpp -o rcpp_init.o +#19 20.22 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/usr/lib/R/lib -lR +#19 20.30 installing to /usr/local/lib/R/site-library/00LOCK-Rcpp/00new/Rcpp/libs +#19 20.30 ** R +#19 20.31 ** inst +#19 20.33 ** byte-compile and prepare package for lazy loading +#19 21.23 ** help +#19 21.28 *** installing help indices +#19 21.31 ** building package indices +#19 21.46 ** installing vignettes +#19 21.46 ** testing if installed package can be loaded from temporary location +#19 21.63 ** checking absolute paths in shared objects and dynamic libraries +#19 21.64 ** testing if installed package can be loaded from final location +#19 21.80 ** testing if installed package keeps a record of temporary installation path +#19 21.81 * DONE (Rcpp) +#19 22.04 * installing *source* package ‘jsonlite’ ... +#19 22.05 ** package ‘jsonlite’ successfully unpacked and MD5 sums checked +#19 22.05 ** using staged installation +#19 22.06 ** libs +#19 22.07 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 22.07 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c base64.c -o base64.o +#19 22.15 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c collapse_array.c -o collapse_array.o +#19 22.19 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c collapse_object.c -o collapse_object.o +#19 22.22 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c collapse_pretty.c -o collapse_pretty.o +#19 22.29 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c escape_chars.c -o escape_chars.o +#19 22.33 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c integer64_to_na.c -o integer64_to_na.o +#19 22.36 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c is_datelist.c -o is_datelist.o +#19 22.39 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c is_recordlist.c -o is_recordlist.o +#19 22.43 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c is_scalarlist.c -o is_scalarlist.o +#19 22.46 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c modp_numtoa.c -o modp_numtoa.o +#19 22.54 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c null_to_na.c -o null_to_na.o +#19 22.58 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c num_to_char.c -o num_to_char.o +#19 22.63 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c parse.c -o parse.o +#19 22.68 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c prettify.c -o prettify.o +#19 22.72 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c push_parser.c -o push_parser.o +#19 22.75 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c r-base64.c -o r-base64.o +#19 22.78 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c register.c -o register.o +#19 22.81 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c row_collapse.c -o row_collapse.o +#19 22.85 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c transpose_list.c -o transpose_list.o +#19 22.88 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c validate.c -o validate.o +#19 22.91 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl.c -o yajl/yajl.o +#19 22.95 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o +#19 22.97 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_buf.c -o yajl/yajl_buf.o +#19 23.00 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_encode.c -o yajl/yajl_encode.o +#19 23.06 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_gen.c -o yajl/yajl_gen.o +#19 23.21 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_lex.c -o yajl/yajl_lex.o +#19 23.36 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_parser.c -o yajl/yajl_parser.o +#19 23.47 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_tree.c -o yajl/yajl_tree.o +#19 23.56 ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o +#19 23.57 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/usr/lib/R/lib -lR +#19 23.58 installing to /usr/local/lib/R/site-library/00LOCK-jsonlite/00new/jsonlite/libs +#19 23.58 ** R +#19 23.59 ** inst +#19 23.59 ** byte-compile and prepare package for lazy loading +#19 24.03 in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs” +#19 24.03 in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime” +#19 24.03 in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms” +#19 24.03 in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json” +#19 24.03 in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64” +#19 24.03 in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist” +#19 24.03 in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob” +#19 24.03 in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar” +#19 24.03 in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf” +#19 24.03 in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc” +#19 24.03 in method for ‘asJSON’ with signature ‘"vctrs_vctr"’: no definition for class “vctrs_vctr” +#19 24.03 ** help +#19 24.04 *** installing help indices +#19 24.06 ** building package indices +#19 24.19 ** installing vignettes +#19 24.19 ** testing if installed package can be loaded from temporary location +#19 24.33 ** checking absolute paths in shared objects and dynamic libraries +#19 24.33 ** testing if installed package can be loaded from final location +#19 24.46 ** testing if installed package keeps a record of temporary installation path +#19 24.46 * DONE (jsonlite) +#19 24.60 * installing *source* package ‘png’ ... +#19 24.60 ** package ‘png’ successfully unpacked and MD5 sums checked +#19 24.60 ** using staged installation +#19 24.60 ** libs +#19 24.61 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 24.61 gcc -I"/usr/share/R/include" -DNDEBUG `libpng-config --cflags` -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dummy.c -o dummy.o +#19 24.62 gcc -I"/usr/share/R/include" -DNDEBUG `libpng-config --cflags` -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read.c -o read.o +#19 24.75 gcc -I"/usr/share/R/include" -DNDEBUG `libpng-config --cflags` -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c write.c -o write.o +#19 24.87 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o png.so dummy.o read.o write.o -lpng16 -lm -lz -lm -L/usr/lib/R/lib -lR +#19 24.88 installing to /usr/local/lib/R/site-library/00LOCK-png/00new/png/libs +#19 24.89 ** R +#19 24.89 ** inst +#19 24.89 ** byte-compile and prepare package for lazy loading +#19 25.03 ** help +#19 25.04 *** installing help indices +#19 25.04 ** building package indices +#19 25.19 ** testing if installed package can be loaded from temporary location +#19 25.32 ** checking absolute paths in shared objects and dynamic libraries +#19 25.32 ** testing if installed package can be loaded from final location +#19 25.45 ** testing if installed package keeps a record of temporary installation path +#19 25.45 * DONE (png) +#19 25.58 * installing *source* package ‘rappdirs’ ... +#19 25.59 ** package ‘rappdirs’ successfully unpacked and MD5 sums checked +#19 25.59 ** using staged installation +#19 25.60 ** libs +#19 25.60 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 25.60 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o +#19 25.63 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c win-path.c -o win-path.o +#19 25.65 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o rappdirs.so init.o win-path.o -L/usr/lib/R/lib -lR +#19 25.66 installing to /usr/local/lib/R/site-library/00LOCK-rappdirs/00new/rappdirs/libs +#19 25.66 ** R +#19 25.67 ** byte-compile and prepare package for lazy loading +#19 25.84 ** help +#19 25.85 *** installing help indices +#19 25.86 ** building package indices +#19 25.99 ** testing if installed package can be loaded from temporary location +#19 26.12 ** checking absolute paths in shared objects and dynamic libraries +#19 26.13 ** testing if installed package can be loaded from final location +#19 26.25 ** testing if installed package keeps a record of temporary installation path +#19 26.25 * DONE (rappdirs) +#19 26.56 * installing *source* package ‘rlang’ ... +#19 26.58 ** package ‘rlang’ successfully unpacked and MD5 sums checked +#19 26.58 ** using staged installation +#19 26.58 ** libs +#19 26.59 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 26.59 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c capture.c -o capture.o +#19 26.64 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c internal.c -o internal.o +#19 29.80 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rlang.c -o rlang.o +#19 30.60 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c version.c -o version.o +#19 30.62 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o rlang.so capture.o internal.o rlang.o version.o -L/usr/lib/R/lib -lR +#19 30.65 installing to /usr/local/lib/R/site-library/00LOCK-rlang/00new/rlang/libs +#19 30.65 ** R +#19 30.69 ** inst +#19 30.69 ** byte-compile and prepare package for lazy loading +#19 33.04 ** help +#19 33.39 *** installing help indices +#19 33.55 *** copying figures +#19 33.55 ** building package indices +#19 33.88 ** testing if installed package can be loaded from temporary location +#19 34.04 ** checking absolute paths in shared objects and dynamic libraries +#19 34.04 ** testing if installed package can be loaded from final location +#19 34.24 ** testing if installed package keeps a record of temporary installation path +#19 34.24 * DONE (rlang) +#19 34.40 * installing *source* package ‘withr’ ... +#19 34.40 ** package ‘withr’ successfully unpacked and MD5 sums checked +#19 34.40 ** using staged installation +#19 34.41 ** R +#19 34.42 ** inst +#19 34.42 ** byte-compile and prepare package for lazy loading +#19 34.79 ** help +#19 34.82 *** installing help indices +#19 34.85 *** copying figures +#19 34.85 ** building package indices +#19 35.00 ** installing vignettes +#19 35.00 ** testing if installed package can be loaded from temporary location +#19 35.12 ** testing if installed package can be loaded from final location +#19 35.25 ** testing if installed package keeps a record of temporary installation path +#19 35.25 * DONE (withr) +#19 35.41 * installing *source* package ‘RcppTOML’ ... +#19 35.42 ** package ‘RcppTOML’ successfully unpacked and MD5 sums checked +#19 35.42 ** using staged installation +#19 35.42 ** libs +#19 35.43 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ +#19 35.43 using C++17 +#19 35.43 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DTOML_ENABLE_FLOAT16=0 -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o +#19 36.84 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DTOML_ENABLE_FLOAT16=0 -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c parse.cpp -o parse.o +#19 41.27 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o RcppTOML.so RcppExports.o parse.o -L/usr/lib/R/lib -lR +#19 41.34 installing to /usr/local/lib/R/site-library/00LOCK-RcppTOML/00new/RcppTOML/libs +#19 41.34 ** R +#19 41.34 ** inst +#19 41.34 ** byte-compile and prepare package for lazy loading +#19 41.53 ** help +#19 41.54 *** installing help indices +#19 41.54 ** building package indices +#19 41.70 ** testing if installed package can be loaded from temporary location +#19 41.90 ** checking absolute paths in shared objects and dynamic libraries +#19 41.90 ** testing if installed package can be loaded from final location +#19 42.07 ** testing if installed package keeps a record of temporary installation path +#19 42.07 * DONE (RcppTOML) +#19 42.22 * installing *source* package ‘here’ ... +#19 42.22 ** package ‘here’ successfully unpacked and MD5 sums checked +#19 42.22 ** using staged installation +#19 42.23 ** R +#19 42.23 ** inst +#19 42.24 ** byte-compile and prepare package for lazy loading +#19 42.40 ** help +#19 42.41 *** installing help indices +#19 42.42 *** copying figures +#19 42.42 ** building package indices +#19 42.54 ** installing vignettes +#19 42.54 ** testing if installed package can be loaded from temporary location +#19 42.67 ** testing if installed package can be loaded from final location +#19 42.79 ** testing if installed package keeps a record of temporary installation path +#19 42.79 * DONE (here) +#19 43.09 * installing *source* package ‘reticulate’ ... +#19 43.10 ** package ‘reticulate’ successfully unpacked and MD5 sums checked +#19 43.10 ** using staged installation +#19 43.11 ** libs +#19 43.12 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ +#19 43.12 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o +#19 46.21 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c event_loop.cpp -o event_loop.o +#19 46.43 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c libpython.cpp -o libpython.o +#19 47.18 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c output.cpp -o output.o +#19 47.76 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c pending_py_calls_notifier.cpp -o pending_py_calls_notifier.o +#19 48.15 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c python.cpp -o python.o +#19 53.68 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c readline.cpp -o readline.o +#19 53.79 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c signals.cpp -o signals.o +#19 53.97 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o reticulate.so RcppExports.o event_loop.o libpython.o output.o pending_py_calls_notifier.o python.o readline.o signals.o -L/usr/lib/R/lib -lR +#19 54.04 installing to /usr/local/lib/R/site-library/00LOCK-reticulate/00new/reticulate/libs +#19 54.04 ** R +#19 54.07 ** inst +#19 54.07 ** byte-compile and prepare package for lazy loading +#19 56.09 ** help +#19 56.17 *** installing help indices +#19 56.23 *** copying figures +#19 56.23 ** building package indices +#19 56.40 ** installing vignettes +#19 56.41 ** testing if installed package can be loaded from temporary location +#19 57.05 ** checking absolute paths in shared objects and dynamic libraries +#19 57.06 ** testing if installed package can be loaded from final location +#19 57.73 ** testing if installed package keeps a record of temporary installation path +#19 57.73 * DONE (reticulate) +#19 57.75 +#19 57.75 The downloaded source packages are in +#19 57.75 ‘/tmp/RtmpZsJzTy/downloaded_packages’ +#19 58.59 Warning message: +#19 58.59 The request to `use_python("/opt/venv/bin/python")` will be ignored because the environment variable RETICULATE_PYTHON is set to "/opt/venv/bin/python3" +#19 58.59 Installing package into ‘/usr/local/lib/R/site-library’ +#19 58.59 (as ‘lib’ is unspecified) +#19 58.80 trying URL 'https://cloud.r-project.org/src/contrib/remotes_2.5.0.tar.gz' +#19 59.36 Content type 'application/x-gzip' length 164496 bytes (160 KB) +#19 59.36 ================================================== +#19 59.38 downloaded 160 KB +#19 59.38 +#19 59.58 * installing *source* package ‘remotes’ ... +#19 59.58 ** package ‘remotes’ successfully unpacked and MD5 sums checked +#19 59.58 ** using staged installation +#19 59.59 ** R +#19 59.61 ** inst +#19 59.61 ** byte-compile and prepare package for lazy loading +#19 60.62 ** help +#19 60.66 *** installing help indices +#19 60.69 ** building package indices +#19 60.84 ** installing vignettes +#19 60.84 ** testing if installed package can be loaded from temporary location +#19 60.98 ** testing if installed package can be loaded from final location +#19 61.13 ** testing if installed package keeps a record of temporary installation path +#19 61.13 * DONE (remotes) +#19 61.13 +#19 61.13 The downloaded source packages are in +#19 61.13 ‘/tmp/RtmpZsJzTy/downloaded_packages’ +#19 62.38 Downloading package from url: https://cloud.r-project.org/src/contrib/Archive/rjson/rjson_0.2.21.tar.gz +#19 63.59 Installing package into ‘/usr/local/lib/R/site-library’ +#19 63.59 (as ‘lib’ is unspecified) +#19 63.72 * installing *source* package ‘rjson’ ... +#19 63.73 ** package ‘rjson’ successfully unpacked and MD5 sums checked +#19 63.73 ** using staged installation +#19 63.73 ** libs +#19 63.74 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 63.74 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ +#19 63.74 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dump.cpp -o dump.o +#19 64.19 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c parser.c -o parser.o +#19 64.36 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c register.c -o register.o +#19 64.38 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o rjson.so dump.o parser.o register.o -L/usr/lib/R/lib -lR +#19 64.42 installing to /usr/local/lib/R/site-library/00LOCK-rjson/00new/rjson/libs +#19 64.42 ** R +#19 64.42 ** inst +#19 64.43 ** byte-compile and prepare package for lazy loading +#19 64.65 ** help +#19 64.67 *** installing help indices +#19 64.67 ** building package indices +#19 64.79 ** installing vignettes +#19 64.79 ** testing if installed package can be loaded from temporary location +#19 64.91 ** checking absolute paths in shared objects and dynamic libraries +#19 64.92 ** testing if installed package can be loaded from final location +#19 65.04 ** testing if installed package keeps a record of temporary installation path +#19 65.04 * DONE (rjson) +#19 65.05 Installing package into ‘/usr/local/lib/R/site-library’ +#19 65.05 (as ‘lib’ is unspecified) +#19 65.93 trying URL 'http://ran.synapse.org/src/contrib/synapser_2.1.1.259.tar.gz' +#19 66.44 Content type 'application/x-tar' length 6046498 bytes (5.8 MB) +#19 66.80 ================================================== +#19 67.95 downloaded 5.8 MB +#19 67.95 +#19 68.32 * installing *source* package ‘synapser’ ... +#19 68.32 ** using staged installation +#19 69.32 [1] "*** Using Python Configuration:" +#19 69.94 python: /opt/venv/bin/python3 +#19 69.94 libpython: /usr/local/lib/libpython3.10.so +#19 69.94 pythonhome: /opt/venv:/opt/venv +#19 69.94 version: 3.10.12 (main, Oct 21 2024, 16:07:16) [GCC 14.2.0] +#19 69.94 numpy: /opt/venv/lib/python3.10/site-packages/numpy +#19 69.94 numpy_version: 1.26.4 +#19 69.94 +#19 69.94 NOTE: Python version was forced by RETICULATE_PYTHON +#19 69.94 Using virtual environment '/opt/venv' ... +#19 69.96 + /opt/venv/bin/python -m pip install --upgrade --no-user 'pandas>=1.5,<=2.0.3' jinja2 markupsafe 'numpy<=1.24.4' +#19 70.27 Collecting pandas<=2.0.3,>=1.5 +#19 70.39 Downloading pandas-2.0.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (18 kB) +#19 70.44 Collecting jinja2 +#19 70.45 Downloading jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB) +#19 70.52 Collecting markupsafe +#19 70.53 Downloading MarkupSafe-3.0.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (4.0 kB) +#19 70.66 Collecting numpy<=1.24.4 +#19 70.67 Downloading numpy-1.24.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (5.6 kB) +#19 70.68 Requirement already satisfied: python-dateutil>=2.8.2 in /opt/venv/lib/python3.10/site-packages (from pandas<=2.0.3,>=1.5) (2.9.0.post0) +#19 70.68 Requirement already satisfied: pytz>=2020.1 in /opt/venv/lib/python3.10/site-packages (from pandas<=2.0.3,>=1.5) (2024.2) +#19 70.68 Requirement already satisfied: tzdata>=2022.1 in /opt/venv/lib/python3.10/site-packages (from pandas<=2.0.3,>=1.5) (2024.2) +#19 70.68 Requirement already satisfied: six>=1.5 in /opt/venv/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas<=2.0.3,>=1.5) (1.16.0) +#19 70.70 Downloading pandas-2.0.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (11.6 MB) +#19 70.89 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 71.9 MB/s eta 0:00:00 +#19 70.91 Downloading jinja2-3.1.4-py3-none-any.whl (133 kB) +#19 70.92 Downloading MarkupSafe-3.0.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (21 kB) +#19 70.94 Downloading numpy-1.24.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (14.0 MB) +#19 71.11 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.0/14.0 MB 82.8 MB/s eta 0:00:00 +#19 71.21 Installing collected packages: numpy, markupsafe, pandas, jinja2 +#19 71.21 Attempting uninstall: numpy +#19 71.21 Found existing installation: numpy 1.26.4 +#19 71.25 Uninstalling numpy-1.26.4: +#19 71.40 Successfully uninstalled numpy-1.26.4 +#19 72.56 Attempting uninstall: pandas +#19 72.56 Found existing installation: pandas 2.2.3 +#19 72.65 Uninstalling pandas-2.2.3: +#19 73.13 Successfully uninstalled pandas-2.2.3 +#19 75.52 Successfully installed jinja2-3.1.4 markupsafe-3.0.2 numpy-1.24.4 pandas-2.0.3 +#19 75.53 +#19 75.53 [notice] A new release of pip is available: 24.2 -> 24.3.1 +#19 75.53 [notice] To update, run: pip install --upgrade pip +#19 75.59 Using virtual environment '/opt/venv' ... +#19 75.61 + /opt/venv/bin/python -m pip install --upgrade --no-user 'synapseclient==4.4.0' +#19 75.83 Collecting synapseclient==4.4.0 +#19 75.89 Downloading synapseclient-4.4.0-py3-none-any.whl.metadata (15 kB) +#19 75.90 Requirement already satisfied: requests<3.0,>=2.22.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (2.32.3) +#19 75.93 Collecting urllib3<2,>=1.26.18 (from synapseclient==4.4.0) +#19 75.95 Downloading urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB) +#19 75.99 Collecting deprecated<2.0,>=1.2.4 (from synapseclient==4.4.0) +#19 76.01 Downloading Deprecated-1.2.15-py2.py3-none-any.whl.metadata (5.5 kB) +#19 76.04 Collecting opentelemetry-api~=1.21.0 (from synapseclient==4.4.0) +#19 76.05 Downloading opentelemetry_api-1.21.0-py3-none-any.whl.metadata (1.4 kB) +#19 76.09 Collecting opentelemetry-sdk~=1.21.0 (from synapseclient==4.4.0) +#19 76.10 Downloading opentelemetry_sdk-1.21.0-py3-none-any.whl.metadata (1.5 kB) +#19 76.13 Collecting opentelemetry-exporter-otlp-proto-http~=1.21.0 (from synapseclient==4.4.0) +#19 76.14 Downloading opentelemetry_exporter_otlp_proto_http-1.21.0-py3-none-any.whl.metadata (2.4 kB) +#19 76.17 Collecting nest-asyncio~=1.6.0 (from synapseclient==4.4.0) +#19 76.18 Downloading nest_asyncio-1.6.0-py3-none-any.whl.metadata (2.8 kB) +#19 76.20 Collecting asyncio-atexit~=1.0.1 (from synapseclient==4.4.0) +#19 76.22 Downloading asyncio_atexit-1.0.1-py3-none-any.whl.metadata (1.5 kB) +#19 76.25 Collecting httpx~=0.27.0 (from synapseclient==4.4.0) +#19 76.27 Downloading httpx-0.27.2-py3-none-any.whl.metadata (7.1 kB) +#19 76.27 Requirement already satisfied: tqdm<5.0,>=4.66.2 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (4.67.0) +#19 76.29 Collecting async-lru~=2.0.4 (from synapseclient==4.4.0) +#19 76.30 Downloading async_lru-2.0.4-py3-none-any.whl.metadata (4.5 kB) +#19 76.39 Collecting psutil~=5.9.8 (from synapseclient==4.4.0) +#19 76.40 Downloading psutil-5.9.8.tar.gz (503 kB) +#19 76.48 Installing build dependencies: started +#19 77.56 Installing build dependencies: finished with status 'done' +#19 77.56 Getting requirements to build wheel: started +#19 77.69 Getting requirements to build wheel: finished with status 'done' +#19 77.69 Preparing metadata (pyproject.toml): started +#19 77.81 Preparing metadata (pyproject.toml): finished with status 'done' +#19 77.84 Collecting typing-extensions>=4.0.0 (from async-lru~=2.0.4->synapseclient==4.4.0) +#19 77.85 Downloading typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB) +#19 77.92 Collecting wrapt<2,>=1.10 (from deprecated<2.0,>=1.2.4->synapseclient==4.4.0) +#19 77.94 Downloading wrapt-1.16.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (6.6 kB) +#19 77.97 Collecting anyio (from httpx~=0.27.0->synapseclient==4.4.0) +#19 77.98 Downloading anyio-4.6.2.post1-py3-none-any.whl.metadata (4.7 kB) +#19 77.98 Requirement already satisfied: certifi in /opt/venv/lib/python3.10/site-packages (from httpx~=0.27.0->synapseclient==4.4.0) (2024.8.30) +#19 78.01 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googleapis-common-protos~=1.52 (from opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) +#19 78.24 Downloading googleapis_common_protos-1.66.0-py2.py3-none-any.whl.metadata (1.5 kB) +#19 78.27 Collecting opentelemetry-exporter-otlp-proto-common==1.21.0 (from opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) +#19 78.28 Downloading opentelemetry_exporter_otlp_proto_common-1.21.0-py3-none-any.whl.metadata (1.8 kB) +#19 78.31 Collecting opentelemetry-proto==1.21.0 (from opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) +#19 78.33 Downloading opentelemetry_proto-1.21.0-py3-none-any.whl.metadata (2.3 kB) +#19 78.46 Collecting protobuf<5.0,>=3.19 (from opentelemetry-proto==1.21.0->opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) +#19 78.47 Downloading protobuf-4.25.5-cp37-abi3-manylinux2014_aarch64.whl.metadata (541 bytes) +#19 78.50 Collecting opentelemetry-semantic-conventions==0.42b0 (from opentelemetry-sdk~=1.21.0->synapseclient==4.4.0) +#19 78.52 Downloading opentelemetry_semantic_conventions-0.42b0-py3-none-any.whl.metadata (2.3 kB) +#19 78.54 Requirement already satisfied: charset-normalizer<4,>=2 in /opt/venv/lib/python3.10/site-packages (from requests<3.0,>=2.22.0->synapseclient==4.4.0) (3.4.0) +#19 78.60 Collecting zipp>=0.5 (from importlib-metadata<7.0,>=6.0->opentelemetry-api~=1.21.0->synapseclient==4.4.0) +#19 78.61 Downloading zipp-3.21.0-py3-none-any.whl.metadata (3.7 kB) +#19 78.64 Collecting exceptiongroup>=1.0.2 (from anyio->httpx~=0.27.0->synapseclient==4.4.0) +#19 78.65 Downloading exceptiongroup-1.2.2-py3-none-any.whl.metadata (6.6 kB) +#19 78.68 Downloading synapseclient-4.4.0-py3-none-any.whl (354 kB) +#19 78.70 Downloading async_lru-2.0.4-py3-none-any.whl (6.1 kB) +#19 78.71 Downloading asyncio_atexit-1.0.1-py3-none-any.whl (3.8 kB) +#19 78.73 Downloading Deprecated-1.2.15-py2.py3-none-any.whl (9.9 kB) +#19 78.75 Downloading httpx-0.27.2-py3-none-any.whl (76 kB) +#19 78.76 Downloading httpcore-1.0.7-py3-none-any.whl (78 kB) +#19 78.78 Downloading nest_asyncio-1.6.0-py3-none-any.whl (5.2 kB) +#19 78.80 Downloading opentelemetry_api-1.21.0-py3-none-any.whl (57 kB) +#19 78.81 Downloading opentelemetry_exporter_otlp_proto_http-1.21.0-py3-none-any.whl (16 kB) +#19 78.83 Downloading opentelemetry_exporter_otlp_proto_common-1.21.0-py3-none-any.whl (17 kB) +#19 78.85 Downloading opentelemetry_proto-1.21.0-py3-none-any.whl (50 kB) +#19 78.87 Downloading opentelemetry_sdk-1.21.0-py3-none-any.whl (105 kB) +#19 78.88 Downloading opentelemetry_semantic_conventions-0.42b0-py3-none-any.whl (36 kB) +#19 78.90 Downloading urllib3-1.26.20-py2.py3-none-any.whl (144 kB) +#19 78.92 Downloading backoff-2.2.1-py3-none-any.whl (15 kB) +#19 78.93 Downloading googleapis_common_protos-1.66.0-py2.py3-none-any.whl (221 kB) +#19 78.95 Downloading importlib_metadata-6.11.0-py3-none-any.whl (23 kB) +#19 78.97 Downloading typing_extensions-4.12.2-py3-none-any.whl (37 kB) +#19 78.99 Downloading wrapt-1.16.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (80 kB) +#19 79.00 Downloading anyio-4.6.2.post1-py3-none-any.whl (90 kB) +#19 79.02 Downloading sniffio-1.3.1-py3-none-any.whl (10 kB) +#19 79.04 Downloading exceptiongroup-1.2.2-py3-none-any.whl (16 kB) +#19 79.06 Downloading h11-0.14.0-py3-none-any.whl (58 kB) +#19 79.08 Downloading protobuf-4.25.5-cp37-abi3-manylinux2014_aarch64.whl (293 kB) +#19 79.24 Downloading zipp-3.21.0-py3-none-any.whl (9.6 kB) +#19 79.26 Building wheels for collected packages: psutil +#19 79.26 Building wheel for psutil (pyproject.toml): started +#19 80.20 Building wheel for psutil (pyproject.toml): finished with status 'done' +#19 80.20 Created wheel for psutil: filename=psutil-5.9.8-cp310-abi3-linux_aarch64.whl size=287191 sha256=64c0012bc080295b71e6b637dcc837bb5e35b963e2fc0c1b152ee743e284fb48 +#19 80.20 Stored in directory: /root/.cache/pip/wheels/3e/93/d6/85cd469d2103627a9e38acdccc834a9997e77d2abe6da25c8b +#19 80.20 Successfully built psutil +#19 80.27 Installing collected packages: zipp, wrapt, urllib3, typing-extensions, sniffio, psutil, protobuf, opentelemetry-semantic-conventions, nest-asyncio, h11, exceptiongroup, backoff, asyncio-atexit, opentelemetry-proto, importlib-metadata, httpcore, googleapis-common-protos, deprecated, async-lru, anyio, opentelemetry-exporter-otlp-proto-common, opentelemetry-api, httpx, opentelemetry-sdk, opentelemetry-exporter-otlp-proto-http, synapseclient +#19 80.29 Attempting uninstall: urllib3 +#19 80.29 Found existing installation: urllib3 2.2.3 +#19 80.30 Uninstalling urllib3-2.2.3: +#19 80.30 Successfully uninstalled urllib3-2.2.3 +#19 80.84 Successfully installed anyio-4.6.2.post1 async-lru-2.0.4 asyncio-atexit-1.0.1 backoff-2.2.1 deprecated-1.2.15 exceptiongroup-1.2.2 googleapis-common-protos-1.66.0 h11-0.14.0 httpcore-1.0.7 httpx-0.27.2 importlib-metadata-6.11.0 nest-asyncio-1.6.0 opentelemetry-api-1.21.0 opentelemetry-exporter-otlp-proto-common-1.21.0 opentelemetry-exporter-otlp-proto-http-1.21.0 opentelemetry-proto-1.21.0 opentelemetry-sdk-1.21.0 opentelemetry-semantic-conventions-0.42b0 protobuf-4.25.5 psutil-5.9.8 sniffio-1.3.1 synapseclient-4.4.0 typing-extensions-4.12.2 urllib3-1.26.20 wrapt-1.16.0 zipp-3.21.0 +#19 80.85 +#19 80.85 [notice] A new release of pip is available: 24.2 -> 24.3.1 +#19 80.85 [notice] To update, run: pip install --upgrade pip +#19 82.20 ** R +#19 82.20 ** inst +#19 82.21 ** byte-compile and prepare package for lazy loading +#19 83.20 ** help +#19 83.31 *** installing help indices +#19 83.37 ** building package indices +#19 83.55 ** installing vignettes +#19 83.56 ** testing if installed package can be loaded from temporary location +#19 85.15 ** testing if installed package can be loaded from final location +#19 86.73 ** testing if installed package keeps a record of temporary installation path +#19 86.73 * DONE (synapser) +#19 86.74 +#19 86.74 The downloaded source packages are in +#19 86.74 ‘/tmp/RtmpZsJzTy/downloaded_packages’ +#19 86.74 Installing package into ‘/usr/local/lib/R/site-library’ +#19 86.74 (as ‘lib’ is unspecified) +#19 86.97 also installing the dependencies ‘fansi’, ‘utf8’, ‘pkgconfig’, ‘cli’, ‘generics’, ‘glue’, ‘lifecycle’, ‘magrittr’, ‘pillar’, ‘R6’, ‘tibble’, ‘tidyselect’, ‘vctrs’ +#19 86.97 +#19 86.97 trying URL 'https://cloud.r-project.org/src/contrib/fansi_1.0.6.tar.gz' +#19 87.43 Content type 'application/x-gzip' length 482480 bytes (471 KB) +#19 87.43 ================================================== +#19 87.47 downloaded 471 KB +#19 87.47 +#19 87.47 trying URL 'https://cloud.r-project.org/src/contrib/utf8_1.2.4.tar.gz' +#19 88.05 Content type 'application/x-gzip' length 241081 bytes (235 KB) +#19 88.05 ================================================== +#19 88.07 downloaded 235 KB +#19 88.07 +#19 88.18 trying URL 'https://cloud.r-project.org/src/contrib/pkgconfig_2.0.3.tar.gz' +#19 88.64 Content type 'application/x-gzip' length 6080 bytes +#19 88.64 ================================================== +#19 88.64 downloaded 6080 bytes +#19 88.64 +#19 88.65 trying URL 'https://cloud.r-project.org/src/contrib/cli_3.6.3.tar.gz' +#19 89.22 Content type 'application/x-gzip' length 568162 bytes (554 KB) +#19 89.22 ================================================== +#19 89.27 downloaded 554 KB +#19 89.27 +#19 89.27 trying URL 'https://cloud.r-project.org/src/contrib/generics_0.1.3.tar.gz' +#19 89.84 Content type 'application/x-gzip' length 172201 bytes (168 KB) +#19 89.84 ================================================== +#19 89.86 downloaded 168 KB +#19 89.86 +#19 89.87 trying URL 'https://cloud.r-project.org/src/contrib/glue_1.8.0.tar.gz' +#19 90.42 Content type 'application/x-gzip' length 126682 bytes (123 KB) +#19 90.42 ================================================== +#19 90.44 downloaded 123 KB +#19 90.44 +#19 90.44 trying URL 'https://cloud.r-project.org/src/contrib/lifecycle_1.0.4.tar.gz' +#19 90.80 Content type 'application/x-gzip' length 107656 bytes (105 KB) +#19 90.80 ================================================== +#19 90.81 downloaded 105 KB +#19 90.81 +#19 90.82 trying URL 'https://cloud.r-project.org/src/contrib/magrittr_2.0.3.tar.gz' +#19 91.38 Content type 'application/x-gzip' length 267074 bytes (260 KB) +#19 91.38 ================================================== +#19 91.41 downloaded 260 KB +#19 91.41 +#19 91.42 trying URL 'https://cloud.r-project.org/src/contrib/pillar_1.9.0.tar.gz' +#19 92.00 Content type 'application/x-gzip' length 444528 bytes (434 KB) +#19 92.00 ================================================== +#19 92.04 downloaded 434 KB +#19 92.04 +#19 92.04 trying URL 'https://cloud.r-project.org/src/contrib/R6_2.5.1.tar.gz' +#19 92.61 Content type 'application/x-gzip' length 63422 bytes (61 KB) +#19 92.61 ================================================== +#19 92.61 downloaded 61 KB +#19 92.61 +#19 92.62 trying URL 'https://cloud.r-project.org/src/contrib/tibble_3.2.1.tar.gz' +#19 93.19 Content type 'application/x-gzip' length 565982 bytes (552 KB) +#19 93.19 ================================================== +#19 93.24 downloaded 552 KB +#19 93.24 +#19 93.24 trying URL 'https://cloud.r-project.org/src/contrib/tidyselect_1.2.1.tar.gz' +#19 93.69 Content type 'application/x-gzip' length 103591 bytes (101 KB) +#19 93.69 ================================================== +#19 93.71 downloaded 101 KB +#19 93.71 +#19 93.71 trying URL 'https://cloud.r-project.org/src/contrib/vctrs_0.6.5.tar.gz' +#19 94.28 Content type 'application/x-gzip' length 969066 bytes (946 KB) +#19 94.28 ================================================== +#19 94.33 downloaded 946 KB +#19 94.33 +#19 94.33 trying URL 'https://cloud.r-project.org/src/contrib/dplyr_1.1.4.tar.gz' +#19 94.90 Content type 'application/x-gzip' length 1207521 bytes (1.2 MB) +#19 94.90 ================================================== +#19 94.97 downloaded 1.2 MB +#19 94.97 +#19 95.16 * installing *source* package ‘fansi’ ... +#19 95.17 ** package ‘fansi’ successfully unpacked and MD5 sums checked +#19 95.17 ** using staged installation +#19 95.17 ** libs +#19 95.18 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 95.18 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c assumptions.c -o assumptions.o +#19 95.21 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c carry.c -o carry.o +#19 95.29 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c has.c -o has.o +#19 95.32 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o +#19 95.34 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c nchar.c -o nchar.o +#19 95.38 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c normalize.c -o normalize.o +#19 95.45 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read.c -o read.o +#19 95.69 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rnchar.c -o rnchar.o +#19 95.71 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c state.c -o state.o +#19 95.81 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c strip.c -o strip.o +#19 95.91 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c substr.c -o substr.o +#19 96.03 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c tabs.c -o tabs.o +#19 96.09 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c tohtml.c -o tohtml.o +#19 96.27 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c trimws.c -o trimws.o +#19 96.33 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c unhandled.c -o unhandled.o +#19 96.39 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8.c -o utf8.o +#19 96.42 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o +#19 96.52 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c wrap.c -o wrap.o +#19 96.69 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c write.c -o write.o +#19 96.87 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o fansi.so assumptions.o carry.o has.o init.o nchar.o normalize.o read.o rnchar.o state.o strip.o substr.o tabs.o tohtml.o trimws.o unhandled.o utf8.o utils.o wrap.o write.o -L/usr/lib/R/lib -lR +#19 96.88 installing to /usr/local/lib/R/site-library/00LOCK-fansi/00new/fansi/libs +#19 96.88 ** R +#19 96.89 ** inst +#19 96.89 ** byte-compile and prepare package for lazy loading +#19 97.22 ** help +#19 97.28 *** installing help indices +#19 97.32 ** building package indices +#19 97.46 ** installing vignettes +#19 97.46 ** testing if installed package can be loaded from temporary location +#19 97.57 ** checking absolute paths in shared objects and dynamic libraries +#19 97.58 ** testing if installed package can be loaded from final location +#19 97.71 ** testing if installed package keeps a record of temporary installation path +#19 97.71 * DONE (fansi) +#19 97.90 * installing *source* package ‘utf8’ ... +#19 97.90 ** package ‘utf8’ successfully unpacked and MD5 sums checked +#19 97.90 ** using staged installation +#19 97.91 ** libs +#19 97.92 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 97.92 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c as_utf8.c -o as_utf8.o +#19 97.96 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c bytes.c -o bytes.o +#19 98.08 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c context.c -o context.o +#19 98.11 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o +#19 98.13 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c render.c -o render.o +#19 98.17 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c render_table.c -o render_table.o +#19 98.27 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c string.c -o string.o +#19 98.31 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c text.c -o text.o +#19 98.39 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8_encode.c -o utf8_encode.o +#19 98.44 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8_format.c -o utf8_format.o +#19 98.49 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8_normalize.c -o utf8_normalize.o +#19 98.54 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8_valid.c -o utf8_valid.o +#19 98.57 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8_width.c -o utf8_width.o +#19 98.61 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c util.c -o util.o +#19 98.64 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/array.c -o utf8lite/src/array.o +#19 98.67 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/char.c -o utf8lite/src/char.o +#19 98.71 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/encode.c -o utf8lite/src/encode.o +#19 98.75 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/error.c -o utf8lite/src/error.o +#19 98.77 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/escape.c -o utf8lite/src/escape.o +#19 98.81 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/graph.c -o utf8lite/src/graph.o +#19 98.84 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/graphscan.c -o utf8lite/src/graphscan.o +#19 98.96 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/normalize.c -o utf8lite/src/normalize.o +#19 99.13 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/render.c -o utf8lite/src/render.o +#19 99.24 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/text.c -o utf8lite/src/text.o +#19 99.28 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/textassign.c -o utf8lite/src/textassign.o +#19 99.31 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/textiter.c -o utf8lite/src/textiter.o +#19 99.36 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/textmap.c -o utf8lite/src/textmap.o +#19 99.41 ar rcs libcutf8lite.a utf8lite/src/array.o utf8lite/src/char.o utf8lite/src/encode.o utf8lite/src/error.o utf8lite/src/escape.o utf8lite/src/graph.o utf8lite/src/graphscan.o utf8lite/src/normalize.o utf8lite/src/render.o utf8lite/src/text.o utf8lite/src/textassign.o utf8lite/src/textiter.o utf8lite/src/textmap.o +#19 99.41 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o utf8.so as_utf8.o bytes.o context.o init.o render.o render_table.o string.o text.o utf8_encode.o utf8_format.o utf8_normalize.o utf8_valid.o utf8_width.o util.o -L. -lcutf8lite -L/usr/lib/R/lib -lR +#19 99.43 installing to /usr/local/lib/R/site-library/00LOCK-utf8/00new/utf8/libs +#19 99.43 ** R +#19 99.43 ** inst +#19 99.43 ** byte-compile and prepare package for lazy loading +#19 99.66 ** help +#19 99.68 *** installing help indices +#19 99.69 ** building package indices +#19 99.83 ** installing vignettes +#19 99.83 ** testing if installed package can be loaded from temporary location +#19 99.95 ** checking absolute paths in shared objects and dynamic libraries +#19 99.95 ** testing if installed package can be loaded from final location +#19 100.1 ** testing if installed package keeps a record of temporary installation path +#19 100.1 * DONE (utf8) +#19 100.2 * installing *source* package ‘pkgconfig’ ... +#19 100.2 ** package ‘pkgconfig’ successfully unpacked and MD5 sums checked +#19 100.2 ** using staged installation +#19 100.2 ** R +#19 100.2 ** inst +#19 100.2 ** byte-compile and prepare package for lazy loading +#19 100.4 ** help +#19 100.4 *** installing help indices +#19 100.4 ** building package indices +#19 100.5 ** testing if installed package can be loaded from temporary location +#19 100.6 ** testing if installed package can be loaded from final location +#19 100.7 ** testing if installed package keeps a record of temporary installation path +#19 100.7 * DONE (pkgconfig) +#19 101.0 * installing *source* package ‘cli’ ... +#19 101.0 ** package ‘cli’ successfully unpacked and MD5 sums checked +#19 101.0 ** using staged installation +#19 101.0 ** libs +#19 101.0 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 101.0 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c ansi.c -o ansi.o +#19 101.3 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cleancall.c -o cleancall.o +#19 101.3 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c diff.c -o diff.o +#19 101.4 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c errors.c -o errors.o +#19 101.4 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c glue.c -o glue.o +#19 101.6 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o +#19 101.6 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c inst.c -o inst.o +#19 101.6 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c keypress-unix.c -o keypress-unix.o +#19 101.7 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c keypress-win.c -o keypress-win.o +#19 101.7 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c keypress.c -o keypress.o +#19 101.7 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c md5.c -o md5.o +#19 101.9 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c progress-altrep.c -o progress-altrep.o +#19 101.9 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c progress.c -o progress.o +#19 102.0 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c sha1.c -o sha1.o +#19 102.1 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c sha256.c -o sha256.o +#19 102.2 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c thread.c -o thread.o +#19 102.3 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c tty.c -o tty.o +#19 102.3 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8.c -o utf8.o +#19 102.5 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o +#19 102.6 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c vt.c -o vt.o +#19 102.7 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c vtparse.c -o vtparse.o +#19 102.8 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c vtparse_table.c -o vtparse_table.o +#19 102.8 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c win-utf8.c -o win-utf8.o +#19 102.8 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c winfiles.c -o winfiles.o +#19 102.8 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o cli.so ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o -lpthread -L/usr/lib/R/lib -lR +#19 102.8 installing to /usr/local/lib/R/site-library/00LOCK-cli/00new/cli/libs +#19 102.8 ** R +#19 102.9 ** exec +#19 102.9 ** inst +#19 102.9 ** byte-compile and prepare package for lazy loading +#19 105.0 ** help +#19 105.2 *** installing help indices +#19 105.3 *** copying figures +#19 105.3 ** building package indices +#19 105.6 ** testing if installed package can be loaded from temporary location +#19 105.7 ** checking absolute paths in shared objects and dynamic libraries +#19 105.7 ** testing if installed package can be loaded from final location +#19 105.9 ** testing if installed package keeps a record of temporary installation path +#19 105.9 * DONE (cli) +#19 106.1 * installing *source* package ‘generics’ ... +#19 106.1 ** package ‘generics’ successfully unpacked and MD5 sums checked +#19 106.1 ** using staged installation +#19 106.1 ** R +#19 106.1 ** byte-compile and prepare package for lazy loading +#19 106.2 ** help +#19 106.3 *** installing help indices +#19 106.3 ** building package indices +#19 106.5 ** testing if installed package can be loaded from temporary location +#19 106.6 ** testing if installed package can be loaded from final location +#19 106.7 ** testing if installed package keeps a record of temporary installation path +#19 106.7 * DONE (generics) +#19 106.9 * installing *source* package ‘glue’ ... +#19 106.9 ** package ‘glue’ successfully unpacked and MD5 sums checked +#19 106.9 ** using staged installation +#19 106.9 ** libs +#19 106.9 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 106.9 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c glue.c -o glue.o +#19 106.9 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o +#19 107.0 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c trim.c -o trim.o +#19 107.0 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o glue.so glue.o init.o trim.o -L/usr/lib/R/lib -lR +#19 107.0 installing to /usr/local/lib/R/site-library/00LOCK-glue/00new/glue/libs +#19 107.0 ** R +#19 107.0 ** inst +#19 107.0 ** byte-compile and prepare package for lazy loading +#19 107.3 ** help +#19 107.3 *** installing help indices +#19 107.3 *** copying figures +#19 107.3 ** building package indices +#19 107.5 ** installing vignettes +#19 107.5 ** testing if installed package can be loaded from temporary location +#19 107.6 ** checking absolute paths in shared objects and dynamic libraries +#19 107.6 ** testing if installed package can be loaded from final location +#19 107.8 ** testing if installed package keeps a record of temporary installation path +#19 107.8 * DONE (glue) +#19 107.9 * installing *source* package ‘magrittr’ ... +#19 107.9 ** package ‘magrittr’ successfully unpacked and MD5 sums checked +#19 107.9 ** using staged installation +#19 107.9 ** libs +#19 107.9 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 107.9 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c pipe.c -o pipe.o +#19 108.0 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o +#19 108.1 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o magrittr.so pipe.o utils.o -L/usr/lib/R/lib -lR +#19 108.1 installing to /usr/local/lib/R/site-library/00LOCK-magrittr/00new/magrittr/libs +#19 108.1 ** R +#19 108.1 ** inst +#19 108.1 ** byte-compile and prepare package for lazy loading +#19 108.2 ** help +#19 108.3 *** installing help indices +#19 108.3 *** copying figures +#19 108.3 ** building package indices +#19 108.4 ** installing vignettes +#19 108.4 ** testing if installed package can be loaded from temporary location +#19 108.5 ** checking absolute paths in shared objects and dynamic libraries +#19 108.5 ** testing if installed package can be loaded from final location +#19 108.6 ** testing if installed package keeps a record of temporary installation path +#19 108.6 * DONE (magrittr) +#19 108.8 * installing *source* package ‘R6’ ... +#19 108.8 ** package ‘R6’ successfully unpacked and MD5 sums checked +#19 108.8 ** using staged installation +#19 108.8 ** R +#19 108.8 ** byte-compile and prepare package for lazy loading +#19 109.1 ** help +#19 109.1 *** installing help indices +#19 109.1 *** copying figures +#19 109.1 ** building package indices +#19 109.2 ** testing if installed package can be loaded from temporary location +#19 109.3 ** testing if installed package can be loaded from final location +#19 109.4 ** testing if installed package keeps a record of temporary installation path +#19 109.4 * DONE (R6) +#19 109.6 * installing *source* package ‘lifecycle’ ... +#19 109.6 ** package ‘lifecycle’ successfully unpacked and MD5 sums checked +#19 109.6 ** using staged installation +#19 109.6 ** R +#19 109.6 ** inst +#19 109.6 ** byte-compile and prepare package for lazy loading +#19 109.9 ** help +#19 109.9 *** installing help indices +#19 110.0 *** copying figures +#19 110.0 ** building package indices +#19 110.1 ** installing vignettes +#19 110.1 ** testing if installed package can be loaded from temporary location +#19 110.3 ** testing if installed package can be loaded from final location +#19 110.4 ** testing if installed package keeps a record of temporary installation path +#19 110.4 * DONE (lifecycle) +#19 110.7 * installing *source* package ‘vctrs’ ... +#19 110.8 ** package ‘vctrs’ successfully unpacked and MD5 sums checked +#19 110.8 ** using staged installation +#19 110.8 ** libs +#19 110.8 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 110.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c altrep-lazy-character.c -o altrep-lazy-character.o +#19 110.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c altrep-rle.c -o altrep-rle.o +#19 110.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c altrep.c -o altrep.o +#19 110.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c arg-counter.c -o arg-counter.o +#19 111.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c arg.c -o arg.o +#19 111.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c assert.c -o assert.o +#19 111.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c bind.c -o bind.o +#19 111.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c c-unchop.c -o c-unchop.o +#19 111.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c c.c -o c.o +#19 111.4 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c callables.c -o callables.o +#19 111.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cast-bare.c -o cast-bare.o +#19 111.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cast-dispatch.c -o cast-dispatch.o +#19 111.7 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cast.c -o cast.o +#19 111.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c compare.c -o compare.o +#19 111.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c complete.c -o complete.o +#19 112.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c conditions.c -o conditions.o +#19 112.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dictionary.c -o dictionary.o +#19 112.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dim.c -o dim.o +#19 112.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c empty.c -o empty.o +#19 112.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c equal.c -o equal.o +#19 112.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c expand.c -o expand.o +#19 112.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fields.c -o fields.o +#19 112.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fill.c -o fill.o +#19 112.7 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c globals.c -o globals.o +#19 112.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c group.c -o group.o +#19 112.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c growable.c -o growable.o +#19 112.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c hash.c -o hash.o +#19 113.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o +#19 113.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c interval.c -o interval.o +#19 113.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c match-joint.c -o match-joint.o +#19 113.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c match.c -o match.o +#19 114.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c missing.c -o missing.o +#19 114.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c names.c -o names.o +#19 114.4 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c order-collate.c -o order-collate.o +#19 114.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c order-groups.c -o order-groups.o +#19 114.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c order-sortedness.c -o order-sortedness.o +#19 114.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c order-truelength.c -o order-truelength.o +#19 114.7 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c order.c -o order.o +#19 115.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c poly-op.c -o poly-op.o +#19 115.4 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c proxy-restore.c -o proxy-restore.o +#19 115.4 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c proxy.c -o proxy.o +#19 115.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c ptype-common.c -o ptype-common.o +#19 115.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c ptype.c -o ptype.o +#19 115.7 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c ptype2-dispatch.c -o ptype2-dispatch.o +#19 115.7 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c ptype2.c -o ptype2.o +#19 115.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rank.c -o rank.o +#19 115.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rep.c -o rep.o +#19 116.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rlang-dev.c -o rlang-dev.o +#19 116.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rlang.c -o rlang.o +#19 116.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c runs.c -o runs.o +#19 116.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c set.c -o set.o +#19 117.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c shape.c -o shape.o +#19 117.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c size-common.c -o size-common.o +#19 117.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c size.c -o size.o +#19 117.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice-array.c -o slice-array.o +#19 117.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice-assign-array.c -o slice-assign-array.o +#19 117.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice-assign.c -o slice-assign.o +#19 117.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice-chop.c -o slice-chop.o +#19 118.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice-interleave.c -o slice-interleave.o +#19 118.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice.c -o slice.o +#19 118.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c split.c -o split.o +#19 118.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c subscript-loc.c -o subscript-loc.o +#19 118.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c subscript.c -o subscript.o +#19 118.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c translate.c -o translate.o +#19 118.7 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c type-data-frame.c -o type-data-frame.o +#19 118.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c type-date-time.c -o type-date-time.o +#19 119.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c type-factor.c -o type-factor.o +#19 119.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c type-info.c -o type-info.o +#19 119.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c type-integer64.c -o type-integer64.o +#19 119.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c type-tibble.c -o type-tibble.o +#19 119.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c typeof2-s3.c -o typeof2-s3.o +#19 119.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c typeof2.c -o typeof2.o +#19 119.4 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c unspecified.c -o unspecified.o +#19 119.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils-dispatch.c -o utils-dispatch.o +#19 119.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o +#19 119.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c vctrs-core.c -o vctrs-core.o +#19 119.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c version.c -o version.o +#19 120.0 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o vctrs.so altrep-lazy-character.o altrep-rle.o altrep.o arg-counter.o arg.o assert.o bind.o c-unchop.o c.o callables.o cast-bare.o cast-dispatch.o cast.o compare.o complete.o conditions.o dictionary.o dim.o empty.o equal.o expand.o fields.o fill.o globals.o group.o growable.o hash.o init.o interval.o match-joint.o match.o missing.o names.o order-collate.o order-groups.o order-sortedness.o order-truelength.o order.o poly-op.o proxy-restore.o proxy.o ptype-common.o ptype.o ptype2-dispatch.o ptype2.o rank.o rep.o rlang-dev.o rlang.o runs.o set.o shape.o size-common.o size.o slice-array.o slice-assign-array.o slice-assign.o slice-chop.o slice-interleave.o slice.o split.o subscript-loc.o subscript.o translate.o type-data-frame.o type-date-time.o type-factor.o type-info.o type-integer64.o type-tibble.o typeof2-s3.o typeof2.o unspecified.o utils-dispatch.o utils.o vctrs-core.o version.o -L/usr/lib/R/lib -lR +#19 120.0 installing to /usr/local/lib/R/site-library/00LOCK-vctrs/00new/vctrs/libs +#19 120.0 ** R +#19 120.0 ** inst +#19 120.0 ** byte-compile and prepare package for lazy loading +#19 121.4 ** help +#19 121.6 *** installing help indices +#19 121.7 *** copying figures +#19 121.7 ** building package indices +#19 121.9 ** installing vignettes +#19 121.9 ** testing if installed package can be loaded from temporary location +#19 122.1 ** checking absolute paths in shared objects and dynamic libraries +#19 122.1 ** testing if installed package can be loaded from final location +#19 122.3 ** testing if installed package keeps a record of temporary installation path +#19 122.3 * DONE (vctrs) +#19 122.5 * installing *source* package ‘pillar’ ... +#19 122.5 ** package ‘pillar’ successfully unpacked and MD5 sums checked +#19 122.5 ** using staged installation +#19 122.5 ** R +#19 122.6 ** inst +#19 122.6 ** byte-compile and prepare package for lazy loading +#19 123.7 ** help +#19 123.7 *** installing help indices +#19 123.8 *** copying figures +#19 123.8 ** building package indices +#19 123.9 ** installing vignettes +#19 123.9 ** testing if installed package can be loaded from temporary location +#19 124.2 ** testing if installed package can be loaded from final location +#19 124.4 ** testing if installed package keeps a record of temporary installation path +#19 124.4 * DONE (pillar) +#19 124.6 * installing *source* package ‘tidyselect’ ... +#19 124.6 ** package ‘tidyselect’ successfully unpacked and MD5 sums checked +#19 124.6 ** using staged installation +#19 124.6 ** R +#19 124.6 ** inst +#19 124.6 ** byte-compile and prepare package for lazy loading +#19 125.3 ** help +#19 125.3 *** installing help indices +#19 125.3 ** building package indices +#19 125.5 ** installing vignettes +#19 125.5 ** testing if installed package can be loaded from temporary location +#19 125.7 ** testing if installed package can be loaded from final location +#19 125.9 ** testing if installed package keeps a record of temporary installation path +#19 125.9 * DONE (tidyselect) +#19 126.1 * installing *source* package ‘tibble’ ... +#19 126.1 ** package ‘tibble’ successfully unpacked and MD5 sums checked +#19 126.1 ** using staged installation +#19 126.1 ** libs +#19 126.1 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 126.1 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c attributes.c -o attributes.o +#19 126.1 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c coerce.c -o coerce.o +#19 126.2 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o +#19 126.2 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c matrixToDataFrame.c -o matrixToDataFrame.o +#19 126.2 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o tibble.so attributes.o coerce.o init.o matrixToDataFrame.o -L/usr/lib/R/lib -lR +#19 126.3 installing to /usr/local/lib/R/site-library/00LOCK-tibble/00new/tibble/libs +#19 126.3 ** R +#19 126.3 ** inst +#19 126.3 ** byte-compile and prepare package for lazy loading +#19 127.1 ** help +#19 127.1 *** installing help indices +#19 127.2 *** copying figures +#19 127.2 ** building package indices +#19 127.3 ** installing vignettes +#19 127.3 ** testing if installed package can be loaded from temporary location +#19 127.6 ** checking absolute paths in shared objects and dynamic libraries +#19 127.6 ** testing if installed package can be loaded from final location +#19 127.9 ** testing if installed package keeps a record of temporary installation path +#19 127.9 * DONE (tibble) +#19 128.2 * installing *source* package ‘dplyr’ ... +#19 128.2 ** package ‘dplyr’ successfully unpacked and MD5 sums checked +#19 128.2 ** using staged installation +#19 128.2 ** libs +#19 128.2 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ +#19 128.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c chop.cpp -o chop.o +#19 128.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c filter.cpp -o filter.o +#19 128.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c funs.cpp -o funs.o +#19 128.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c group_by.cpp -o group_by.o +#19 129.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c group_data.cpp -o group_data.o +#19 129.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c imports.cpp -o imports.o +#19 129.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.cpp -o init.o +#19 129.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mask.cpp -o mask.o +#19 129.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mutate.cpp -o mutate.o +#19 129.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c reconstruct.cpp -o reconstruct.o +#19 129.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice.cpp -o slice.o +#19 129.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c summarise.cpp -o summarise.o +#19 129.9 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o dplyr.so chop.o filter.o funs.o group_by.o group_data.o imports.o init.o mask.o mutate.o reconstruct.o slice.o summarise.o -L/usr/lib/R/lib -lR +#19 130.0 installing to /usr/local/lib/R/site-library/00LOCK-dplyr/00new/dplyr/libs +#19 130.0 ** R +#19 130.0 ** data +#19 130.0 *** moving datasets to lazyload DB +#19 130.1 ** inst +#19 130.1 ** byte-compile and prepare package for lazy loading +#19 132.5 ** help +#19 132.7 *** installing help indices +#19 132.8 *** copying figures +#19 132.8 ** building package indices +#19 133.0 ** installing vignettes +#19 133.0 ** testing if installed package can be loaded from temporary location +#19 133.3 ** checking absolute paths in shared objects and dynamic libraries +#19 133.3 ** testing if installed package can be loaded from final location +#19 133.7 ** testing if installed package keeps a record of temporary installation path +#19 133.7 * DONE (dplyr) +#19 133.7 +#19 133.7 The downloaded source packages are in +#19 133.7 ‘/tmp/RtmpZsJzTy/downloaded_packages’ +#19 133.7 Installing package into ‘/usr/local/lib/R/site-library’ +#19 133.7 (as ‘lib’ is unspecified) +#19 133.9 trying URL 'https://cloud.r-project.org/src/contrib/data.table_1.16.2.tar.gz' +#19 134.4 Content type 'application/x-gzip' length 5490076 bytes (5.2 MB) +#19 134.4 ================================================== +#19 134.5 downloaded 5.2 MB +#19 134.5 +#19 135.0 * installing *source* package ‘data.table’ ... +#19 135.0 ** package ‘data.table’ successfully unpacked and MD5 sums checked +#19 135.0 ** using staged installation +#19 135.2 gcc 14.2.0 +#19 135.2 zlib 1.3.1 is available ok +#19 135.2 * checking if R installation supports OpenMP without any extra hints... yes +#19 135.3 ** libs +#19 135.3 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 135.3 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c assign.c -o assign.o +#19 136.3 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c between.c -o between.o +#19 136.4 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c bmerge.c -o bmerge.o +#19 136.8 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c chmatch.c -o chmatch.o +#19 136.9 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cj.c -o cj.o +#19 137.0 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c coalesce.c -o coalesce.o +#19 137.1 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dogroups.c -o dogroups.o +#19 137.4 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fastmean.c -o fastmean.o +#19 137.5 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fcast.c -o fcast.o +#19 137.5 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fifelse.c -o fifelse.o +#19 137.8 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fmelt.c -o fmelt.o +#19 138.2 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c forder.c -o forder.o +#19 138.9 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c frank.c -o frank.o +#19 139.0 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fread.c -o fread.o +#19 140.1 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c freadR.c -o freadR.o +#19 140.4 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c froll.c -o froll.o +#19 140.6 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c frollR.c -o frollR.o +#19 140.8 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c frolladaptive.c -o frolladaptive.o +#19 140.9 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fsort.c -o fsort.o +#19 141.1 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fwrite.c -o fwrite.o +#19 141.4 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fwriteR.c -o fwriteR.o +#19 141.5 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c gsumm.c -o gsumm.o +#19 142.5 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c idatetime.c -o idatetime.o +#19 142.5 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c ijoin.c -o ijoin.o +#19 142.8 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o +#19 142.9 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c inrange.c -o inrange.o +#19 142.9 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c nafill.c -o nafill.o +#19 143.0 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c negate.c -o negate.o +#19 143.1 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c nqrecreateindices.c -o nqrecreateindices.o +#19 143.1 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c openmp-utils.c -o openmp-utils.o +#19 143.2 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c programming.c -o programming.o +#19 143.2 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c quickselect.c -o quickselect.o +#19 143.3 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rbindlist.c -o rbindlist.o +#19 143.6 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c reorder.c -o reorder.o +#19 143.7 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c shift.c -o shift.o +#19 143.8 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c snprintf.c -o snprintf.o +#19 143.9 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c subset.c -o subset.o +#19 144.2 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c transpose.c -o transpose.o +#19 144.2 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c types.c -o types.o +#19 144.3 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c uniqlist.c -o uniqlist.o +#19 144.5 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o +#19 144.7 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c vecseq.c -o vecseq.o +#19 144.7 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c wrappers.c -o wrappers.o +#19 144.8 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -lz -L/usr/lib/R/lib -lR +#19 144.8 PKG_CFLAGS = -fopenmp +#19 144.8 PKG_LIBS = -fopenmp -lz +#19 144.8 if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi +#19 144.8 if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi +#19 144.8 installing to /usr/local/lib/R/site-library/00LOCK-data.table/00new/data.table/libs +#19 144.8 ** R +#19 144.8 ** inst +#19 144.8 ** byte-compile and prepare package for lazy loading +#19 147.7 ** help +#19 147.8 *** installing help indices +#19 147.9 ** building package indices +#19 148.1 ** installing vignettes +#19 148.1 ** testing if installed package can be loaded from temporary location +#19 148.3 ** checking absolute paths in shared objects and dynamic libraries +#19 148.3 ** testing if installed package can be loaded from final location +#19 148.5 ** testing if installed package keeps a record of temporary installation path +#19 148.6 * DONE (data.table) +#19 148.6 +#19 148.6 The downloaded source packages are in +#19 148.6 ‘/tmp/RtmpZsJzTy/downloaded_packages’ +#19 148.6 Installing package into ‘/usr/local/lib/R/site-library’ +#19 148.6 (as ‘lib’ is unspecified) +#19 148.8 trying URL 'http://ran.synapse.org/src/contrib/synapser_2.1.1.259.tar.gz' +#19 149.3 Content type 'application/x-tar' length 6046498 bytes (5.8 MB) +#19 149.6 ================================================== +#19 151.5 downloaded 5.8 MB +#19 151.5 +#19 151.8 * installing *source* package ‘synapser’ ... +#19 151.8 ** using staged installation +#19 152.8 [1] "*** Using Python Configuration:" +#19 153.5 python: /opt/venv/bin/python3 +#19 153.5 libpython: /usr/local/lib/libpython3.10.so +#19 153.5 pythonhome: /opt/venv:/opt/venv +#19 153.5 version: 3.10.12 (main, Oct 21 2024, 16:07:16) [GCC 14.2.0] +#19 153.5 numpy: /opt/venv/lib/python3.10/site-packages/numpy +#19 153.5 numpy_version: 1.24.4 +#19 153.5 +#19 153.5 NOTE: Python version was forced by RETICULATE_PYTHON +#19 153.5 Using virtual environment '/opt/venv' ... +#19 153.5 + /opt/venv/bin/python -m pip install --upgrade --no-user 'pandas>=1.5,<=2.0.3' jinja2 markupsafe 'numpy<=1.24.4' +#19 153.6 Requirement already satisfied: pandas<=2.0.3,>=1.5 in /opt/venv/lib/python3.10/site-packages (2.0.3) +#19 153.8 Requirement already satisfied: jinja2 in /opt/venv/lib/python3.10/site-packages (3.1.4) +#19 153.8 Requirement already satisfied: markupsafe in /opt/venv/lib/python3.10/site-packages (3.0.2) +#19 153.8 Requirement already satisfied: numpy<=1.24.4 in /opt/venv/lib/python3.10/site-packages (1.24.4) +#19 154.0 Requirement already satisfied: python-dateutil>=2.8.2 in /opt/venv/lib/python3.10/site-packages (from pandas<=2.0.3,>=1.5) (2.9.0.post0) +#19 154.0 Requirement already satisfied: pytz>=2020.1 in /opt/venv/lib/python3.10/site-packages (from pandas<=2.0.3,>=1.5) (2024.2) +#19 154.0 Requirement already satisfied: tzdata>=2022.1 in /opt/venv/lib/python3.10/site-packages (from pandas<=2.0.3,>=1.5) (2024.2) +#19 154.0 Requirement already satisfied: six>=1.5 in /opt/venv/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas<=2.0.3,>=1.5) (1.16.0) +#19 154.1 +#19 154.1 [notice] A new release of pip is available: 24.2 -> 24.3.1 +#19 154.1 [notice] To update, run: pip install --upgrade pip +#19 154.2 Using virtual environment '/opt/venv' ... +#19 154.3 + /opt/venv/bin/python -m pip install --upgrade --no-user 'synapseclient==4.4.0' +#19 154.4 Requirement already satisfied: synapseclient==4.4.0 in /opt/venv/lib/python3.10/site-packages (4.4.0) +#19 154.5 Requirement already satisfied: requests<3.0,>=2.22.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (2.32.3) +#19 154.5 Requirement already satisfied: urllib3<2,>=1.26.18 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.26.20) +#19 154.5 Requirement already satisfied: deprecated<2.0,>=1.2.4 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.2.15) +#19 154.5 Requirement already satisfied: opentelemetry-api~=1.21.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.21.0) +#19 154.5 Requirement already satisfied: opentelemetry-sdk~=1.21.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.21.0) +#19 154.5 Requirement already satisfied: opentelemetry-exporter-otlp-proto-http~=1.21.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.21.0) +#19 154.5 Requirement already satisfied: nest-asyncio~=1.6.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.6.0) +#19 154.5 Requirement already satisfied: asyncio-atexit~=1.0.1 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.0.1) +#19 154.5 Requirement already satisfied: httpx~=0.27.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (0.27.2) +#19 154.5 Requirement already satisfied: tqdm<5.0,>=4.66.2 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (4.67.0) +#19 154.5 Requirement already satisfied: async-lru~=2.0.4 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (2.0.4) +#19 154.5 Requirement already satisfied: psutil~=5.9.8 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (5.9.8) +#19 154.5 Requirement already satisfied: typing-extensions>=4.0.0 in /opt/venv/lib/python3.10/site-packages (from async-lru~=2.0.4->synapseclient==4.4.0) (4.12.2) +#19 154.5 Requirement already satisfied: wrapt<2,>=1.10 in /opt/venv/lib/python3.10/site-packages (from deprecated<2.0,>=1.2.4->synapseclient==4.4.0) (1.16.0) +#19 154.5 Requirement already satisfied: anyio in /opt/venv/lib/python3.10/site-packages (from httpx~=0.27.0->synapseclient==4.4.0) (4.6.2.post1) +#19 154.5 Requirement already satisfied: certifi in /opt/venv/lib/python3.10/site-packages (from httpx~=0.27.0->synapseclient==4.4.0) (2024.8.30) +#19 154.5 Requirement already satisfied: httpcore==1.* in /opt/venv/lib/python3.10/site-packages (from httpx~=0.27.0->synapseclient==4.4.0) (1.0.7) +#19 154.5 Requirement already satisfied: idna in /opt/venv/lib/python3.10/site-packages (from httpx~=0.27.0->synapseclient==4.4.0) (3.10) +#19 154.5 Requirement already satisfied: sniffio in /opt/venv/lib/python3.10/site-packages (from httpx~=0.27.0->synapseclient==4.4.0) (1.3.1) +#19 154.5 Requirement already satisfied: h11<0.15,>=0.13 in /opt/venv/lib/python3.10/site-packages (from httpcore==1.*->httpx~=0.27.0->synapseclient==4.4.0) (0.14.0) +#19 154.5 Requirement already satisfied: importlib-metadata<7.0,>=6.0 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-api~=1.21.0->synapseclient==4.4.0) (6.11.0) +#19 154.5 Requirement already satisfied: backoff<3.0.0,>=1.10.0 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) (2.2.1) +#19 154.5 Requirement already satisfied: googleapis-common-protos~=1.52 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) (1.66.0) +#19 154.5 Requirement already satisfied: opentelemetry-exporter-otlp-proto-common==1.21.0 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) (1.21.0) +#19 154.5 Requirement already satisfied: opentelemetry-proto==1.21.0 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) (1.21.0) +#19 154.5 Requirement already satisfied: protobuf<5.0,>=3.19 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-proto==1.21.0->opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) (4.25.5) +#19 154.5 Requirement already satisfied: opentelemetry-semantic-conventions==0.42b0 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-sdk~=1.21.0->synapseclient==4.4.0) (0.42b0) +#19 154.5 Requirement already satisfied: charset-normalizer<4,>=2 in /opt/venv/lib/python3.10/site-packages (from requests<3.0,>=2.22.0->synapseclient==4.4.0) (3.4.0) +#19 154.5 Requirement already satisfied: zipp>=0.5 in /opt/venv/lib/python3.10/site-packages (from importlib-metadata<7.0,>=6.0->opentelemetry-api~=1.21.0->synapseclient==4.4.0) (3.21.0) +#19 154.6 Requirement already satisfied: exceptiongroup>=1.0.2 in /opt/venv/lib/python3.10/site-packages (from anyio->httpx~=0.27.0->synapseclient==4.4.0) (1.2.2) +#19 154.6 +#19 154.6 [notice] A new release of pip is available: 24.2 -> 24.3.1 +#19 154.6 [notice] To update, run: pip install --upgrade pip +#19 155.8 ** R +#19 155.8 ** inst +#19 155.8 ** byte-compile and prepare package for lazy loading +#19 156.7 ** help +#19 156.8 *** installing help indices +#19 156.8 ** building package indices +#19 157.0 ** installing vignettes +#19 157.0 ** testing if installed package can be loaded from temporary location +#19 158.6 ** testing if installed package can be loaded from final location +#19 160.2 ** testing if installed package keeps a record of temporary installation path +#19 160.2 * DONE (synapser) +#19 160.2 +#19 160.2 The downloaded source packages are in +#19 160.2 ‘/tmp/RtmpZsJzTy/downloaded_packages’ +#19 160.2 Installing package into ‘/usr/local/lib/R/site-library’ +#19 160.2 (as ‘lib’ is unspecified) +#19 160.4 also installing the dependencies ‘R.oo’, ‘R.methodsS3’ +#19 160.4 +#19 160.4 trying URL 'https://cloud.r-project.org/src/contrib/R.oo_1.27.0.tar.gz' +#19 160.9 Content type 'application/x-gzip' length 384222 bytes (375 KB) +#19 160.9 ================================================== +#19 160.9 downloaded 375 KB +#19 160.9 +#19 160.9 trying URL 'https://cloud.r-project.org/src/contrib/R.methodsS3_1.8.2.tar.gz' +#19 161.3 Content type 'application/x-gzip' length 24131 bytes (23 KB) +#19 161.3 ================================================== +#19 161.3 downloaded 23 KB +#19 161.3 +#19 161.3 trying URL 'https://cloud.r-project.org/src/contrib/R.utils_2.12.3.tar.gz' +#19 161.9 Content type 'application/x-gzip' length 364188 bytes (355 KB) +#19 161.9 ================================================== +#19 161.9 downloaded 355 KB +#19 161.9 +#19 162.1 * installing *source* package ‘R.methodsS3’ ... +#19 162.1 ** package ‘R.methodsS3’ successfully unpacked and MD5 sums checked +#19 162.1 ** using staged installation +#19 162.1 ** R +#19 162.1 ** inst +#19 162.1 ** byte-compile and prepare package for lazy loading +#19 162.3 ** help +#19 162.3 *** installing help indices +#19 162.4 ** building package indices +#19 162.5 ** testing if installed package can be loaded from temporary location +#19 162.6 ** testing if installed package can be loaded from final location +#19 162.7 ** testing if installed package keeps a record of temporary installation path +#19 162.7 * DONE (R.methodsS3) +#19 162.9 * installing *source* package ‘R.oo’ ... +#19 163.0 ** package ‘R.oo’ successfully unpacked and MD5 sums checked +#19 163.0 ** using staged installation +#19 163.0 ** R +#19 163.0 ** inst +#19 163.0 ** byte-compile and prepare package for lazy loading +#19 164.2 Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : +#19 164.2 Renamed the preexisting function getMethods to getMethods.default, which was defined in environment R.oo. +#19 164.2 Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : +#19 164.2 Renamed the preexisting function getClasses to getClasses.default, which was defined in environment R.oo. +#19 164.2 ** help +#19 164.4 *** installing help indices +#19 164.6 ** building package indices +#19 164.8 ** testing if installed package can be loaded from temporary location +#19 165.0 ** testing if installed package can be loaded from final location +#19 165.1 ** testing if installed package keeps a record of temporary installation path +#19 165.1 * DONE (R.oo) +#19 165.4 * installing *source* package ‘R.utils’ ... +#19 165.4 ** package ‘R.utils’ successfully unpacked and MD5 sums checked +#19 165.4 ** using staged installation +#19 165.4 ** R +#19 165.4 ** inst +#19 165.4 ** byte-compile and prepare package for lazy loading +#19 167.9 Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : +#19 167.9 Renamed the preexisting function warnings to warnings.default, which was defined in environment R.utils. +#19 167.9 ** help +#19 168.3 *** installing help indices +#19 168.5 ** building package indices +#19 168.8 ** testing if installed package can be loaded from temporary location +#19 169.0 ** testing if installed package can be loaded from final location +#19 169.2 ** testing if installed package keeps a record of temporary installation path +#19 169.2 * DONE (R.utils) +#19 169.2 +#19 169.2 The downloaded source packages are in +#19 169.2 ‘/tmp/RtmpZsJzTy/downloaded_packages’ +#19 169.2 Installing package into ‘/usr/local/lib/R/site-library’ +#19 169.2 (as ‘lib’ is unspecified) +#19 169.4 also installing the dependency ‘stringi’ +#19 169.4 +#19 169.4 trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.8.4.tar.gz' +#19 169.9 Content type 'application/x-gzip' length 11917497 bytes (11.4 MB) +#19 169.9 ================================================== +#19 170.1 downloaded 11.4 MB +#19 170.1 +#19 170.1 trying URL 'https://cloud.r-project.org/src/contrib/stringr_1.5.1.tar.gz' +#19 170.6 Content type 'application/x-gzip' length 176599 bytes (172 KB) +#19 170.6 ================================================== +#19 170.7 downloaded 172 KB +#19 170.7 +#19 171.6 * installing *source* package ‘stringi’ ... +#19 171.6 ** package ‘stringi’ successfully unpacked and MD5 sums checked +#19 171.6 ** using staged installation +#19 171.7 checking for R_HOME... /usr/lib/R +#19 171.7 checking for R... /usr/lib/R/bin/R +#19 171.7 checking for endianness... little +#19 171.9 checking for cat... /usr/bin/cat +#19 171.9 checking whether the C++ compiler works... yes +#19 172.0 checking for C++ compiler default output file name... a.out +#19 172.0 checking for suffix of executables... +#19 172.0 checking whether we are cross compiling... no +#19 172.0 checking for suffix of object files... o +#19 172.0 checking whether the compiler supports GNU C++... yes +#19 172.0 checking whether g++ -std=gnu++17 accepts -g... yes +#19 172.1 checking for g++ -std=gnu++17 option to enable C++11 features... none needed +#19 172.1 checking whether the C++ compiler supports the 'long long' type... yes +#19 172.3 checking whether the compiler implements namespaces... yes +#19 172.4 checking whether the compiler supports the Standard Template Library... yes +#19 172.5 checking whether std::map is available... yes +#19 172.8 checking for pkg-config... /usr/bin/pkg-config +#19 172.8 checking with 'pkg-config' for the system ICU4C (icu-i18n icu-uc)... 72.1 +#19 172.8 checking for ICU4C >= 61... yes +#19 172.8 checking for additional CPPFLAGS, LDFLAGS, and LIBS required... done +#19 172.8 checking whether an ICU4C-based project can be built... yes +#19 173.0 checking programmatically for sufficient U_ICU_VERSION_MAJOR_NUM... yes +#19 173.0 checking the capabilities of the ICU data library (ucnv, uloc, utrans)... yes +#19 173.3 checking the capabilities of the ICU data library (ucol)... yes +#19 173.6 checking for stdio.h... yes +#19 173.6 checking for stdlib.h... yes +#19 173.6 checking for string.h... yes +#19 173.6 checking for inttypes.h... yes +#19 173.7 checking for stdint.h... yes +#19 173.7 checking for strings.h... yes +#19 173.7 checking for sys/stat.h... yes +#19 173.7 checking for sys/types.h... yes +#19 173.8 checking for unistd.h... yes +#19 173.8 checking for elf.h... yes +#19 173.8 configure: creating ./config.status +#19 173.9 config.status: creating src/Makevars +#19 173.9 config.status: creating src/uconfig_local.h +#19 173.9 config.status: creating src/install.libs.R +#19 173.9 +#19 173.9 *** stringi configure summary: +#19 173.9 ICU_FOUND=1 +#19 173.9 STRINGI_CXXSTD= +#19 173.9 STRINGI_CXXFLAGS= -fPIC +#19 173.9 STRINGI_CPPFLAGS=-I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H +#19 173.9 STRINGI_LDFLAGS= -L/usr/lib/aarch64-linux-gnu +#19 173.9 STRINGI_LIBS= -licui18n -licuuc -licudata +#19 173.9 +#19 173.9 *** Compiler settings used: +#19 173.9 CXX=g++ -std=gnu++17 +#19 173.9 LD=g++ -std=gnu++17 +#19 173.9 CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 +#19 173.9 CPPFLAGS= +#19 173.9 LDFLAGS= +#19 173.9 LIBS= +#19 173.9 +#19 173.9 ** libs +#19 173.9 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ +#19 173.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_brkiter.cpp -o stri_brkiter.o +#19 174.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_collator.cpp -o stri_collator.o +#19 174.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_common.cpp -o stri_common.o +#19 175.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_compare.cpp -o stri_compare.o +#19 175.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_base.cpp -o stri_container_base.o +#19 175.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_bytesearch.cpp -o stri_container_bytesearch.o +#19 176.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_listint.cpp -o stri_container_listint.o +#19 176.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_listraw.cpp -o stri_container_listraw.o +#19 176.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_listutf8.cpp -o stri_container_listutf8.o +#19 177.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_regex.cpp -o stri_container_regex.o +#19 177.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_usearch.cpp -o stri_container_usearch.o +#19 177.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_utf16.cpp -o stri_container_utf16.o +#19 178.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_utf8.cpp -o stri_container_utf8.o +#19 178.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_utf8_indexable.cpp -o stri_container_utf8_indexable.o +#19 178.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_encoding_conversion.cpp -o stri_encoding_conversion.o +#19 179.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_encoding_detection.cpp -o stri_encoding_detection.o +#19 180.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_encoding_management.cpp -o stri_encoding_management.o +#19 180.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_escape.cpp -o stri_escape.o +#19 181.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_exception.cpp -o stri_exception.o +#19 181.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_ICU_settings.cpp -o stri_ICU_settings.o +#19 181.6 In file included from stri_ICU_settings.cpp:37: +#19 181.6 uconfig_local.h:42:9: warning: "UCONFIG_USE_WINDOWS_LCID_MAPPING_API" redefined +#19 181.6 42 | #define UCONFIG_USE_WINDOWS_LCID_MAPPING_API 0 +#19 181.6 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +#19 181.6 In file included from /usr/include/unicode/platform.h:24, +#19 181.6 from /usr/include/unicode/ptypes.h:52, +#19 181.6 from stri_external.h:52, +#19 181.6 from stri_stringi.h:36, +#19 181.6 from stri_ICU_settings.cpp:33: +#19 181.6 /usr/include/unicode/uconfig.h:381:12: note: this is the location of the previous definition +#19 181.6 381 | # define UCONFIG_USE_WINDOWS_LCID_MAPPING_API 1 +#19 181.6 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +#19 181.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_join.cpp -o stri_join.o +#19 182.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_length.cpp -o stri_length.o +#19 182.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_pad.cpp -o stri_pad.o +#19 183.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_prepare_arg.cpp -o stri_prepare_arg.o +#19 183.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_random.cpp -o stri_random.o +#19 184.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_reverse.cpp -o stri_reverse.o +#19 184.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_count.cpp -o stri_search_class_count.o +#19 184.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_detect.cpp -o stri_search_class_detect.o +#19 185.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_extract.cpp -o stri_search_class_extract.o +#19 185.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_locate.cpp -o stri_search_class_locate.o +#19 186.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_replace.cpp -o stri_search_class_replace.o +#19 186.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_split.cpp -o stri_search_class_split.o +#19 187.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_startsendswith.cpp -o stri_search_class_startsendswith.o +#19 187.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_subset.cpp -o stri_search_class_subset.o +#19 187.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_trim.cpp -o stri_search_class_trim.o +#19 188.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_common.cpp -o stri_search_common.o +#19 188.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_count.cpp -o stri_search_coll_count.o +#19 188.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_detect.cpp -o stri_search_coll_detect.o +#19 189.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_extract.cpp -o stri_search_coll_extract.o +#19 189.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_locate.cpp -o stri_search_coll_locate.o +#19 190.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_replace.cpp -o stri_search_coll_replace.o +#19 190.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_split.cpp -o stri_search_coll_split.o +#19 191.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_startsendswith.cpp -o stri_search_coll_startsendswith.o +#19 191.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_subset.cpp -o stri_search_coll_subset.o +#19 192.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_boundaries_count.cpp -o stri_search_boundaries_count.o +#19 192.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_boundaries_extract.cpp -o stri_search_boundaries_extract.o +#19 192.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_boundaries_locate.cpp -o stri_search_boundaries_locate.o +#19 193.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_boundaries_split.cpp -o stri_search_boundaries_split.o +#19 193.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_count.cpp -o stri_search_fixed_count.o +#19 193.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_detect.cpp -o stri_search_fixed_detect.o +#19 194.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_extract.cpp -o stri_search_fixed_extract.o +#19 194.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_locate.cpp -o stri_search_fixed_locate.o +#19 195.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_replace.cpp -o stri_search_fixed_replace.o +#19 195.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_split.cpp -o stri_search_fixed_split.o +#19 196.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_subset.cpp -o stri_search_fixed_subset.o +#19 196.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_startsendswith.cpp -o stri_search_fixed_startsendswith.o +#19 196.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_in.cpp -o stri_search_in.o +#19 196.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_other_split.cpp -o stri_search_other_split.o +#19 197.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_count.cpp -o stri_search_regex_count.o +#19 197.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_detect.cpp -o stri_search_regex_detect.o +#19 197.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_extract.cpp -o stri_search_regex_extract.o +#19 198.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_locate.cpp -o stri_search_regex_locate.o +#19 199.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_match.cpp -o stri_search_regex_match.o +#19 199.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_replace.cpp -o stri_search_regex_replace.o +#19 200.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_split.cpp -o stri_search_regex_split.o +#19 200.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_subset.cpp -o stri_search_regex_subset.o +#19 200.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_sort.cpp -o stri_sort.o +#19 201.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_sprintf.cpp -o stri_sprintf.o +#19 202.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_stats.cpp -o stri_stats.o +#19 203.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_string8.cpp -o stri_string8.o +#19 203.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_stringi.cpp -o stri_stringi.o +#19 203.4 In file included from stri_stringi.cpp:39: +#19 203.4 uconfig_local.h:42:9: warning: "UCONFIG_USE_WINDOWS_LCID_MAPPING_API" redefined +#19 203.4 42 | #define UCONFIG_USE_WINDOWS_LCID_MAPPING_API 0 +#19 203.4 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +#19 203.4 In file included from /usr/include/unicode/platform.h:24, +#19 203.4 from /usr/include/unicode/ptypes.h:52, +#19 203.4 from stri_external.h:52, +#19 203.4 from stri_stringi.h:36, +#19 203.4 from stri_stringi.cpp:33: +#19 203.4 /usr/include/unicode/uconfig.h:381:12: note: this is the location of the previous definition +#19 203.4 381 | # define UCONFIG_USE_WINDOWS_LCID_MAPPING_API 1 +#19 203.4 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +#19 203.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_sub.cpp -o stri_sub.o +#19 204.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_test.cpp -o stri_test.o +#19 204.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_time_zone.cpp -o stri_time_zone.o +#19 204.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_time_calendar.cpp -o stri_time_calendar.o +#19 205.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_time_symbols.cpp -o stri_time_symbols.o +#19 205.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_time_format.cpp -o stri_time_format.o +#19 206.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_trans_casemap.cpp -o stri_trans_casemap.o +#19 206.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_trans_other.cpp -o stri_trans_other.o +#19 207.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_trans_normalization.cpp -o stri_trans_normalization.o +#19 207.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_trans_transliterate.cpp -o stri_trans_transliterate.o +#19 207.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_ucnv.cpp -o stri_ucnv.o +#19 208.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_uloc.cpp -o stri_uloc.o +#19 208.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_utils.cpp -o stri_utils.o +#19 208.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_wrap.cpp -o stri_wrap.o +#19 209.2 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o stringi.so stri_brkiter.o stri_collator.o stri_common.o stri_compare.o stri_container_base.o stri_container_bytesearch.o stri_container_listint.o stri_container_listraw.o stri_container_listutf8.o stri_container_regex.o stri_container_usearch.o stri_container_utf16.o stri_container_utf8.o stri_container_utf8_indexable.o stri_encoding_conversion.o stri_encoding_detection.o stri_encoding_management.o stri_escape.o stri_exception.o stri_ICU_settings.o stri_join.o stri_length.o stri_pad.o stri_prepare_arg.o stri_random.o stri_reverse.o stri_search_class_count.o stri_search_class_detect.o stri_search_class_extract.o stri_search_class_locate.o stri_search_class_replace.o stri_search_class_split.o stri_search_class_startsendswith.o stri_search_class_subset.o stri_search_class_trim.o stri_search_common.o stri_search_coll_count.o stri_search_coll_detect.o stri_search_coll_extract.o stri_search_coll_locate.o stri_search_coll_replace.o stri_search_coll_split.o stri_search_coll_startsendswith.o stri_search_coll_subset.o stri_search_boundaries_count.o stri_search_boundaries_extract.o stri_search_boundaries_locate.o stri_search_boundaries_split.o stri_search_fixed_count.o stri_search_fixed_detect.o stri_search_fixed_extract.o stri_search_fixed_locate.o stri_search_fixed_replace.o stri_search_fixed_split.o stri_search_fixed_subset.o stri_search_fixed_startsendswith.o stri_search_in.o stri_search_other_split.o stri_search_regex_count.o stri_search_regex_detect.o stri_search_regex_extract.o stri_search_regex_locate.o stri_search_regex_match.o stri_search_regex_replace.o stri_search_regex_split.o stri_search_regex_subset.o stri_sort.o stri_sprintf.o stri_stats.o stri_string8.o stri_stringi.o stri_sub.o stri_test.o stri_time_zone.o stri_time_calendar.o stri_time_symbols.o stri_time_format.o stri_trans_casemap.o stri_trans_other.o stri_trans_normalization.o stri_trans_transliterate.o stri_ucnv.o stri_uloc.o stri_utils.o stri_wrap.o -L/usr/lib/aarch64-linux-gnu -licui18n -licuuc -licudata -L/usr/lib/R/lib -lR +#19 209.4 installing via 'install.libs.R' to /usr/local/lib/R/site-library/00LOCK-stringi/00new/stringi +#19 209.4 ** R +#19 209.4 ** inst +#19 209.4 ** byte-compile and prepare package for lazy loading +#19 209.9 ** help +#19 210.3 *** installing help indices +#19 210.4 ** building package indices +#19 210.7 ** testing if installed package can be loaded from temporary location +#19 210.8 ** checking absolute paths in shared objects and dynamic libraries +#19 210.8 ** testing if installed package can be loaded from final location +#19 210.9 ** testing if installed package keeps a record of temporary installation path +#19 210.9 * DONE (stringi) +#19 211.1 * installing *source* package ‘stringr’ ... +#19 211.1 ** package ‘stringr’ successfully unpacked and MD5 sums checked +#19 211.1 ** using staged installation +#19 211.1 ** R +#19 211.1 ** data +#19 211.1 *** moving datasets to lazyload DB +#19 211.1 ** inst +#19 211.1 ** byte-compile and prepare package for lazy loading +#19 211.7 ** help +#19 211.7 *** installing help indices +#19 211.7 *** copying figures +#19 211.7 ** building package indices +#19 211.9 ** installing vignettes +#19 211.9 ** testing if installed package can be loaded from temporary location +#19 212.1 ** testing if installed package can be loaded from final location +#19 212.3 ** testing if installed package keeps a record of temporary installation path +#19 212.3 * DONE (stringr) +#19 212.3 +#19 212.3 The downloaded source packages are in +#19 212.3 ‘/tmp/RtmpZsJzTy/downloaded_packages’ +#19 212.3 Installing package into ‘/usr/local/lib/R/site-library’ +#19 212.3 (as ‘lib’ is unspecified) +#19 212.5 also installing the dependencies ‘purrr’, ‘cpp11’ +#19 212.5 +#19 212.5 trying URL 'https://cloud.r-project.org/src/contrib/purrr_1.0.2.tar.gz' +#19 213.2 Content type 'application/x-gzip' length 220868 bytes (215 KB) +#19 213.2 ================================================== +#19 213.2 downloaded 215 KB +#19 213.2 +#19 213.2 trying URL 'https://cloud.r-project.org/src/contrib/cpp11_0.5.0.tar.gz' +#19 213.7 Content type 'application/x-gzip' length 275693 bytes (269 KB) +#19 213.7 ================================================== +#19 213.7 downloaded 269 KB +#19 213.7 +#19 213.7 trying URL 'https://cloud.r-project.org/src/contrib/tidyr_1.3.1.tar.gz' +#19 214.2 Content type 'application/x-gzip' length 809058 bytes (790 KB) +#19 214.2 ================================================== +#19 214.2 downloaded 790 KB +#19 214.2 +#19 214.5 * installing *source* package ‘purrr’ ... +#19 214.5 ** package ‘purrr’ successfully unpacked and MD5 sums checked +#19 214.5 ** using staged installation +#19 214.7 ** libs +#19 214.7 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ +#19 214.7 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c backports.c -o backports.o +#19 214.7 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cleancall.c -o cleancall.o +#19 214.8 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c coerce.c -o coerce.o +#19 214.8 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c conditions.c -o conditions.o +#19 214.9 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c flatten.c -o flatten.o +#19 215.1 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o +#19 215.1 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c map.c -o map.o +#19 215.2 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c pluck.c -o pluck.o +#19 215.3 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c transpose.c -o transpose.o +#19 215.3 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o +#19 215.4 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o purrr.so backports.o cleancall.o coerce.o conditions.o flatten.o init.o map.o pluck.o transpose.o utils.o -L/usr/lib/R/lib -lR +#19 215.4 installing to /usr/local/lib/R/site-library/00LOCK-purrr/00new/purrr/libs +#19 215.4 ** R +#19 215.4 ** inst +#19 215.4 ** byte-compile and prepare package for lazy loading +#19 216.2 ** help +#19 216.3 *** installing help indices +#19 216.4 *** copying figures +#19 216.4 ** building package indices +#19 216.6 ** installing vignettes +#19 216.6 ** testing if installed package can be loaded from temporary location +#19 216.8 ** checking absolute paths in shared objects and dynamic libraries +#19 216.8 ** testing if installed package can be loaded from final location +#19 217.0 ** testing if installed package keeps a record of temporary installation path +#19 217.0 * DONE (purrr) +#19 217.2 * installing *source* package ‘cpp11’ ... +#19 217.2 ** package ‘cpp11’ successfully unpacked and MD5 sums checked +#19 217.2 ** using staged installation +#19 217.2 ** R +#19 217.2 ** inst +#19 217.2 ** byte-compile and prepare package for lazy loading +#19 217.4 ** help +#19 217.4 *** installing help indices +#19 217.4 ** building package indices +#19 217.6 ** installing vignettes +#19 217.6 ** testing if installed package can be loaded from temporary location +#19 217.7 ** testing if installed package can be loaded from final location +#19 217.8 ** testing if installed package keeps a record of temporary installation path +#19 217.8 * DONE (cpp11) +#19 218.1 * installing *source* package ‘tidyr’ ... +#19 218.1 ** package ‘tidyr’ successfully unpacked and MD5 sums checked +#19 218.1 ** using staged installation +#19 218.1 ** libs +#19 218.1 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ +#19 218.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cpp11/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cpp11.cpp -o cpp11.o +#19 218.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cpp11/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c melt.cpp -o melt.o +#19 219.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cpp11/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c simplifyPieces.cpp -o simplifyPieces.o +#19 220.2 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o tidyr.so cpp11.o melt.o simplifyPieces.o -L/usr/lib/R/lib -lR +#19 220.2 installing to /usr/local/lib/R/site-library/00LOCK-tidyr/00new/tidyr/libs +#19 220.2 ** R +#19 220.2 ** data +#19 220.2 *** moving datasets to lazyload DB +#19 220.6 ** inst +#19 220.6 ** byte-compile and prepare package for lazy loading +#19 221.7 ** help +#19 221.8 *** installing help indices +#19 221.9 *** copying figures +#19 221.9 ** building package indices +#19 222.0 ** installing vignettes +#19 222.0 ** testing if installed package can be loaded from temporary location +#19 222.4 ** checking absolute paths in shared objects and dynamic libraries +#19 222.4 ** testing if installed package can be loaded from final location +#19 222.7 ** testing if installed package keeps a record of temporary installation path +#19 222.7 * DONE (tidyr) +#19 222.7 +#19 222.7 The downloaded source packages are in +#19 222.7 ‘/tmp/RtmpZsJzTy/downloaded_packages’ +#19 DONE 222.9s + +#20 exporting to image +#20 exporting layers +#20 exporting layers 2.6s done +#20 writing image sha256:3812c88e7d3f4e4bbcc71ca3d6d1c53c4601dab50a410c8579086533a58b83d2 done +#20 naming to docker.io/library/mpnstpdx done +#20 DONE 2.6s + + 1 warning found (use --debug to expand): + - UndefinedVar: Usage of undefined variable '$PYTHONPATH' (line 34) + +View build details: docker-desktop://dashboard/build/desktop-linux/desktop-linux/rjrwxqzbvz2qr9uxna8wl95zm + +What's next: + View a summary of image vulnerabilities and recommendations → docker scout quickview  diff --git a/build/build_dataset.py b/build/build_dataset.py new file mode 100644 index 00000000..88863090 --- /dev/null +++ b/build/build_dataset.py @@ -0,0 +1,321 @@ +""" +Script that builds a single dataset. +""" + +import os +import argparse +import subprocess +import shutil +import gzip +from concurrent.futures import ThreadPoolExecutor +import glob + +def run_docker_cmd(cmd_arr, filename): + ''' + Wrapper for 'docker run' command. Executes a Docker container with the specified command. + ''' + print('Running...', filename) + env = os.environ.copy() + if 'SYNAPSE_AUTH_TOKEN' not in env: + print('You need to set the SYNAPSE_AUTH_TOKEN to access the MPNST and beatAML datasets') + docker_run = ['docker', 'run', '-v', f"{env['PWD']}/local/:/tmp/", '--platform=linux/amd64'] + else: + docker_run = ['docker', 'run', '-v', f"{env['PWD']}/local/:/tmp/", '-e', f"SYNAPSE_AUTH_TOKEN={env['SYNAPSE_AUTH_TOKEN']}", '--platform=linux/amd64'] + + cmd = docker_run + cmd_arr + print('Executing command:', ' '.join(cmd)) + res = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + if res.returncode != 0: + print(res.stderr.decode()) + exit(f'{filename} failed') + else: + print(f'{filename} completed successfully') + +def process_docker(dataset,validate): + ''' + Build Docker images required for the specified dataset. + ''' + compose_file = 'build/docker/docker-compose.yml' + dataset_map = { + 'broad_sanger': ['broad_sanger_exp', 'broad_sanger_omics'], + 'hcmi': ['hcmi'], + 'beataml': ['beataml'], + 'mpnst': ['mpnst'], + 'mpnstpdx': ['mpnstpdx'], + 'cptac': ['cptac'], + 'genes': ['genes'], + 'upload': ['upload'] + } + + # Collect container names to build based on the dataset provided. Always build 'genes'. + datasets_to_build = ['genes'] + # Append upload if validation step is included + if validate is True: + datasets_to_build.append('upload') + + datasets_to_build.extend(dataset_map.get(dataset, [])) + + compose_command = ['docker-compose', '-f', compose_file, 'build'] + datasets_to_build + + log_file_path = 'local/docker.log' + env = os.environ.copy() + + print(f"Docker-compose is building images for {', '.join(datasets_to_build)}. View output in {log_file_path}.") + + with open(log_file_path, 'w') as log_file: + try: + subprocess.run(compose_command, env=env, stdout=log_file, stderr=log_file, text=True, check=True) + log_file.write("Docker images built successfully.\n") + print(f"Docker images for {', '.join(datasets_to_build)} built successfully. Details logged in {log_file_path}.") + except subprocess.CalledProcessError as e: + log_file.write(f"Docker compose build failed with error: {e}\n") + print(f"Docker compose build failed. See {log_file_path} for details.") + raise + +def process_genes(executor): + ''' + Build the genes file if it does not exist. + ''' + if not os.path.exists('local/genes.csv'): + executor.submit(run_docker_cmd, ['genes', 'bash', 'build_genes.sh'], 'genes file') + +def process_samples(executor, dataset, use_prev_dataset, should_continue): + ''' + Build the samples file for the specified dataset. + ''' + samples_file = f'local/{dataset}_samples.csv' + if should_continue and os.path.exists(samples_file): + print(f"Samples file for {dataset} already exists. Skipping samples build.") + return + + prev_samples_file = f'/tmp/{use_prev_dataset}_samples.csv' if use_prev_dataset else '' + di = 'broad_sanger_omics' if dataset == 'broad_sanger' else dataset + filename = f'{dataset} samples' + executor.submit(run_docker_cmd, [di, 'bash', 'build_samples.sh', prev_samples_file], filename) + +def process_drugs(executor, dataset, use_prev_dataset, should_continue): + ''' + Build the drugs file for the specified dataset. + ''' + if dataset in ['cptac', 'hcmi']: + return # No drugs to process for these datasets + + drugs_file = f'local/{dataset}_drugs.tsv' + if should_continue and os.path.exists(drugs_file): + print(f"Drugs file for {dataset} already exists. Skipping drugs build.") + return + + prev_drugs_file = f'/tmp/{use_prev_dataset}_drugs.tsv' if use_prev_dataset else '' + dflist = [prev_drugs_file] if use_prev_dataset else [] + di = 'broad_sanger_exp' if dataset == 'broad_sanger' else dataset + filename = f'{dataset} drugs' + executor.submit(run_docker_cmd, [di, 'bash', 'build_drugs.sh', ','.join(dflist)], filename) + + +def process_omics(executor, dataset, should_continue): + ''' + Build the omics files for the specified dataset. + ''' + # Map datasets to their expected omics files + dataset_omics_files = { + 'beataml': ['mutations', 'proteomics', 'transcriptomics'], + 'mpnst': ['copy_number', 'mutations', 'proteomics', 'transcriptomics'], + 'broad_sanger': ['copy_number', 'mutations', 'proteomics', 'transcriptomics'], + 'cptac': ['copy_number', 'mutations', 'proteomics', 'transcriptomics'], + 'hcmi': ['mutations', 'transcriptomics'], + 'mpnstpdx':['copy_number', 'mutations', 'proteomics', 'transcriptomics'] + } + + expected_omics = dataset_omics_files.get(dataset, []) + + if not expected_omics: + print(f"No omics data expected for dataset {dataset}. Skipping omics build.") + return + + # Check if all expected omics files exist + omics_files_exist = True + for omics_type in expected_omics: + patterns = [ + f'local/{dataset}_{omics_type}.csv', + f'local/{dataset}_{omics_type}.csv.gz', + f'local/{dataset}_{omics_type}.tsv', + f'local/{dataset}_{omics_type}.tsv.gz' + ] + file_found = False + for pattern in patterns: + matches = glob.glob(pattern) + if matches: + file_found = True + break + if not file_found: + omics_files_exist = False + break # If any omics files are missing, just build / rebuild them all. + + if should_continue and omics_files_exist: + print(f"Omics files for {dataset} already exist. Skipping omics build.") + return + + di = 'broad_sanger_omics' if dataset == 'broad_sanger' else dataset + filename = f'{dataset} omics' + executor.submit(run_docker_cmd, [di, 'bash', 'build_omics.sh', '/tmp/genes.csv', f'/tmp/{dataset}_samples.csv'], filename) + + +def process_experiments(executor, dataset, should_continue): + ''' + Build the experiments files for the specified dataset. + ''' + if dataset in ['cptac', 'hcmi']: + return # No experiments to process for these datasets + + experiments_file = f'local/{dataset}_experiments.tsv' + if should_continue and os.path.exists(experiments_file): + print(f"Experiments file for {dataset} already exists. Skipping experiments build.") + return + + di = 'broad_sanger_exp' if dataset == 'broad_sanger' else dataset + filename = f'{dataset} experiments' + executor.submit(run_docker_cmd, [di, 'bash', 'build_exp.sh', f'/tmp/{dataset}_samples.csv', f'/tmp/{dataset}_drugs.tsv'], filename) + + + +def process_misc(executor, datasets): + ''' + Run all misc scripts concurrently or one at a time. + ''' + last_misc_future = None + #Currently this only applies to broad_sanger. Add others here if they need a final step. + if "broad_sanger" in datasets: + datasets = ["broad_sanger"] + else: + return + for da in datasets: + di = 'broad_sanger_omics' if da == 'broad_sanger' else da + #Run all at once: + if last_misc_future: + last_misc_future.result() + last_misc_future = executor.submit(run_docker_cmd, [di, 'bash', 'build_misc.sh'], f'{da} misc') + + + +def decompress_file(file_path): + """Decompress a gzip file and delete the original compressed file.""" + with gzip.open(file_path, 'rb') as f_in: + decompressed_file_path = file_path[:-3] # Remove '.gz' from the filename + with open(decompressed_file_path, 'wb') as f_out: + shutil.copyfileobj(f_in, f_out) + os.remove(file_path) + +def compress_file(file_path): + """Compress a file using gzip and delete the original uncompressed file.""" + compressed_file_path = file_path + '.gz' + with open(file_path, 'rb') as f_in: + with gzip.open(compressed_file_path, 'wb') as f_out: + shutil.copyfileobj(f_in, f_out) + os.remove(file_path) + +def run_docker_validate_cmd(cmd_arr, all_files_dir, name): + ''' + Wrapper for 'docker run' command used during validation and uploads. + ''' + env = os.environ.copy() + docker_run = ['docker', 'run', '-v', f"{env['PWD']}/local/{all_files_dir}:/tmp"] + docker_run.extend(['upload']) + docker_run.extend(cmd_arr) + print('Executing:', ' '.join(docker_run)) + res = subprocess.run(docker_run, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + if res.returncode != 0: + print(res.stderr.decode()) + exit(f'{name} failed') + else: + print(f'{name} completed successfully') + +def run_schema_checker(dataset): + ''' + Run schema checker on the built files for the specified dataset. + ''' + # Prepare the directory with the built files + prefixes = ['genes', dataset] + datasets = [dataset] + broad_sanger_datasets = ["ccle","ctrpv2","fimm","gdscv1","gdscv2","gcsi","prism","nci60"] + all_files_dir = 'all_files_dir' + if "broad_sanger" == dataset: + prefixes.extend(broad_sanger_datasets) + datasets.extend(broad_sanger_datasets) + datasets.remove("broad_sanger") + prefixes.remove("broad_sanger") + + if not os.path.exists(f'local/{all_files_dir}'): + os.makedirs(f'local/{all_files_dir}') + + # Move relevant files to all_files_dir + for file in os.listdir('local'): + if any(file.startswith(prefix) for prefix in prefixes): + shutil.move(os.path.join('local', file), os.path.join('local', all_files_dir, file)) + + # Decompress any compressed files + for file in os.listdir(f'local/{all_files_dir}'): + if file.endswith('.gz'): + decompress_file(os.path.join('local', all_files_dir, file)) + + # Run schema checker + schema_check_command = ['python3', 'scripts/check_schema.py', '--datasets'] + datasets + run_docker_validate_cmd(schema_check_command, all_files_dir, 'Validation') + +def main(): + parser = argparse.ArgumentParser( + description="This script builds a single dataset." + ) + parser.add_argument('--dataset', required=True, help='Name of the dataset to build') + parser.add_argument('--use_prev_dataset', help='Prefix of the previous dataset for sample and drug ID assignment') + parser.add_argument('--build', action='store_true', help='Run data build.') + parser.add_argument('--validate', action='store_true', help='Run schema checker on the built files') + parser.add_argument('--continue', dest='should_continue', action='store_true', help='Continue from where the build left off by skipping existing files') + + args = parser.parse_args() + + if not os.path.exists('local'): + os.mkdir('local') + + # Build Docker Image + process_docker(args.dataset,args.validate) + + if args.build: + # Use ThreadPoolExecutor for parallel execution + with ThreadPoolExecutor() as executor: + # Always build genes file + process_genes(executor) + + # Build samples and drugs + samples_future = executor.submit(process_samples, executor, args.dataset, args.use_prev_dataset, args.should_continue) + drugs_future = executor.submit(process_drugs, executor, args.dataset, args.use_prev_dataset, args.should_continue) + + samples_future.result() + drugs_future.result() + + print("Samples and Drugs Files Completed.") + + with ThreadPoolExecutor() as executor: + + # Build omics and experiments + omics_future = executor.submit(process_omics, executor, args.dataset, args.should_continue) + experiments_future = executor.submit(process_experiments, executor, args.dataset, args.should_continue) + + omics_future.result() + experiments_future.result() + + print("Experiments and Omics Files completed.") + + with ThreadPoolExecutor() as executor: + + if args.build: + misc_thread = executor.submit(process_misc, executor, args.dataset) + if args.build: + misc_thread.result() + print("Final build step complete.") + + if args.validate: + run_schema_checker(args.dataset) + print("Validation completed.") + +if __name__ == '__main__': + main() diff --git a/build/docker/Dockerfile.mpnst b/build/docker/Dockerfile.mpnst index 0204144b..92fe9c6d 100755 --- a/build/docker/Dockerfile.mpnst +++ b/build/docker/Dockerfile.mpnst @@ -1,16 +1,44 @@ FROM r-base:4.3.2 + +# Set environment to noninteractive ENV DEBIAN_FRONTEND=noninteractive -RUN apt-get update --allow-insecure-repositories -#RUN apt-get install -y --allow-unauthenticated build-essential --fix-missing libpq-dev python3-pip python3-setuptools python3-dev python3-venv libcurl4-openssl-dev libxml2-dev -RUN apt-get install -y --allow-unauthenticated build-essential --fix-missing python3-pip python3-setuptools python3-dev python3-venv libcurl4-openssl-dev libxml2-dev +# Update package list and install required packages +RUN apt-get update && \ + apt-get install -y build-essential wget curl libcurl4-openssl-dev libxml2-dev \ + zlib1g-dev libssl-dev libbz2-dev libreadline-dev libsqlite3-dev libffi-dev + +# Download and compile Python 3.10 with shared library support +RUN wget https://www.python.org/ftp/python/3.10.12/Python-3.10.12.tgz && \ + tar -xf Python-3.10.12.tgz && \ + cd Python-3.10.12 && \ + ./configure --enable-optimizations --enable-shared && \ + make -j$(nproc) && \ + make altinstall && \ + cd .. && \ + rm -rf Python-3.10.12.tgz Python-3.10.12 + +# Set Python 3.10 as default +RUN ln -s /usr/local/bin/python3.10 /usr/bin/python3 && \ + ln -s /usr/local/bin/pip3.10 /usr/bin/pip3 + +# Update library paths for Python shared library +RUN echo "/usr/local/lib" >> /etc/ld.so.conf.d/python3.10.conf && ldconfig + +# Create a Python virtual environment RUN python3 -m venv /opt/venv -RUN /opt/venv/bin/pip3 install --upgrade pip - +RUN /opt/venv/bin/pip install --upgrade pip -ENV PYTHONPATH "${PYTHONPATH}:/app" +# Set environment variables for reticulate +ENV RETICULATE_PYTHON="/opt/venv/bin/python3" +ENV PYTHONPATH=/app#"${PYTHONPATH}:/app" WORKDIR /app +# Set MPLCONFIGDIR to a writable directory +ENV MPLCONFIGDIR=/app/tmp/matplotlib +RUN mkdir -p /app/tmp/matplotlib + +# Add necessary files to the container ADD build/mpnst/requirements.txt . ADD build/mpnst/requirements.r . ADD build/mpnst/* ./ @@ -19,8 +47,8 @@ ADD build/utils/* ./ # installing python libraries RUN /opt/venv/bin/pip3 install -r requirements.txt -# installing r libraries +# Install all R libraries from requirements.r RUN Rscript requirements.r - +# Set up volume for temporary storage VOLUME ["/tmp"] diff --git a/build/docker/Dockerfile.mpnstPDX b/build/docker/Dockerfile.mpnstPDX index 070d676c..88e4ff53 100755 --- a/build/docker/Dockerfile.mpnstPDX +++ b/build/docker/Dockerfile.mpnstPDX @@ -1,16 +1,44 @@ FROM r-base:4.3.2 + +# Set environment to noninteractive ENV DEBIAN_FRONTEND=noninteractive -RUN apt-get update --allow-insecure-repositories -#RUN apt-get install -y --allow-unauthenticated build-essential --fix-missing libpq-dev python3-pip python3-setuptools python3-dev python3-venv libcurl4-openssl-dev libxml2-dev -RUN apt-get install -y --allow-unauthenticated build-essential --fix-missing python3-pip python3-setuptools python3-dev python3-venv libcurl4-openssl-dev libxml2-dev +# Update package list and install required packages +RUN apt-get update && \ + apt-get install -y build-essential wget curl libcurl4-openssl-dev libxml2-dev \ + zlib1g-dev libssl-dev libbz2-dev libreadline-dev libsqlite3-dev libffi-dev + +# Download and compile Python 3.10 with shared library support +RUN wget https://www.python.org/ftp/python/3.10.12/Python-3.10.12.tgz && \ + tar -xf Python-3.10.12.tgz && \ + cd Python-3.10.12 && \ + ./configure --enable-optimizations --enable-shared && \ + make -j$(nproc) && \ + make altinstall && \ + cd .. && \ + rm -rf Python-3.10.12.tgz Python-3.10.12 + +# Set Python 3.10 as default +RUN ln -s /usr/local/bin/python3.10 /usr/bin/python3 && \ + ln -s /usr/local/bin/pip3.10 /usr/bin/pip3 + +# Update library paths for Python shared library +RUN echo "/usr/local/lib" >> /etc/ld.so.conf.d/python3.10.conf && ldconfig + +# Create a Python virtual environment RUN python3 -m venv /opt/venv -RUN /opt/venv/bin/pip3 install --upgrade pip - +RUN /opt/venv/bin/pip install --upgrade pip -ENV PYTHONPATH "${PYTHONPATH}:/app" +# Set environment variables for reticulate +ENV RETICULATE_PYTHON="/opt/venv/bin/python3" +ENV PYTHONPATH=/app#"${PYTHONPATH}:/app" WORKDIR /app +# Set MPLCONFIGDIR to a writable directory +ENV MPLCONFIGDIR=/app/tmp/matplotlib +RUN mkdir -p /app/tmp/matplotlib + +# Add necessary files to the container ADD build/mpnstPDX/requirements.txt . ADD build/mpnstPDX/requirements.r . ADD build/mpnstPDX/* ./ @@ -19,8 +47,8 @@ ADD build/utils/* ./ # installing python libraries RUN /opt/venv/bin/pip3 install -r requirements.txt -# installing r libraries +# Install all R libraries from requirements.r RUN Rscript requirements.r - +# Set up volume for temporary storage VOLUME ["/tmp"] diff --git a/build/docker/docker-compose.yml b/build/docker/docker-compose.yml index fb9c9ab8..bf28ef65 100644 --- a/build/docker/docker-compose.yml +++ b/build/docker/docker-compose.yml @@ -44,7 +44,14 @@ services: HTTPS_PROXY: ${HTTPS_PROXY} platform: linux/amd64 image: mpnst:latest - + mpnstpdx: + build: + context: ../../ + dockerfile: build/docker/Dockerfile.mpnstpdx + args: + HTTPS_PROXY: ${HTTPS_PROXY} + platform: linux/amd64 + image: mpnstpdx:latest cptac: build: context: ../../ diff --git a/build/mpnst/requirements.r b/build/mpnst/requirements.r index 160a55bc..72dd457d 100755 --- a/build/mpnst/requirements.r +++ b/build/mpnst/requirements.r @@ -1,9 +1,11 @@ +install.packages('reticulate', repos='https://cloud.r-project.org') +reticulate::use_virtualenv('/opt/venv', required = TRUE) +install.packages('remotes') +remotes::install_version('rjson', version = '0.2.21', repos = 'https://cloud.r-project.org') +install.packages('synapser', repos = c('http://ran.synapse.org', 'https://cloud.r-project.org')) install.packages("dplyr") install.packages("data.table") -install.packages("synapser", repos = c("http://ran.synapse.org", "http://cran.fhcrc.org")) -install.packages('R.utils') +install.packages("synapser", repos = c("http://ran.synapse.org", "https://cloud.r-project.org")) +install.packages("R.utils") install.packages("stringr") -install.packages('reticulate') -install.packages("tidyr") - - +install.packages("tidyr") \ No newline at end of file diff --git a/build/mpnst/requirements.txt b/build/mpnst/requirements.txt index 99f3c960..27c4dc2a 100755 --- a/build/mpnst/requirements.txt +++ b/build/mpnst/requirements.txt @@ -8,4 +8,4 @@ scikit-learn scipy requests mordredcommunity -rdkit +rdkit \ No newline at end of file diff --git a/build/mpnstPDX/README.md b/build/mpnstPDX/README.md index 392f4b5c..b0059283 100755 --- a/build/mpnstPDX/README.md +++ b/build/mpnstPDX/README.md @@ -1,6 +1,6 @@ ## Build Instructions for MPNST PDX Dataset -To build the MPNST dataset, follow these steps from the coderdata root +To build the MPNST PDX dataset, follow these steps from the coderdata root directory. Currently using the test files as input. 1. Build the Docker image: @@ -9,16 +9,16 @@ directory. Currently using the test files as input. ``` 2. Generate new identifiers for these samples to create a - `mpnst_samples.csv` file. This pulls from the latest synapse + `mpnstpdx_samples.csv` file. This pulls from the latest synapse project metadata table. ``` - docker run -v $PWD:/tmp -e -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN mpnstpdx sh build_samples.sh /tmp/build/build_test/test_samples.csv + docker run -v $PWD:/tmp -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN mpnstpdx sh build_samples.sh /tmp/build/build_test/test_samples.csv ``` 3. Pull the data and map it to the samples. This uses the metadata table pulled above. ``` - docker run -v $PWD:/tmp -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN mpnstpdx sh build_omics.sh /tmp/build/build_test/test_genes.csv /tmp/mpnst_samples.csv + docker run -v $PWD:/tmp -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN mpnstpdx sh build_omics.sh /tmp/build/build_test/test_genes.csv /tmp/mpnstpdx_samples.csv ``` 4. Process drug data @@ -28,7 +28,7 @@ directory. Currently using the test files as input. 5. Process experiment data. This uses the metadata from above as well as the file directory on synapse: ``` - docker run -v $PWD:/tmp -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN mpnstpdx sh build_exp.sh /tmp/mpnst_samples.csv /tmp/mpnst_drugs.tsv.gz + docker run -v $PWD:/tmp -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN mpnstpdx sh build_exp.sh /tmp/mpnstpdx_samples.csv /tmp/mpnstpdx_drugs.tsv.gz ``` Please ensure that each step is followed in order for correct dataset compilation. diff --git a/build/mpnstPDX/build_exp.sh b/build/mpnstPDX/build_exp.sh index f11f8616..4e34f6b3 100644 --- a/build/mpnstPDX/build_exp.sh +++ b/build/mpnstPDX/build_exp.sh @@ -1,2 +1,2 @@ Rscript 03_get_drug_response_data.R $SYNAPSE_AUTH_TOKEN $1 $2 -/opt/venv/bin/python3 compute_metrics.py /tmp/curve_data.tsv --drugfile=/tmp/mpnstpdx_drugs.tsv --outprefix=/tmp/mpnstpdx +/opt/venv/bin/python3 calc_pdx_metrics.py /tmp/curve_data.tsv --drugfile=/tmp/mpnstpdx_drugs.tsv --outprefix=/tmp/mpnstpdx diff --git a/build/mpnstPDX/requirements.r b/build/mpnstPDX/requirements.r index 59013bf5..72dd457d 100755 --- a/build/mpnstPDX/requirements.r +++ b/build/mpnstPDX/requirements.r @@ -1,8 +1,11 @@ -install.packages("tidyverse") -install.packages("synapser", repos = c("http://ran.synapse.org", "http://cran.fhcrc.org")) -#install.packages('reticulate') -install.packages('R.utils') +install.packages('reticulate', repos='https://cloud.r-project.org') +reticulate::use_virtualenv('/opt/venv', required = TRUE) +install.packages('remotes') +remotes::install_version('rjson', version = '0.2.21', repos = 'https://cloud.r-project.org') +install.packages('synapser', repos = c('http://ran.synapse.org', 'https://cloud.r-project.org')) +install.packages("dplyr") install.packages("data.table") - - - +install.packages("synapser", repos = c("http://ran.synapse.org", "https://cloud.r-project.org")) +install.packages("R.utils") +install.packages("stringr") +install.packages("tidyr") \ No newline at end of file diff --git a/build/mpnstPDX/requirements.txt b/build/mpnstPDX/requirements.txt index 7dc03410..b0944928 100755 --- a/build/mpnstPDX/requirements.txt +++ b/build/mpnstPDX/requirements.txt @@ -1,5 +1,5 @@ pyarrow -pandas==2.1.1 +pandas matplotlib numpy==1.26.4 argparse @@ -9,3 +9,4 @@ scipy requests mordredcommunity rdkit +statsmodels diff --git a/mpnstpdx_ignore_chems.txt b/mpnstpdx_ignore_chems.txt new file mode 100644 index 00000000..eac569e9 --- /dev/null +++ b/mpnstpdx_ignore_chems.txt @@ -0,0 +1,130 @@ +vks +tno 155 [who-dd] +bdbm50553783 +(3s,4s)-8-[6-amino-5-(2-amino-3-chloropyridin-4-yl)sulfanylpyrazin-2-yl]-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine +nsc825523 +(3s,4s)-8-{6-amino-5-[(2-amino-3-chloropyridin-4- yl)sulfanyl]pyrazin-2-yl}-3-methyl-2-oxa-8- azaspiro[4.5]decan-4-amine +batoprotafib [inn] +ptpn11 inhibitor tno155 +(3s,4s)-8-{6-amino-5-[(2-amino-3-chloropyridin-4-yl)sulfanyl]pyrazin-2-yl}-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine +schembl16914359 +(3s,4s)-8-[6-amino-5-[(2-amino-3-chloro-4-pyridinyl)thio]-2-pyrazinyl]-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine +1801765-04-7 +compound 1 (pmid: 32910655) +tno 155 +nsc-825523 +ac-36494 +ms-27407 +d81634 +cs-0120271 +(3s,4s)-8-(6-amino-5-((2-amino-3-chloropyridin-4-yl)sulfanyl)pyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro(4.5)decan-4-amine +2-oxa-8-azaspiro[4.5]decan-4-amine, 8-[6-amino-5-[(2-amino-3-chloro-4-pyridinyl)thio]-2-pyrazinyl]-3-methyl-, (3s,4s)- +(3s,4s)-8-(6-amino-5-((2-amino-3-chloropyridin-4-yl)thio)pyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine +fpjworqegi +gtpl12068 +batoprotafib +unii-fpjworqegi +tno-155; tno 155 +akos040740434 +tno-155 +tno155 +compound 1 [pmid: 32910655] +tno155? +ex-a3645 +hy-136173 +bcp33299 +db-130941 +(3s,4s)-8-(6-amino-5-(2-amino-3-chloropyridin-4-ylthio)pyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine +mfcd32693919 +chembl4650521 +shp2 inhibitor tno155 +(3s,4s)-8-(6-amino-5-(2-amino-3-chloropyridin-4-yl)sulfanylpyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro(4.5)decan-4-amine +brd-k13514097-001-01-2 +(1r,9s,12s,15r,16e,18r,19r,21r,23s,24e,26e,28e,30s,32s,35r)-1,18-dihydroxy-12-((1r)-2-((1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl)-1-methylethyl)-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo(30.3.1.0(sup 4,9))hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentaone +(3s,6r,7e,9r,10r,12r,14s,15e,17e,19e,21s,23s,26r,27r,34as)-9,10,12,13,14,21,22,23,24,25,26,27,32,33,34,34a-hexadecahydro-9,27-dihydroxy-3-((1r)-2-((1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl)-1-methylethyl)-10,21-dimethoxy-6,8,12,14,20,26-hexamethyl-23,27-epoxy-3h-pyrido(2,1-c)(1,4)oxaazacyclohentriacontine-1,5,11,28,29(4h,6h,31h)-pentone +42-o-(2-hydroxy)ethyl rapamycin +xience v +bdbm50088378 +everolimus [ema epar] +everolimus, analytical standard +everolimus (mart.) +everolimus [vandf] +dihydroxy-[(1r)-2-[(1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxy-cyclohexyl]-1-methyl-ethyl]-dimethoxy-hexamethyl-[?]pentone +rad 001 +everolimus (rad001) +ncgc00167512-01 +everolimus [ep monograph] +159351-69-6 +brd-k13514097-001-05-3 +votubia +rapamycin, 42-o-(2-hydroxyethyl)- +(1r,9s,12s,15r,16e,18r,19r,21r,23s,24e,26e,28e,30s,35r)-1,18-dihydroxy-12-{(2r)-1-[(1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl]propan-2-yl}-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo[30.3.1.0(4,9)]hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentone +40-o-(2-hydroxyethyl)-rapamycin +everolimus (inn) +rad-001c +l04aa18 +everolimus [mi] +rad, sdz +q421052 +db01590 +everolimus [usan:inn:ban] +gtpl5889 +42-o-(2-hydroxyethyl)-rapamycin +zortress +rad001 +sdz-rad +(3s,6r,7e,9r,10r,12r,14s,15e,17e,19e,21s,23s,26r,27r,34as)-9,27-dihydroxy-3-((2r)-1-((1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl)propan-2-yl)-10,21-dimethoxy-6,8,12,14,20,26-hexamethyl-9,10,12,13,14,21,22,23,24,25,26,27,32,33,34,34a-hexadecahydro-3h-23,27-epoxypyrido(2,1-c)(1,4)oxazacyclohentriacontine-1,5,11,28,29(4h,6h,31h)-pentone +everolimus [usp-rs] +(1r,9s,12s,15r,16e,18r,19r,21r,23s,24e,26e,28e,30s,35r)-1,18-dihydroxy-12-((2r)-1-((1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl)propan-2-yl)-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo(30.3.1.0(4,9))hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentone +afinitordisperz +everolimus tablets +001, rad +everolimus (ep monograph) +tox21_112510 +dtxsid0040599 +everolimus [inn] +everolimus [orange book] +(1r,9s,12s,15r,16e,18r,19r,21r,23s,24e,26e,28e,30s,32s,35r)-1,18-dihydroxy-12-[(2r)-1-[(1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl]propan-2-yl]-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo[30.3.1.04,9]hexatriaconta-16,24,2 +everolimus (rad-001, sdz-rad) +everolimus +eve - everolimus +(3s,6r,7e,9r,10r,12r,14s,15e,17e,19e,21s,23s,26r,27r,34as)-9,27-dihydroxy-3-{(2r)-1-[(1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl]propan-2-yl}-10,21-dimethoxy-6,8,12,14,20,26-hexamethyl-9,10,12,13,14,21,22,23,24,25,26,27,32,33,34,34a-hexadecahydro-3h-23,27-epoxypyrido[2,1-c][1,4]oxazacyclohentriacontine-1,5,11,28,29(4h,6h,31h)-pentone +dtxcid8020599 +everolimusum +ex-a2057 +hy-10218r +everolimus [mart.] +afinitor +unii-9hw64q8g6g +rad-001 +chembl1908360 +cas-159351-69-6 +everolimus (~90% pure) +rad +akos015850977 +9hw64q8g6g +(1r,9s,12s,15r,16e,18r,19r,21r,23s,24e,26e,28e,30s,32s,35r)-1,18-dihydroxy-12-((1r)-2-((1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl)-1-methylethyl)-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo(30.3.1.04,9)hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentaone +everolimus (usp-rs) +everolimus? +chebi:68478 +everolimus (standard) +as-16971 +q-101413 +nsc733504 +everolimus; rad001; sdz-rad +hsdb 8255 +everolimus [who-dd] +sdz rad +schembl4378 +afinitor disperz +42-o-(2-hydroxyethyl)rapamycin +40-o-(2-hydroxyethyl)rapamycin +certican +hy-10218 +rad-666 +rad 666 +everolimus [jan] +nvp-rad-001 +l01xe10 +cs-0064 +everolimus [usan] From c4f0db88c494ddec1b0a70aa358b26368128df2b Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Thu, 21 Nov 2024 16:02:22 -0800 Subject: [PATCH 06/17] got single dataset build to work with script --- build.out | 1721 -------------------- build/docker/Dockerfile.mpnstPDX | 6 +- build/docker/docker-compose.yml | 1 + build/mpnst/build_drugs.sh | 10 +- build/mpnstPDX/01_mpnst_get_omics.R | 12 +- build/mpnstPDX/03_get_drug_response_data.R | 2 +- build/mpnstPDX/build_samples.sh | 2 +- build/mpnstPDX/requirements.r | 4 +- 8 files changed, 24 insertions(+), 1734 deletions(-) delete mode 100644 build.out diff --git a/build.out b/build.out deleted file mode 100644 index 36a601f4..00000000 --- a/build.out +++ /dev/null @@ -1,1721 +0,0 @@ -#0 building with "desktop-linux" instance using docker driver - -#1 [internal] load build definition from Dockerfile.mpnstpdx -#1 transferring dockerfile: 1.79kB done -#1 DONE 0.0s - -#2 [internal] load metadata for docker.io/library/r-base:4.3.2 -#2 DONE 0.4s - -#3 [internal] load .dockerignore -#3 transferring context: 116B 0.0s done -#3 DONE 0.0s - -#4 [ 1/15] FROM docker.io/library/r-base:4.3.2@sha256:4bdf68161b2ed65fa6ca8285d1dc445ceb8100e94f503c56f59d2cfc453c7cdd -#4 DONE 0.0s - -#5 [internal] load build context -#5 transferring context: 2.62kB 0.0s done -#5 DONE 0.0s - -#6 [ 2/15] RUN apt-get update && apt-get install -y build-essential wget curl libcurl4-openssl-dev libxml2-dev zlib1g-dev libssl-dev libbz2-dev libreadline-dev libsqlite3-dev libffi-dev -#6 CACHED - -#7 [ 7/15] RUN /opt/venv/bin/pip install --upgrade pip -#7 CACHED - -#8 [ 5/15] RUN echo "/usr/local/lib" >> /etc/ld.so.conf.d/python3.10.conf && ldconfig -#8 CACHED - -#9 [ 8/15] WORKDIR /app -#9 CACHED - -#10 [ 4/15] RUN ln -s /usr/local/bin/python3.10 /usr/bin/python3 && ln -s /usr/local/bin/pip3.10 /usr/bin/pip3 -#10 CACHED - -#11 [ 6/15] RUN python3 -m venv /opt/venv -#11 CACHED - -#12 [ 3/15] RUN wget https://www.python.org/ftp/python/3.10.12/Python-3.10.12.tgz && tar -xf Python-3.10.12.tgz && cd Python-3.10.12 && ./configure --enable-optimizations --enable-shared && make -j$(nproc) && make altinstall && cd .. && rm -rf Python-3.10.12.tgz Python-3.10.12 -#12 CACHED - -#13 [ 9/15] RUN mkdir -p /app/tmp/matplotlib -#13 CACHED - -#14 [10/15] ADD build/mpnstPDX/requirements.txt . -#14 DONE 0.0s - -#15 [11/15] ADD build/mpnstPDX/requirements.r . -#15 DONE 0.0s - -#16 [12/15] ADD build/mpnstPDX/* ./ -#16 DONE 0.0s - -#17 [13/15] ADD build/utils/* ./ -#17 DONE 0.0s - -#18 [14/15] RUN /opt/venv/bin/pip3 install -r requirements.txt -#18 0.470 Collecting pyarrow (from -r requirements.txt (line 1)) -#18 0.536 Downloading pyarrow-18.0.0-cp310-cp310-manylinux_2_28_aarch64.whl.metadata (3.3 kB) -#18 0.647 Collecting pandas (from -r requirements.txt (line 2)) -#18 0.663 Downloading pandas-2.2.3-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.whl.metadata (89 kB) -#18 0.801 Collecting matplotlib (from -r requirements.txt (line 3)) -#18 0.816 Downloading matplotlib-3.9.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (11 kB) -#18 0.947 Collecting numpy==1.26.4 (from -r requirements.txt (line 4)) -#18 0.962 Downloading numpy-1.26.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (62 kB) -#18 0.994 Collecting argparse (from -r requirements.txt (line 5)) -#18 1.010 Downloading argparse-1.4.0-py2.py3-none-any.whl.metadata (2.8 kB) -#18 1.095 Collecting tqdm (from -r requirements.txt (line 6)) -#18 1.110 Downloading tqdm-4.67.0-py3-none-any.whl.metadata (57 kB) -#18 1.185 Collecting scikit-learn (from -r requirements.txt (line 7)) -#18 1.200 Downloading scikit_learn-1.5.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (13 kB) -#18 1.295 Collecting scipy (from -r requirements.txt (line 8)) -#18 1.311 Downloading scipy-1.14.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (60 kB) -#18 1.352 Collecting requests (from -r requirements.txt (line 9)) -#18 1.366 Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB) -#18 1.388 Collecting mordredcommunity (from -r requirements.txt (line 10)) -#18 1.406 Downloading mordredcommunity-2.0.6-py3-none-any.whl.metadata (6.2 kB) -#18 1.449 Collecting rdkit (from -r requirements.txt (line 11)) -#18 1.463 Downloading rdkit-2024.3.6-cp310-cp310-manylinux_2_28_aarch64.whl.metadata (4.0 kB) -#18 1.503 Collecting python-dateutil>=2.8.2 (from pandas->-r requirements.txt (line 2)) -#18 1.518 Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) -#18 1.585 Collecting pytz>=2020.1 (from pandas->-r requirements.txt (line 2)) -#18 1.599 Downloading pytz-2024.2-py2.py3-none-any.whl.metadata (22 kB) -#18 1.625 Collecting tzdata>=2022.7 (from pandas->-r requirements.txt (line 2)) -#18 1.638 Downloading tzdata-2024.2-py2.py3-none-any.whl.metadata (1.4 kB) -#18 1.701 Collecting contourpy>=1.0.1 (from matplotlib->-r requirements.txt (line 3)) -#18 1.715 Downloading contourpy-1.3.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (5.4 kB) -#18 1.742 Collecting cycler>=0.10 (from matplotlib->-r requirements.txt (line 3)) -#18 1.755 Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB) -#18 1.853 Collecting fonttools>=4.22.0 (from matplotlib->-r requirements.txt (line 3)) -#18 1.888 Downloading fonttools-4.55.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (164 kB) -#18 1.947 Collecting kiwisolver>=1.3.1 (from matplotlib->-r requirements.txt (line 3)) -#18 1.963 Downloading kiwisolver-1.4.7-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (6.3 kB) -#18 1.997 Collecting packaging>=20.0 (from matplotlib->-r requirements.txt (line 3)) -#18 2.011 Downloading packaging-24.2-py3-none-any.whl.metadata (3.2 kB) -#18 2.155 Collecting pillow>=8 (from matplotlib->-r requirements.txt (line 3)) -#18 2.169 Downloading pillow-11.0.0-cp310-cp310-manylinux_2_28_aarch64.whl.metadata (9.1 kB) -#18 2.207 Collecting pyparsing>=2.3.1 (from matplotlib->-r requirements.txt (line 3)) -#18 2.221 Downloading pyparsing-3.2.0-py3-none-any.whl.metadata (5.0 kB) -#18 2.258 Collecting joblib>=1.2.0 (from scikit-learn->-r requirements.txt (line 7)) -#18 2.278 Downloading joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB) -#18 2.299 Collecting threadpoolctl>=3.1.0 (from scikit-learn->-r requirements.txt (line 7)) -#18 2.312 Downloading threadpoolctl-3.5.0-py3-none-any.whl.metadata (13 kB) -#18 2.377 Collecting charset-normalizer<4,>=2 (from requests->-r requirements.txt (line 9)) -#18 2.390 Downloading charset_normalizer-3.4.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (34 kB) -#18 2.414 Collecting idna<4,>=2.5 (from requests->-r requirements.txt (line 9)) -#18 2.428 Downloading idna-3.10-py3-none-any.whl.metadata (10 kB) -#18 2.469 Collecting urllib3<3,>=1.21.1 (from requests->-r requirements.txt (line 9)) -#18 2.483 Downloading urllib3-2.2.3-py3-none-any.whl.metadata (6.5 kB) -#18 2.510 Collecting certifi>=2017.4.17 (from requests->-r requirements.txt (line 9)) -#18 2.523 Downloading certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB) -#18 2.551 Collecting six (from mordredcommunity->-r requirements.txt (line 10)) -#18 2.564 Downloading six-1.16.0-py2.py3-none-any.whl.metadata (1.8 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contourpy-1.3.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (312 kB) -#18 6.251 Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB) -#18 6.268 Downloading fonttools-4.55.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (4.6 MB) -#18 6.334 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 68.9 MB/s eta 0:00:00 -#18 6.349 Downloading idna-3.10-py3-none-any.whl (70 kB) -#18 6.366 Downloading joblib-1.4.2-py3-none-any.whl (301 kB) -#18 6.386 Downloading kiwisolver-1.4.7-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (1.4 MB) -#18 6.405 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 73.5 MB/s eta 0:00:00 -#18 6.418 Downloading packaging-24.2-py3-none-any.whl (65 kB) -#18 6.442 Downloading pillow-11.0.0-cp310-cp310-manylinux_2_28_aarch64.whl (4.2 MB) -#18 6.498 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.2/4.2 MB 74.8 MB/s eta 0:00:00 -#18 6.512 Downloading pyparsing-3.2.0-py3-none-any.whl (106 kB) -#18 6.529 Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) -#18 6.547 Downloading pytz-2024.2-py2.py3-none-any.whl (508 kB) -#18 6.566 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) -#18 6.582 Downloading threadpoolctl-3.5.0-py3-none-any.whl (18 kB) -#18 6.600 Downloading tzdata-2024.2-py2.py3-none-any.whl (346 kB) -#18 6.618 Downloading urllib3-2.2.3-py3-none-any.whl (126 kB) -#18 6.636 Downloading networkx-3.4.2-py3-none-any.whl (1.7 MB) -#18 6.658 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 75.7 MB/s eta 0:00:00 -#18 6.966 Installing collected packages: pytz, argparse, urllib3, tzdata, tqdm, threadpoolctl, six, pyparsing, pyarrow, pillow, packaging, numpy, networkx, kiwisolver, joblib, idna, fonttools, cycler, charset-normalizer, certifi, scipy, requests, rdkit, python-dateutil, contourpy, scikit-learn, pandas, mordredcommunity, matplotlib -#18 19.01 Successfully installed argparse-1.4.0 certifi-2024.8.30 charset-normalizer-3.4.0 contourpy-1.3.1 cycler-0.12.1 fonttools-4.55.0 idna-3.10 joblib-1.4.2 kiwisolver-1.4.7 matplotlib-3.9.2 mordredcommunity-2.0.6 networkx-3.4.2 numpy-1.26.4 packaging-24.2 pandas-2.2.3 pillow-11.0.0 pyarrow-18.0.0 pyparsing-3.2.0 python-dateutil-2.9.0.post0 pytz-2024.2 rdkit-2024.3.6 requests-2.32.3 scikit-learn-1.5.2 scipy-1.14.1 six-1.16.0 threadpoolctl-3.5.0 tqdm-4.67.0 tzdata-2024.2 urllib3-2.2.3 -#18 19.11 -#18 19.11 [notice] A new release of pip is available: 24.2 -> 24.3.1 -#18 19.11 [notice] To update, run: python3 -m pip install --upgrade pip -#18 DONE 19.8s - -#19 [15/15] RUN Rscript requirements.r -#19 0.252 Installing package into ‘/usr/local/lib/R/site-library’ -#19 0.252 (as ‘lib’ is unspecified) -#19 1.128 also installing the dependencies ‘rprojroot’, ‘Rcpp’, ‘RcppTOML’, ‘here’, ‘jsonlite’, ‘png’, ‘rappdirs’, ‘rlang’, ‘withr’ -#19 1.128 -#19 1.129 trying URL 'https://cloud.r-project.org/src/contrib/rprojroot_2.0.4.tar.gz' -#19 1.576 Content type 'application/x-gzip' length 59946 bytes (58 KB) -#19 1.576 ================================================== -#19 1.595 downloaded 58 KB -#19 1.595 -#19 1.599 trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.13-1.tar.gz' -#19 2.063 Content type 'application/x-gzip' length 3435726 bytes (3.3 MB) -#19 2.077 ================================================== -#19 2.183 downloaded 3.3 MB -#19 2.183 -#19 2.185 trying URL 'https://cloud.r-project.org/src/contrib/RcppTOML_0.2.2.tar.gz' -#19 2.792 Content type 'application/x-gzip' length 141195 bytes (137 KB) -#19 2.792 ================================================== -#19 2.860 downloaded 137 KB -#19 2.860 -#19 2.862 trying URL 'https://cloud.r-project.org/src/contrib/here_1.0.1.tar.gz' -#19 3.320 Content type 'application/x-gzip' length 32954 bytes (32 KB) -#19 3.320 ================================================== -#19 3.322 downloaded 32 KB -#19 3.322 -#19 3.325 trying URL 'https://cloud.r-project.org/src/contrib/jsonlite_1.8.9.tar.gz' -#19 3.796 Content type 'application/x-gzip' length 1055633 bytes (1.0 MB) -#19 3.797 ================================================== -#19 3.854 downloaded 1.0 MB -#19 3.854 -#19 3.857 trying URL 'https://cloud.r-project.org/src/contrib/png_0.1-8.tar.gz' -#19 4.445 Content type 'application/x-gzip' length 24880 bytes (24 KB) -#19 4.445 ================================================== -#19 4.445 downloaded 24 KB -#19 4.445 -#19 4.450 trying URL 'https://cloud.r-project.org/src/contrib/rappdirs_0.3.3.tar.gz' -#19 5.016 Content type 'application/x-gzip' length 12288 bytes (12 KB) -#19 5.016 ================================================== -#19 5.016 downloaded 12 KB -#19 5.016 -#19 5.024 trying URL 'https://cloud.r-project.org/src/contrib/rlang_1.1.4.tar.gz' -#19 5.582 Content type 'application/x-gzip' length 767041 bytes (749 KB) -#19 5.582 ================================================== -#19 5.631 downloaded 749 KB -#19 5.631 -#19 5.634 trying URL 'https://cloud.r-project.org/src/contrib/withr_3.0.2.tar.gz' -#19 6.192 Content type 'application/x-gzip' length 103240 bytes (100 KB) -#19 6.192 ================================================== -#19 6.207 downloaded 100 KB -#19 6.207 -#19 6.212 trying URL 'https://cloud.r-project.org/src/contrib/reticulate_1.40.0.tar.gz' -#19 6.789 Content type 'application/x-gzip' length 1640550 bytes (1.6 MB) -#19 6.794 ================================================== -#19 6.856 downloaded 1.6 MB -#19 6.856 -#19 7.024 * installing *source* package ‘rprojroot’ ... -#19 7.025 ** package ‘rprojroot’ successfully unpacked and MD5 sums checked -#19 7.025 ** using staged installation -#19 7.033 ** R -#19 7.036 ** inst -#19 7.037 ** byte-compile and prepare package for lazy loading -#19 7.325 ** help -#19 7.341 *** installing help indices -#19 7.353 *** copying figures -#19 7.353 ** building package indices -#19 7.491 ** installing vignettes -#19 7.494 ** testing if installed package can be loaded from temporary location -#19 7.609 ** testing if installed package can be loaded from final location -#19 7.719 ** testing if installed package keeps a record of temporary installation path -#19 7.719 * DONE (rprojroot) -#19 8.206 * installing *source* package ‘Rcpp’ ... -#19 8.237 ** package ‘Rcpp’ successfully unpacked and MD5 sums checked -#19 8.237 ** using staged installation -#19 8.244 ** libs -#19 8.254 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ -#19 8.255 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c api.cpp -o api.o -#19 9.262 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c attributes.cpp -o attributes.o -#19 15.62 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c barrier.cpp -o barrier.o -#19 15.73 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c date.cpp -o date.o -#19 16.79 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c module.cpp -o module.o -#19 19.45 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rcpp_init.cpp -o rcpp_init.o -#19 20.22 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/usr/lib/R/lib -lR -#19 20.30 installing to /usr/local/lib/R/site-library/00LOCK-Rcpp/00new/Rcpp/libs -#19 20.30 ** R -#19 20.31 ** inst -#19 20.33 ** byte-compile and prepare package for lazy loading -#19 21.23 ** help -#19 21.28 *** installing help indices -#19 21.31 ** building package indices -#19 21.46 ** installing vignettes -#19 21.46 ** testing if installed package can be loaded from temporary location -#19 21.63 ** checking absolute paths in shared objects and dynamic libraries -#19 21.64 ** testing if installed package can be loaded from final location -#19 21.80 ** testing if installed package keeps a record of temporary installation path -#19 21.81 * DONE (Rcpp) -#19 22.04 * installing *source* package ‘jsonlite’ ... -#19 22.05 ** package ‘jsonlite’ successfully unpacked and MD5 sums checked -#19 22.05 ** using staged installation -#19 22.06 ** libs -#19 22.07 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 22.07 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c base64.c -o base64.o -#19 22.15 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c collapse_array.c -o collapse_array.o -#19 22.19 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c collapse_object.c -o collapse_object.o -#19 22.22 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c collapse_pretty.c -o collapse_pretty.o -#19 22.29 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c escape_chars.c -o escape_chars.o -#19 22.33 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c integer64_to_na.c -o integer64_to_na.o -#19 22.36 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c is_datelist.c -o is_datelist.o -#19 22.39 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c is_recordlist.c -o is_recordlist.o -#19 22.43 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c is_scalarlist.c -o is_scalarlist.o -#19 22.46 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c modp_numtoa.c -o modp_numtoa.o -#19 22.54 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c null_to_na.c -o null_to_na.o -#19 22.58 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c num_to_char.c -o num_to_char.o -#19 22.63 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c parse.c -o parse.o -#19 22.68 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c prettify.c -o prettify.o -#19 22.72 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c push_parser.c -o push_parser.o -#19 22.75 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c r-base64.c -o r-base64.o -#19 22.78 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c register.c -o register.o -#19 22.81 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c row_collapse.c -o row_collapse.o -#19 22.85 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c transpose_list.c -o transpose_list.o -#19 22.88 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c validate.c -o validate.o -#19 22.91 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl.c -o yajl/yajl.o -#19 22.95 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o -#19 22.97 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_buf.c -o yajl/yajl_buf.o -#19 23.00 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_encode.c -o yajl/yajl_encode.o -#19 23.06 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_gen.c -o yajl/yajl_gen.o -#19 23.21 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_lex.c -o yajl/yajl_lex.o -#19 23.36 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_parser.c -o yajl/yajl_parser.o -#19 23.47 gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c yajl/yajl_tree.c -o yajl/yajl_tree.o -#19 23.56 ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o -#19 23.57 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/usr/lib/R/lib -lR -#19 23.58 installing to /usr/local/lib/R/site-library/00LOCK-jsonlite/00new/jsonlite/libs -#19 23.58 ** R -#19 23.59 ** inst -#19 23.59 ** byte-compile and prepare package for lazy loading -#19 24.03 in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs” -#19 24.03 in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime” -#19 24.03 in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms” -#19 24.03 in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json” -#19 24.03 in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64” -#19 24.03 in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist” -#19 24.03 in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob” -#19 24.03 in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar” -#19 24.03 in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf” -#19 24.03 in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc” -#19 24.03 in method for ‘asJSON’ with signature ‘"vctrs_vctr"’: no definition for class “vctrs_vctr” -#19 24.03 ** help -#19 24.04 *** installing help indices -#19 24.06 ** building package indices -#19 24.19 ** installing vignettes -#19 24.19 ** testing if installed package can be loaded from temporary location -#19 24.33 ** checking absolute paths in shared objects and dynamic libraries -#19 24.33 ** testing if installed package can be loaded from final location -#19 24.46 ** testing if installed package keeps a record of temporary installation path -#19 24.46 * DONE (jsonlite) -#19 24.60 * installing *source* package ‘png’ ... -#19 24.60 ** package ‘png’ successfully unpacked and MD5 sums checked -#19 24.60 ** using staged installation -#19 24.60 ** libs -#19 24.61 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 24.61 gcc -I"/usr/share/R/include" -DNDEBUG `libpng-config --cflags` -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dummy.c -o dummy.o -#19 24.62 gcc -I"/usr/share/R/include" -DNDEBUG `libpng-config --cflags` -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read.c -o read.o -#19 24.75 gcc -I"/usr/share/R/include" -DNDEBUG `libpng-config --cflags` -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c write.c -o write.o -#19 24.87 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o png.so dummy.o read.o write.o -lpng16 -lm -lz -lm -L/usr/lib/R/lib -lR -#19 24.88 installing to /usr/local/lib/R/site-library/00LOCK-png/00new/png/libs -#19 24.89 ** R -#19 24.89 ** inst -#19 24.89 ** byte-compile and prepare package for lazy loading -#19 25.03 ** help -#19 25.04 *** installing help indices -#19 25.04 ** building package indices -#19 25.19 ** testing if installed package can be loaded from temporary location -#19 25.32 ** checking absolute paths in shared objects and dynamic libraries -#19 25.32 ** testing if installed package can be loaded from final location -#19 25.45 ** testing if installed package keeps a record of temporary installation path -#19 25.45 * DONE (png) -#19 25.58 * installing *source* package ‘rappdirs’ ... -#19 25.59 ** package ‘rappdirs’ successfully unpacked and MD5 sums checked -#19 25.59 ** using staged installation -#19 25.60 ** libs -#19 25.60 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 25.60 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o -#19 25.63 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c win-path.c -o win-path.o -#19 25.65 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o rappdirs.so init.o win-path.o -L/usr/lib/R/lib -lR -#19 25.66 installing to /usr/local/lib/R/site-library/00LOCK-rappdirs/00new/rappdirs/libs -#19 25.66 ** R -#19 25.67 ** byte-compile and prepare package for lazy loading -#19 25.84 ** help -#19 25.85 *** installing help indices -#19 25.86 ** building package indices -#19 25.99 ** testing if installed package can be loaded from temporary location -#19 26.12 ** checking absolute paths in shared objects and dynamic libraries -#19 26.13 ** testing if installed package can be loaded from final location -#19 26.25 ** testing if installed package keeps a record of temporary installation path -#19 26.25 * DONE (rappdirs) -#19 26.56 * installing *source* package ‘rlang’ ... -#19 26.58 ** package ‘rlang’ successfully unpacked and MD5 sums checked -#19 26.58 ** using staged installation -#19 26.58 ** libs -#19 26.59 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 26.59 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c capture.c -o capture.o -#19 26.64 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c internal.c -o internal.o -#19 29.80 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rlang.c -o rlang.o -#19 30.60 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang/ -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c version.c -o version.o -#19 30.62 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o rlang.so capture.o internal.o rlang.o version.o -L/usr/lib/R/lib -lR -#19 30.65 installing to /usr/local/lib/R/site-library/00LOCK-rlang/00new/rlang/libs -#19 30.65 ** R -#19 30.69 ** inst -#19 30.69 ** byte-compile and prepare package for lazy loading -#19 33.04 ** help -#19 33.39 *** installing help indices -#19 33.55 *** copying figures -#19 33.55 ** building package indices -#19 33.88 ** testing if installed package can be loaded from temporary location -#19 34.04 ** checking absolute paths in shared objects and dynamic libraries -#19 34.04 ** testing if installed package can be loaded from final location -#19 34.24 ** testing if installed package keeps a record of temporary installation path -#19 34.24 * DONE (rlang) -#19 34.40 * installing *source* package ‘withr’ ... -#19 34.40 ** package ‘withr’ successfully unpacked and MD5 sums checked -#19 34.40 ** using staged installation -#19 34.41 ** R -#19 34.42 ** inst -#19 34.42 ** byte-compile and prepare package for lazy loading -#19 34.79 ** help -#19 34.82 *** installing help indices -#19 34.85 *** copying figures -#19 34.85 ** building package indices -#19 35.00 ** installing vignettes -#19 35.00 ** testing if installed package can be loaded from temporary location -#19 35.12 ** testing if installed package can be loaded from final location -#19 35.25 ** testing if installed package keeps a record of temporary installation path -#19 35.25 * DONE (withr) -#19 35.41 * installing *source* package ‘RcppTOML’ ... -#19 35.42 ** package ‘RcppTOML’ successfully unpacked and MD5 sums checked -#19 35.42 ** using staged installation -#19 35.42 ** libs -#19 35.43 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ -#19 35.43 using C++17 -#19 35.43 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DTOML_ENABLE_FLOAT16=0 -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o -#19 36.84 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DTOML_ENABLE_FLOAT16=0 -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c parse.cpp -o parse.o -#19 41.27 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o RcppTOML.so RcppExports.o parse.o -L/usr/lib/R/lib -lR -#19 41.34 installing to /usr/local/lib/R/site-library/00LOCK-RcppTOML/00new/RcppTOML/libs -#19 41.34 ** R -#19 41.34 ** inst -#19 41.34 ** byte-compile and prepare package for lazy loading -#19 41.53 ** help -#19 41.54 *** installing help indices -#19 41.54 ** building package indices -#19 41.70 ** testing if installed package can be loaded from temporary location -#19 41.90 ** checking absolute paths in shared objects and dynamic libraries -#19 41.90 ** testing if installed package can be loaded from final location -#19 42.07 ** testing if installed package keeps a record of temporary installation path -#19 42.07 * DONE (RcppTOML) -#19 42.22 * installing *source* package ‘here’ ... -#19 42.22 ** package ‘here’ successfully unpacked and MD5 sums checked -#19 42.22 ** using staged installation -#19 42.23 ** R -#19 42.23 ** inst -#19 42.24 ** byte-compile and prepare package for lazy loading -#19 42.40 ** help -#19 42.41 *** installing help indices -#19 42.42 *** copying figures -#19 42.42 ** building package indices -#19 42.54 ** installing vignettes -#19 42.54 ** testing if installed package can be loaded from temporary location -#19 42.67 ** testing if installed package can be loaded from final location -#19 42.79 ** testing if installed package keeps a record of temporary installation path -#19 42.79 * DONE (here) -#19 43.09 * installing *source* package ‘reticulate’ ... -#19 43.10 ** package ‘reticulate’ successfully unpacked and MD5 sums checked -#19 43.10 ** using staged installation -#19 43.11 ** libs -#19 43.12 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ -#19 43.12 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o -#19 46.21 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c event_loop.cpp -o event_loop.o -#19 46.43 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c libpython.cpp -o libpython.o -#19 47.18 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c output.cpp -o output.o -#19 47.76 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c pending_py_calls_notifier.cpp -o pending_py_calls_notifier.o -#19 48.15 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c python.cpp -o python.o -#19 53.68 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c readline.cpp -o readline.o -#19 53.79 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c signals.cpp -o signals.o -#19 53.97 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o reticulate.so RcppExports.o event_loop.o libpython.o output.o pending_py_calls_notifier.o python.o readline.o signals.o -L/usr/lib/R/lib -lR -#19 54.04 installing to /usr/local/lib/R/site-library/00LOCK-reticulate/00new/reticulate/libs -#19 54.04 ** R -#19 54.07 ** inst -#19 54.07 ** byte-compile and prepare package for lazy loading -#19 56.09 ** help -#19 56.17 *** installing help indices -#19 56.23 *** copying figures -#19 56.23 ** building package indices -#19 56.40 ** installing vignettes -#19 56.41 ** testing if installed package can be loaded from temporary location -#19 57.05 ** checking absolute paths in shared objects and dynamic libraries -#19 57.06 ** testing if installed package can be loaded from final location -#19 57.73 ** testing if installed package keeps a record of temporary installation path -#19 57.73 * DONE (reticulate) -#19 57.75 -#19 57.75 The downloaded source packages are in -#19 57.75 ‘/tmp/RtmpZsJzTy/downloaded_packages’ -#19 58.59 Warning message: -#19 58.59 The request to `use_python("/opt/venv/bin/python")` will be ignored because the environment variable RETICULATE_PYTHON is set to "/opt/venv/bin/python3" -#19 58.59 Installing package into ‘/usr/local/lib/R/site-library’ -#19 58.59 (as ‘lib’ is unspecified) -#19 58.80 trying URL 'https://cloud.r-project.org/src/contrib/remotes_2.5.0.tar.gz' -#19 59.36 Content type 'application/x-gzip' length 164496 bytes (160 KB) -#19 59.36 ================================================== -#19 59.38 downloaded 160 KB -#19 59.38 -#19 59.58 * installing *source* package ‘remotes’ ... -#19 59.58 ** package ‘remotes’ successfully unpacked and MD5 sums checked -#19 59.58 ** using staged installation -#19 59.59 ** R -#19 59.61 ** inst -#19 59.61 ** byte-compile and prepare package for lazy loading -#19 60.62 ** help -#19 60.66 *** installing help indices -#19 60.69 ** building package indices -#19 60.84 ** installing vignettes -#19 60.84 ** testing if installed package can be loaded from temporary location -#19 60.98 ** testing if installed package can be loaded from final location -#19 61.13 ** testing if installed package keeps a record of temporary installation path -#19 61.13 * DONE (remotes) -#19 61.13 -#19 61.13 The downloaded source packages are in -#19 61.13 ‘/tmp/RtmpZsJzTy/downloaded_packages’ -#19 62.38 Downloading package from url: https://cloud.r-project.org/src/contrib/Archive/rjson/rjson_0.2.21.tar.gz -#19 63.59 Installing package into ‘/usr/local/lib/R/site-library’ -#19 63.59 (as ‘lib’ is unspecified) -#19 63.72 * installing *source* package ‘rjson’ ... -#19 63.73 ** package ‘rjson’ successfully unpacked and MD5 sums checked -#19 63.73 ** using staged installation -#19 63.73 ** libs -#19 63.74 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 63.74 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ -#19 63.74 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dump.cpp -o dump.o -#19 64.19 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c parser.c -o parser.o -#19 64.36 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c register.c -o register.o -#19 64.38 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o rjson.so dump.o parser.o register.o -L/usr/lib/R/lib -lR -#19 64.42 installing to /usr/local/lib/R/site-library/00LOCK-rjson/00new/rjson/libs -#19 64.42 ** R -#19 64.42 ** inst -#19 64.43 ** byte-compile and prepare package for lazy loading -#19 64.65 ** help -#19 64.67 *** installing help indices -#19 64.67 ** building package indices -#19 64.79 ** installing vignettes -#19 64.79 ** testing if installed package can be loaded from temporary location -#19 64.91 ** checking absolute paths in shared objects and dynamic libraries -#19 64.92 ** testing if installed package can be loaded from final location -#19 65.04 ** testing if installed package keeps a record of temporary installation path -#19 65.04 * DONE (rjson) -#19 65.05 Installing package into ‘/usr/local/lib/R/site-library’ -#19 65.05 (as ‘lib’ is unspecified) -#19 65.93 trying URL 'http://ran.synapse.org/src/contrib/synapser_2.1.1.259.tar.gz' -#19 66.44 Content type 'application/x-tar' length 6046498 bytes (5.8 MB) -#19 66.80 ================================================== -#19 67.95 downloaded 5.8 MB -#19 67.95 -#19 68.32 * installing *source* package ‘synapser’ ... -#19 68.32 ** using staged installation -#19 69.32 [1] "*** Using Python Configuration:" -#19 69.94 python: /opt/venv/bin/python3 -#19 69.94 libpython: /usr/local/lib/libpython3.10.so -#19 69.94 pythonhome: /opt/venv:/opt/venv -#19 69.94 version: 3.10.12 (main, Oct 21 2024, 16:07:16) [GCC 14.2.0] -#19 69.94 numpy: /opt/venv/lib/python3.10/site-packages/numpy -#19 69.94 numpy_version: 1.26.4 -#19 69.94 -#19 69.94 NOTE: Python version was forced by RETICULATE_PYTHON -#19 69.94 Using virtual environment '/opt/venv' ... -#19 69.96 + /opt/venv/bin/python -m pip install --upgrade --no-user 'pandas>=1.5,<=2.0.3' jinja2 markupsafe 'numpy<=1.24.4' -#19 70.27 Collecting pandas<=2.0.3,>=1.5 -#19 70.39 Downloading pandas-2.0.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (18 kB) -#19 70.44 Collecting jinja2 -#19 70.45 Downloading jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB) -#19 70.52 Collecting markupsafe -#19 70.53 Downloading MarkupSafe-3.0.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (4.0 kB) -#19 70.66 Collecting numpy<=1.24.4 -#19 70.67 Downloading numpy-1.24.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (5.6 kB) -#19 70.68 Requirement already satisfied: python-dateutil>=2.8.2 in /opt/venv/lib/python3.10/site-packages (from pandas<=2.0.3,>=1.5) (2.9.0.post0) -#19 70.68 Requirement already satisfied: pytz>=2020.1 in /opt/venv/lib/python3.10/site-packages (from pandas<=2.0.3,>=1.5) (2024.2) -#19 70.68 Requirement already satisfied: tzdata>=2022.1 in /opt/venv/lib/python3.10/site-packages (from pandas<=2.0.3,>=1.5) (2024.2) -#19 70.68 Requirement already satisfied: six>=1.5 in /opt/venv/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas<=2.0.3,>=1.5) (1.16.0) -#19 70.70 Downloading pandas-2.0.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (11.6 MB) -#19 70.89 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 71.9 MB/s eta 0:00:00 -#19 70.91 Downloading jinja2-3.1.4-py3-none-any.whl (133 kB) -#19 70.92 Downloading MarkupSafe-3.0.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (21 kB) -#19 70.94 Downloading numpy-1.24.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (14.0 MB) -#19 71.11 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.0/14.0 MB 82.8 MB/s eta 0:00:00 -#19 71.21 Installing collected packages: numpy, markupsafe, pandas, jinja2 -#19 71.21 Attempting uninstall: numpy -#19 71.21 Found existing installation: numpy 1.26.4 -#19 71.25 Uninstalling numpy-1.26.4: -#19 71.40 Successfully uninstalled numpy-1.26.4 -#19 72.56 Attempting uninstall: pandas -#19 72.56 Found existing installation: pandas 2.2.3 -#19 72.65 Uninstalling pandas-2.2.3: -#19 73.13 Successfully uninstalled pandas-2.2.3 -#19 75.52 Successfully installed jinja2-3.1.4 markupsafe-3.0.2 numpy-1.24.4 pandas-2.0.3 -#19 75.53 -#19 75.53 [notice] A new release of pip is available: 24.2 -> 24.3.1 -#19 75.53 [notice] To update, run: pip install --upgrade pip -#19 75.59 Using virtual environment '/opt/venv' ... -#19 75.61 + /opt/venv/bin/python -m pip install --upgrade --no-user 'synapseclient==4.4.0' -#19 75.83 Collecting synapseclient==4.4.0 -#19 75.89 Downloading synapseclient-4.4.0-py3-none-any.whl.metadata (15 kB) -#19 75.90 Requirement already satisfied: requests<3.0,>=2.22.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (2.32.3) -#19 75.93 Collecting urllib3<2,>=1.26.18 (from synapseclient==4.4.0) -#19 75.95 Downloading urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB) -#19 75.99 Collecting deprecated<2.0,>=1.2.4 (from synapseclient==4.4.0) -#19 76.01 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opentelemetry-proto==1.21.0 (from opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) -#19 78.33 Downloading opentelemetry_proto-1.21.0-py3-none-any.whl.metadata (2.3 kB) -#19 78.46 Collecting protobuf<5.0,>=3.19 (from opentelemetry-proto==1.21.0->opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) -#19 78.47 Downloading protobuf-4.25.5-cp37-abi3-manylinux2014_aarch64.whl.metadata (541 bytes) -#19 78.50 Collecting opentelemetry-semantic-conventions==0.42b0 (from opentelemetry-sdk~=1.21.0->synapseclient==4.4.0) -#19 78.52 Downloading opentelemetry_semantic_conventions-0.42b0-py3-none-any.whl.metadata (2.3 kB) -#19 78.54 Requirement already satisfied: charset-normalizer<4,>=2 in /opt/venv/lib/python3.10/site-packages (from requests<3.0,>=2.22.0->synapseclient==4.4.0) (3.4.0) -#19 78.60 Collecting zipp>=0.5 (from importlib-metadata<7.0,>=6.0->opentelemetry-api~=1.21.0->synapseclient==4.4.0) -#19 78.61 Downloading zipp-3.21.0-py3-none-any.whl.metadata 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Downloading opentelemetry_sdk-1.21.0-py3-none-any.whl (105 kB) -#19 78.88 Downloading opentelemetry_semantic_conventions-0.42b0-py3-none-any.whl (36 kB) -#19 78.90 Downloading urllib3-1.26.20-py2.py3-none-any.whl (144 kB) -#19 78.92 Downloading backoff-2.2.1-py3-none-any.whl (15 kB) -#19 78.93 Downloading googleapis_common_protos-1.66.0-py2.py3-none-any.whl (221 kB) -#19 78.95 Downloading importlib_metadata-6.11.0-py3-none-any.whl (23 kB) -#19 78.97 Downloading typing_extensions-4.12.2-py3-none-any.whl (37 kB) -#19 78.99 Downloading wrapt-1.16.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (80 kB) -#19 79.00 Downloading anyio-4.6.2.post1-py3-none-any.whl (90 kB) -#19 79.02 Downloading sniffio-1.3.1-py3-none-any.whl (10 kB) -#19 79.04 Downloading exceptiongroup-1.2.2-py3-none-any.whl (16 kB) -#19 79.06 Downloading h11-0.14.0-py3-none-any.whl (58 kB) -#19 79.08 Downloading protobuf-4.25.5-cp37-abi3-manylinux2014_aarch64.whl (293 kB) -#19 79.24 Downloading zipp-3.21.0-py3-none-any.whl (9.6 kB) -#19 79.26 Building wheels for collected packages: psutil -#19 79.26 Building wheel for psutil (pyproject.toml): started -#19 80.20 Building wheel for psutil (pyproject.toml): finished with status 'done' -#19 80.20 Created wheel for psutil: filename=psutil-5.9.8-cp310-abi3-linux_aarch64.whl size=287191 sha256=64c0012bc080295b71e6b637dcc837bb5e35b963e2fc0c1b152ee743e284fb48 -#19 80.20 Stored in directory: /root/.cache/pip/wheels/3e/93/d6/85cd469d2103627a9e38acdccc834a9997e77d2abe6da25c8b -#19 80.20 Successfully built psutil -#19 80.27 Installing collected packages: zipp, wrapt, urllib3, typing-extensions, sniffio, psutil, protobuf, opentelemetry-semantic-conventions, nest-asyncio, h11, exceptiongroup, backoff, asyncio-atexit, opentelemetry-proto, importlib-metadata, httpcore, googleapis-common-protos, deprecated, async-lru, anyio, opentelemetry-exporter-otlp-proto-common, opentelemetry-api, httpx, opentelemetry-sdk, opentelemetry-exporter-otlp-proto-http, synapseclient -#19 80.29 Attempting uninstall: urllib3 -#19 80.29 Found existing installation: urllib3 2.2.3 -#19 80.30 Uninstalling urllib3-2.2.3: -#19 80.30 Successfully uninstalled urllib3-2.2.3 -#19 80.84 Successfully installed anyio-4.6.2.post1 async-lru-2.0.4 asyncio-atexit-1.0.1 backoff-2.2.1 deprecated-1.2.15 exceptiongroup-1.2.2 googleapis-common-protos-1.66.0 h11-0.14.0 httpcore-1.0.7 httpx-0.27.2 importlib-metadata-6.11.0 nest-asyncio-1.6.0 opentelemetry-api-1.21.0 opentelemetry-exporter-otlp-proto-common-1.21.0 opentelemetry-exporter-otlp-proto-http-1.21.0 opentelemetry-proto-1.21.0 opentelemetry-sdk-1.21.0 opentelemetry-semantic-conventions-0.42b0 protobuf-4.25.5 psutil-5.9.8 sniffio-1.3.1 synapseclient-4.4.0 typing-extensions-4.12.2 urllib3-1.26.20 wrapt-1.16.0 zipp-3.21.0 -#19 80.85 -#19 80.85 [notice] A new release of pip is available: 24.2 -> 24.3.1 -#19 80.85 [notice] To update, run: pip install --upgrade pip -#19 82.20 ** R -#19 82.20 ** inst -#19 82.21 ** byte-compile and prepare package for lazy loading -#19 83.20 ** help -#19 83.31 *** installing help indices -#19 83.37 ** building package indices -#19 83.55 ** installing vignettes -#19 83.56 ** testing if installed package can be loaded from temporary location -#19 85.15 ** testing if installed package can be loaded from final location -#19 86.73 ** testing if installed package keeps a record of temporary installation path -#19 86.73 * DONE (synapser) -#19 86.74 -#19 86.74 The downloaded source packages are in -#19 86.74 ‘/tmp/RtmpZsJzTy/downloaded_packages’ -#19 86.74 Installing package into ‘/usr/local/lib/R/site-library’ -#19 86.74 (as ‘lib’ is unspecified) -#19 86.97 also installing the dependencies ‘fansi’, ‘utf8’, ‘pkgconfig’, ‘cli’, ‘generics’, ‘glue’, ‘lifecycle’, ‘magrittr’, ‘pillar’, ‘R6’, ‘tibble’, ‘tidyselect’, ‘vctrs’ -#19 86.97 -#19 86.97 trying URL 'https://cloud.r-project.org/src/contrib/fansi_1.0.6.tar.gz' -#19 87.43 Content type 'application/x-gzip' length 482480 bytes (471 KB) -#19 87.43 ================================================== -#19 87.47 downloaded 471 KB -#19 87.47 -#19 87.47 trying URL 'https://cloud.r-project.org/src/contrib/utf8_1.2.4.tar.gz' -#19 88.05 Content type 'application/x-gzip' length 241081 bytes (235 KB) -#19 88.05 ================================================== -#19 88.07 downloaded 235 KB -#19 88.07 -#19 88.18 trying URL 'https://cloud.r-project.org/src/contrib/pkgconfig_2.0.3.tar.gz' -#19 88.64 Content type 'application/x-gzip' length 6080 bytes -#19 88.64 ================================================== -#19 88.64 downloaded 6080 bytes -#19 88.64 -#19 88.65 trying URL 'https://cloud.r-project.org/src/contrib/cli_3.6.3.tar.gz' -#19 89.22 Content type 'application/x-gzip' length 568162 bytes (554 KB) -#19 89.22 ================================================== -#19 89.27 downloaded 554 KB -#19 89.27 -#19 89.27 trying URL 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downloaded 260 KB -#19 91.41 -#19 91.42 trying URL 'https://cloud.r-project.org/src/contrib/pillar_1.9.0.tar.gz' -#19 92.00 Content type 'application/x-gzip' length 444528 bytes (434 KB) -#19 92.00 ================================================== -#19 92.04 downloaded 434 KB -#19 92.04 -#19 92.04 trying URL 'https://cloud.r-project.org/src/contrib/R6_2.5.1.tar.gz' -#19 92.61 Content type 'application/x-gzip' length 63422 bytes (61 KB) -#19 92.61 ================================================== -#19 92.61 downloaded 61 KB -#19 92.61 -#19 92.62 trying URL 'https://cloud.r-project.org/src/contrib/tibble_3.2.1.tar.gz' -#19 93.19 Content type 'application/x-gzip' length 565982 bytes (552 KB) -#19 93.19 ================================================== -#19 93.24 downloaded 552 KB -#19 93.24 -#19 93.24 trying URL 'https://cloud.r-project.org/src/contrib/tidyselect_1.2.1.tar.gz' -#19 93.69 Content type 'application/x-gzip' length 103591 bytes (101 KB) -#19 93.69 ================================================== -#19 93.71 downloaded 101 KB -#19 93.71 -#19 93.71 trying URL 'https://cloud.r-project.org/src/contrib/vctrs_0.6.5.tar.gz' -#19 94.28 Content type 'application/x-gzip' length 969066 bytes (946 KB) -#19 94.28 ================================================== -#19 94.33 downloaded 946 KB -#19 94.33 -#19 94.33 trying URL 'https://cloud.r-project.org/src/contrib/dplyr_1.1.4.tar.gz' -#19 94.90 Content type 'application/x-gzip' length 1207521 bytes (1.2 MB) -#19 94.90 ================================================== -#19 94.97 downloaded 1.2 MB -#19 94.97 -#19 95.16 * installing *source* package ‘fansi’ ... -#19 95.17 ** package ‘fansi’ successfully unpacked and MD5 sums checked -#19 95.17 ** using staged installation -#19 95.17 ** libs -#19 95.18 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 95.18 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c assumptions.c -o assumptions.o -#19 95.21 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c carry.c -o carry.o -#19 95.29 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c has.c -o has.o -#19 95.32 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o -#19 95.34 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c nchar.c -o nchar.o -#19 95.38 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c normalize.c -o normalize.o -#19 95.45 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c read.c -o read.o -#19 95.69 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rnchar.c -o rnchar.o -#19 95.71 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c state.c -o state.o -#19 95.81 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c strip.c -o strip.o -#19 95.91 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c substr.c -o substr.o -#19 96.03 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c tabs.c -o tabs.o -#19 96.09 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c tohtml.c -o tohtml.o -#19 96.27 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c trimws.c -o trimws.o -#19 96.33 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c unhandled.c -o unhandled.o -#19 96.39 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8.c -o utf8.o -#19 96.42 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o -#19 96.52 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c wrap.c -o wrap.o -#19 96.69 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c write.c -o write.o -#19 96.87 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o fansi.so assumptions.o carry.o has.o init.o nchar.o normalize.o read.o rnchar.o state.o strip.o substr.o tabs.o tohtml.o trimws.o unhandled.o utf8.o utils.o wrap.o write.o -L/usr/lib/R/lib -lR -#19 96.88 installing to /usr/local/lib/R/site-library/00LOCK-fansi/00new/fansi/libs -#19 96.88 ** R -#19 96.89 ** inst -#19 96.89 ** byte-compile and prepare package for lazy loading -#19 97.22 ** help -#19 97.28 *** installing help indices -#19 97.32 ** building package indices -#19 97.46 ** installing vignettes -#19 97.46 ** testing if installed package can be loaded from temporary location -#19 97.57 ** checking absolute paths in shared objects and dynamic libraries -#19 97.58 ** testing if installed package can be loaded from final location -#19 97.71 ** testing if installed package keeps a record of temporary installation path -#19 97.71 * DONE (fansi) -#19 97.90 * installing *source* package ‘utf8’ ... -#19 97.90 ** package ‘utf8’ successfully unpacked and MD5 sums checked -#19 97.90 ** using staged installation -#19 97.91 ** libs -#19 97.92 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 97.92 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c as_utf8.c -o as_utf8.o -#19 97.96 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c bytes.c -o bytes.o -#19 98.08 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c context.c -o context.o -#19 98.11 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o -#19 98.13 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c render.c -o render.o -#19 98.17 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c render_table.c -o render_table.o -#19 98.27 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c string.c -o string.o -#19 98.31 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c text.c -o text.o -#19 98.39 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8_encode.c -o utf8_encode.o -#19 98.44 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8_format.c -o utf8_format.o -#19 98.49 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8_normalize.c -o utf8_normalize.o -#19 98.54 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8_valid.c -o utf8_valid.o -#19 98.57 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8_width.c -o utf8_width.o -#19 98.61 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c util.c -o util.o -#19 98.64 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/array.c -o utf8lite/src/array.o -#19 98.67 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/char.c -o utf8lite/src/char.o -#19 98.71 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/encode.c -o utf8lite/src/encode.o -#19 98.75 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/error.c -o utf8lite/src/error.o -#19 98.77 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/escape.c -o utf8lite/src/escape.o -#19 98.81 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/graph.c -o utf8lite/src/graph.o -#19 98.84 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/graphscan.c -o utf8lite/src/graphscan.o -#19 98.96 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/normalize.c -o utf8lite/src/normalize.o -#19 99.13 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/render.c -o utf8lite/src/render.o -#19 99.24 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/text.c -o utf8lite/src/text.o -#19 99.28 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/textassign.c -o utf8lite/src/textassign.o -#19 99.31 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/textiter.c -o utf8lite/src/textiter.o -#19 99.36 gcc -I"/usr/share/R/include" -DNDEBUG -Iutf8lite/src -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8lite/src/textmap.c -o utf8lite/src/textmap.o -#19 99.41 ar rcs libcutf8lite.a utf8lite/src/array.o utf8lite/src/char.o utf8lite/src/encode.o utf8lite/src/error.o utf8lite/src/escape.o utf8lite/src/graph.o utf8lite/src/graphscan.o utf8lite/src/normalize.o utf8lite/src/render.o utf8lite/src/text.o utf8lite/src/textassign.o utf8lite/src/textiter.o utf8lite/src/textmap.o -#19 99.41 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o utf8.so as_utf8.o bytes.o context.o init.o render.o render_table.o string.o text.o utf8_encode.o utf8_format.o utf8_normalize.o utf8_valid.o utf8_width.o util.o -L. -lcutf8lite -L/usr/lib/R/lib -lR -#19 99.43 installing to /usr/local/lib/R/site-library/00LOCK-utf8/00new/utf8/libs -#19 99.43 ** R -#19 99.43 ** inst -#19 99.43 ** byte-compile and prepare package for lazy loading -#19 99.66 ** help -#19 99.68 *** installing help indices -#19 99.69 ** building package indices -#19 99.83 ** installing vignettes -#19 99.83 ** testing if installed package can be loaded from temporary location -#19 99.95 ** checking absolute paths in shared objects and dynamic libraries -#19 99.95 ** testing if installed package can be loaded from final location -#19 100.1 ** testing if installed package keeps a record of temporary installation path -#19 100.1 * DONE (utf8) -#19 100.2 * installing *source* package ‘pkgconfig’ ... -#19 100.2 ** package ‘pkgconfig’ successfully unpacked and MD5 sums checked -#19 100.2 ** using staged installation -#19 100.2 ** R -#19 100.2 ** inst -#19 100.2 ** byte-compile and prepare package for lazy loading -#19 100.4 ** help -#19 100.4 *** installing help indices -#19 100.4 ** building package indices -#19 100.5 ** testing if installed package can be loaded from temporary location -#19 100.6 ** testing if installed package can be loaded from final location -#19 100.7 ** testing if installed package keeps a record of temporary installation path -#19 100.7 * DONE (pkgconfig) -#19 101.0 * installing *source* package ‘cli’ ... -#19 101.0 ** package ‘cli’ successfully unpacked and MD5 sums checked -#19 101.0 ** using staged installation -#19 101.0 ** libs -#19 101.0 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 101.0 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c ansi.c -o ansi.o -#19 101.3 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cleancall.c -o cleancall.o -#19 101.3 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c diff.c -o diff.o -#19 101.4 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c errors.c -o errors.o -#19 101.4 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c glue.c -o glue.o -#19 101.6 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o -#19 101.6 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c inst.c -o inst.o -#19 101.6 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c keypress-unix.c -o keypress-unix.o -#19 101.7 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c keypress-win.c -o keypress-win.o -#19 101.7 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c keypress.c -o keypress.o -#19 101.7 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c md5.c -o md5.o -#19 101.9 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c progress-altrep.c -o progress-altrep.o -#19 101.9 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c progress.c -o progress.o -#19 102.0 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c sha1.c -o sha1.o -#19 102.1 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c sha256.c -o sha256.o -#19 102.2 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c thread.c -o thread.o -#19 102.3 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c tty.c -o tty.o -#19 102.3 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8.c -o utf8.o -#19 102.5 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o -#19 102.6 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c vt.c -o vt.o -#19 102.7 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c vtparse.c -o vtparse.o -#19 102.8 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c vtparse_table.c -o vtparse_table.o -#19 102.8 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c win-utf8.c -o win-utf8.o -#19 102.8 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c winfiles.c -o winfiles.o -#19 102.8 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o cli.so ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o -lpthread -L/usr/lib/R/lib -lR -#19 102.8 installing to /usr/local/lib/R/site-library/00LOCK-cli/00new/cli/libs -#19 102.8 ** R -#19 102.9 ** exec -#19 102.9 ** inst -#19 102.9 ** byte-compile and prepare package for lazy loading -#19 105.0 ** help -#19 105.2 *** installing help indices -#19 105.3 *** copying figures -#19 105.3 ** building package indices -#19 105.6 ** testing if installed package can be loaded from temporary location -#19 105.7 ** checking absolute paths in shared objects and dynamic libraries -#19 105.7 ** testing if installed package can be loaded from final location -#19 105.9 ** testing if installed package keeps a record of temporary installation path -#19 105.9 * DONE (cli) -#19 106.1 * installing *source* package ‘generics’ ... -#19 106.1 ** package ‘generics’ successfully unpacked and MD5 sums checked -#19 106.1 ** using staged installation -#19 106.1 ** R -#19 106.1 ** byte-compile and prepare package for lazy loading -#19 106.2 ** help -#19 106.3 *** installing help indices -#19 106.3 ** building package indices -#19 106.5 ** testing if installed package can be loaded from temporary location -#19 106.6 ** testing if installed package can be loaded from final location -#19 106.7 ** testing if installed package keeps a record of temporary installation path -#19 106.7 * DONE (generics) -#19 106.9 * installing *source* package ‘glue’ ... -#19 106.9 ** package ‘glue’ successfully unpacked and MD5 sums checked -#19 106.9 ** using staged installation -#19 106.9 ** libs -#19 106.9 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 106.9 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c glue.c -o glue.o -#19 106.9 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o -#19 107.0 gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c trim.c -o trim.o -#19 107.0 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o glue.so glue.o init.o trim.o -L/usr/lib/R/lib -lR -#19 107.0 installing to /usr/local/lib/R/site-library/00LOCK-glue/00new/glue/libs -#19 107.0 ** R -#19 107.0 ** inst -#19 107.0 ** byte-compile and prepare package for lazy loading -#19 107.3 ** help -#19 107.3 *** installing help indices -#19 107.3 *** copying figures -#19 107.3 ** building package indices -#19 107.5 ** installing vignettes -#19 107.5 ** testing if installed package can be loaded from temporary location -#19 107.6 ** checking absolute paths in shared objects and dynamic libraries -#19 107.6 ** testing if installed package can be loaded from final location -#19 107.8 ** testing if installed package keeps a record of temporary installation path -#19 107.8 * DONE (glue) -#19 107.9 * installing *source* package ‘magrittr’ ... -#19 107.9 ** package ‘magrittr’ successfully unpacked and MD5 sums checked -#19 107.9 ** using staged installation -#19 107.9 ** libs -#19 107.9 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 107.9 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c pipe.c -o pipe.o -#19 108.0 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o -#19 108.1 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o magrittr.so pipe.o utils.o -L/usr/lib/R/lib -lR -#19 108.1 installing to /usr/local/lib/R/site-library/00LOCK-magrittr/00new/magrittr/libs -#19 108.1 ** R -#19 108.1 ** inst -#19 108.1 ** byte-compile and prepare package for lazy loading -#19 108.2 ** help -#19 108.3 *** installing help indices -#19 108.3 *** copying figures -#19 108.3 ** building package indices -#19 108.4 ** installing vignettes -#19 108.4 ** testing if installed package can be loaded from temporary location -#19 108.5 ** checking absolute paths in shared objects and dynamic libraries -#19 108.5 ** testing if installed package can be loaded from final location -#19 108.6 ** testing if installed package keeps a record of temporary installation path -#19 108.6 * DONE (magrittr) -#19 108.8 * installing *source* package ‘R6’ ... -#19 108.8 ** package ‘R6’ successfully unpacked and MD5 sums checked -#19 108.8 ** using staged installation -#19 108.8 ** R -#19 108.8 ** byte-compile and prepare package for lazy loading -#19 109.1 ** help -#19 109.1 *** installing help indices -#19 109.1 *** copying figures -#19 109.1 ** building package indices -#19 109.2 ** testing if installed package can be loaded from temporary location -#19 109.3 ** testing if installed package can be loaded from final location -#19 109.4 ** testing if installed package keeps a record of temporary installation path -#19 109.4 * DONE (R6) -#19 109.6 * installing *source* package ‘lifecycle’ ... -#19 109.6 ** package ‘lifecycle’ successfully unpacked and MD5 sums checked -#19 109.6 ** using staged installation -#19 109.6 ** R -#19 109.6 ** inst -#19 109.6 ** byte-compile and prepare package for lazy loading -#19 109.9 ** help -#19 109.9 *** installing help indices -#19 110.0 *** copying figures -#19 110.0 ** building package indices -#19 110.1 ** installing vignettes -#19 110.1 ** testing if installed package can be loaded from temporary location -#19 110.3 ** testing if installed package can be loaded from final location -#19 110.4 ** testing if installed package keeps a record of temporary installation path -#19 110.4 * DONE (lifecycle) -#19 110.7 * installing *source* package ‘vctrs’ ... -#19 110.8 ** package ‘vctrs’ successfully unpacked and MD5 sums checked -#19 110.8 ** using staged installation -#19 110.8 ** libs -#19 110.8 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 110.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c altrep-lazy-character.c -o altrep-lazy-character.o -#19 110.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c altrep-rle.c -o altrep-rle.o -#19 110.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c altrep.c -o altrep.o -#19 110.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c arg-counter.c -o arg-counter.o -#19 111.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c arg.c -o arg.o -#19 111.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c assert.c -o assert.o -#19 111.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c bind.c -o bind.o -#19 111.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c c-unchop.c -o c-unchop.o -#19 111.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c c.c -o c.o -#19 111.4 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c callables.c -o callables.o -#19 111.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cast-bare.c -o cast-bare.o -#19 111.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cast-dispatch.c -o cast-dispatch.o -#19 111.7 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cast.c -o cast.o -#19 111.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c compare.c -o compare.o -#19 111.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c complete.c -o complete.o -#19 112.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c conditions.c -o conditions.o -#19 112.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dictionary.c -o dictionary.o -#19 112.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dim.c -o dim.o -#19 112.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c empty.c -o empty.o -#19 112.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c equal.c -o equal.o -#19 112.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c expand.c -o expand.o -#19 112.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fields.c -o fields.o -#19 112.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fill.c -o fill.o -#19 112.7 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c globals.c -o globals.o -#19 112.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c group.c -o group.o -#19 112.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c growable.c -o growable.o -#19 112.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c hash.c -o hash.o -#19 113.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o -#19 113.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c interval.c -o interval.o -#19 113.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c match-joint.c -o match-joint.o -#19 113.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c match.c -o match.o -#19 114.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c missing.c -o missing.o -#19 114.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c names.c -o names.o -#19 114.4 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c order-collate.c -o order-collate.o -#19 114.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c order-groups.c -o order-groups.o -#19 114.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c order-sortedness.c -o order-sortedness.o -#19 114.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c order-truelength.c -o order-truelength.o -#19 114.7 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c order.c -o order.o -#19 115.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c poly-op.c -o poly-op.o -#19 115.4 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c proxy-restore.c -o proxy-restore.o -#19 115.4 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c proxy.c -o proxy.o -#19 115.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c ptype-common.c -o ptype-common.o -#19 115.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c ptype.c -o ptype.o -#19 115.7 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c ptype2-dispatch.c -o ptype2-dispatch.o -#19 115.7 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c ptype2.c -o ptype2.o -#19 115.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rank.c -o rank.o -#19 115.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rep.c -o rep.o -#19 116.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rlang-dev.c -o rlang-dev.o -#19 116.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rlang.c -o rlang.o -#19 116.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c runs.c -o runs.o -#19 116.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c set.c -o set.o -#19 117.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c shape.c -o shape.o -#19 117.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c size-common.c -o size-common.o -#19 117.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c size.c -o size.o -#19 117.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice-array.c -o slice-array.o -#19 117.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice-assign-array.c -o slice-assign-array.o -#19 117.8 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice-assign.c -o slice-assign.o -#19 117.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice-chop.c -o slice-chop.o -#19 118.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice-interleave.c -o slice-interleave.o -#19 118.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice.c -o slice.o -#19 118.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c split.c -o split.o -#19 118.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c subscript-loc.c -o subscript-loc.o -#19 118.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c subscript.c -o subscript.o -#19 118.6 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c translate.c -o translate.o -#19 118.7 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c type-data-frame.c -o type-data-frame.o -#19 118.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c type-date-time.c -o type-date-time.o -#19 119.0 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c type-factor.c -o type-factor.o -#19 119.1 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c type-info.c -o type-info.o -#19 119.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c type-integer64.c -o type-integer64.o -#19 119.2 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c type-tibble.c -o type-tibble.o -#19 119.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c typeof2-s3.c -o typeof2-s3.o -#19 119.3 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c typeof2.c -o typeof2.o -#19 119.4 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c unspecified.c -o unspecified.o -#19 119.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils-dispatch.c -o utils-dispatch.o -#19 119.5 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o -#19 119.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c vctrs-core.c -o vctrs-core.o -#19 119.9 gcc -I"/usr/share/R/include" -DNDEBUG -I./rlang -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c version.c -o version.o -#19 120.0 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o vctrs.so altrep-lazy-character.o altrep-rle.o altrep.o arg-counter.o arg.o assert.o bind.o c-unchop.o c.o callables.o cast-bare.o cast-dispatch.o cast.o compare.o complete.o conditions.o dictionary.o dim.o empty.o equal.o expand.o fields.o fill.o globals.o group.o growable.o hash.o init.o interval.o match-joint.o match.o missing.o names.o order-collate.o order-groups.o order-sortedness.o order-truelength.o order.o poly-op.o proxy-restore.o proxy.o ptype-common.o ptype.o ptype2-dispatch.o ptype2.o rank.o rep.o rlang-dev.o rlang.o runs.o set.o shape.o size-common.o size.o slice-array.o slice-assign-array.o slice-assign.o slice-chop.o slice-interleave.o slice.o split.o subscript-loc.o subscript.o translate.o type-data-frame.o type-date-time.o type-factor.o type-info.o type-integer64.o type-tibble.o typeof2-s3.o typeof2.o unspecified.o utils-dispatch.o utils.o vctrs-core.o version.o -L/usr/lib/R/lib -lR -#19 120.0 installing to /usr/local/lib/R/site-library/00LOCK-vctrs/00new/vctrs/libs -#19 120.0 ** R -#19 120.0 ** inst -#19 120.0 ** byte-compile and prepare package for lazy loading -#19 121.4 ** help -#19 121.6 *** installing help indices -#19 121.7 *** copying figures -#19 121.7 ** building package indices -#19 121.9 ** installing vignettes -#19 121.9 ** testing if installed package can be loaded from temporary location -#19 122.1 ** checking absolute paths in shared objects and dynamic libraries -#19 122.1 ** testing if installed package can be loaded from final location -#19 122.3 ** testing if installed package keeps a record of temporary installation path -#19 122.3 * DONE (vctrs) -#19 122.5 * installing *source* package ‘pillar’ ... -#19 122.5 ** package ‘pillar’ successfully unpacked and MD5 sums checked -#19 122.5 ** using staged installation -#19 122.5 ** R -#19 122.6 ** inst -#19 122.6 ** byte-compile and prepare package for lazy loading -#19 123.7 ** help -#19 123.7 *** installing help indices -#19 123.8 *** copying figures -#19 123.8 ** building package indices -#19 123.9 ** installing vignettes -#19 123.9 ** testing if installed package can be loaded from temporary location -#19 124.2 ** testing if installed package can be loaded from final location -#19 124.4 ** testing if installed package keeps a record of temporary installation path -#19 124.4 * DONE (pillar) -#19 124.6 * installing *source* package ‘tidyselect’ ... -#19 124.6 ** package ‘tidyselect’ successfully unpacked and MD5 sums checked -#19 124.6 ** using staged installation -#19 124.6 ** R -#19 124.6 ** inst -#19 124.6 ** byte-compile and prepare package for lazy loading -#19 125.3 ** help -#19 125.3 *** installing help indices -#19 125.3 ** building package indices -#19 125.5 ** installing vignettes -#19 125.5 ** testing if installed package can be loaded from temporary location -#19 125.7 ** testing if installed package can be loaded from final location -#19 125.9 ** testing if installed package keeps a record of temporary installation path -#19 125.9 * DONE (tidyselect) -#19 126.1 * installing *source* package ‘tibble’ ... -#19 126.1 ** package ‘tibble’ successfully unpacked and MD5 sums checked -#19 126.1 ** using staged installation -#19 126.1 ** libs -#19 126.1 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 126.1 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c attributes.c -o attributes.o -#19 126.1 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c coerce.c -o coerce.o -#19 126.2 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o -#19 126.2 gcc -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c matrixToDataFrame.c -o matrixToDataFrame.o -#19 126.2 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o tibble.so attributes.o coerce.o init.o matrixToDataFrame.o -L/usr/lib/R/lib -lR -#19 126.3 installing to /usr/local/lib/R/site-library/00LOCK-tibble/00new/tibble/libs -#19 126.3 ** R -#19 126.3 ** inst -#19 126.3 ** byte-compile and prepare package for lazy loading -#19 127.1 ** help -#19 127.1 *** installing help indices -#19 127.2 *** copying figures -#19 127.2 ** building package indices -#19 127.3 ** installing vignettes -#19 127.3 ** testing if installed package can be loaded from temporary location -#19 127.6 ** checking absolute paths in shared objects and dynamic libraries -#19 127.6 ** testing if installed package can be loaded from final location -#19 127.9 ** testing if installed package keeps a record of temporary installation path -#19 127.9 * DONE (tibble) -#19 128.2 * installing *source* package ‘dplyr’ ... -#19 128.2 ** package ‘dplyr’ successfully unpacked and MD5 sums checked -#19 128.2 ** using staged installation -#19 128.2 ** libs -#19 128.2 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ -#19 128.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c chop.cpp -o chop.o -#19 128.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c filter.cpp -o filter.o -#19 128.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c funs.cpp -o funs.o -#19 128.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c group_by.cpp -o group_by.o -#19 129.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c group_data.cpp -o group_data.o -#19 129.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c imports.cpp -o imports.o -#19 129.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.cpp -o init.o -#19 129.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mask.cpp -o mask.o -#19 129.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mutate.cpp -o mutate.o -#19 129.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c reconstruct.cpp -o reconstruct.o -#19 129.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c slice.cpp -o slice.o -#19 129.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c summarise.cpp -o summarise.o -#19 129.9 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o dplyr.so chop.o filter.o funs.o group_by.o group_data.o imports.o init.o mask.o mutate.o reconstruct.o slice.o summarise.o -L/usr/lib/R/lib -lR -#19 130.0 installing to /usr/local/lib/R/site-library/00LOCK-dplyr/00new/dplyr/libs -#19 130.0 ** R -#19 130.0 ** data -#19 130.0 *** moving datasets to lazyload DB -#19 130.1 ** inst -#19 130.1 ** byte-compile and prepare package for lazy loading -#19 132.5 ** help -#19 132.7 *** installing help indices -#19 132.8 *** copying figures -#19 132.8 ** building package indices -#19 133.0 ** installing vignettes -#19 133.0 ** testing if installed package can be loaded from temporary location -#19 133.3 ** checking absolute paths in shared objects and dynamic libraries -#19 133.3 ** testing if installed package can be loaded from final location -#19 133.7 ** testing if installed package keeps a record of temporary installation path -#19 133.7 * DONE (dplyr) -#19 133.7 -#19 133.7 The downloaded source packages are in -#19 133.7 ‘/tmp/RtmpZsJzTy/downloaded_packages’ -#19 133.7 Installing package into ‘/usr/local/lib/R/site-library’ -#19 133.7 (as ‘lib’ is unspecified) -#19 133.9 trying URL 'https://cloud.r-project.org/src/contrib/data.table_1.16.2.tar.gz' -#19 134.4 Content type 'application/x-gzip' length 5490076 bytes (5.2 MB) -#19 134.4 ================================================== -#19 134.5 downloaded 5.2 MB -#19 134.5 -#19 135.0 * installing *source* package ‘data.table’ ... -#19 135.0 ** package ‘data.table’ successfully unpacked and MD5 sums checked -#19 135.0 ** using staged installation -#19 135.2 gcc 14.2.0 -#19 135.2 zlib 1.3.1 is available ok -#19 135.2 * checking if R installation supports OpenMP without any extra hints... yes -#19 135.3 ** libs -#19 135.3 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 135.3 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c assign.c -o assign.o -#19 136.3 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c between.c -o between.o -#19 136.4 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c bmerge.c -o bmerge.o -#19 136.8 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c chmatch.c -o chmatch.o -#19 136.9 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cj.c -o cj.o -#19 137.0 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c coalesce.c -o coalesce.o -#19 137.1 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dogroups.c -o dogroups.o -#19 137.4 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fastmean.c -o fastmean.o -#19 137.5 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fcast.c -o fcast.o -#19 137.5 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fifelse.c -o fifelse.o -#19 137.8 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fmelt.c -o fmelt.o -#19 138.2 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c forder.c -o forder.o -#19 138.9 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c frank.c -o frank.o -#19 139.0 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fread.c -o fread.o -#19 140.1 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c freadR.c -o freadR.o -#19 140.4 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c froll.c -o froll.o -#19 140.6 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c frollR.c -o frollR.o -#19 140.8 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c frolladaptive.c -o frolladaptive.o -#19 140.9 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fsort.c -o fsort.o -#19 141.1 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fwrite.c -o fwrite.o -#19 141.4 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c fwriteR.c -o fwriteR.o -#19 141.5 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c gsumm.c -o gsumm.o -#19 142.5 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c idatetime.c -o idatetime.o -#19 142.5 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c ijoin.c -o ijoin.o -#19 142.8 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o -#19 142.9 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c inrange.c -o inrange.o -#19 142.9 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c nafill.c -o nafill.o -#19 143.0 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c negate.c -o negate.o -#19 143.1 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c nqrecreateindices.c -o nqrecreateindices.o -#19 143.1 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c openmp-utils.c -o openmp-utils.o -#19 143.2 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c programming.c -o programming.o -#19 143.2 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c quickselect.c -o quickselect.o -#19 143.3 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c rbindlist.c -o rbindlist.o -#19 143.6 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c reorder.c -o reorder.o -#19 143.7 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c shift.c -o shift.o -#19 143.8 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c snprintf.c -o snprintf.o -#19 143.9 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c subset.c -o subset.o -#19 144.2 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c transpose.c -o transpose.o -#19 144.2 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c types.c -o types.o -#19 144.3 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c uniqlist.c -o uniqlist.o -#19 144.5 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o -#19 144.7 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c vecseq.c -o vecseq.o -#19 144.7 gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c wrappers.c -o wrappers.o -#19 144.8 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -lz -L/usr/lib/R/lib -lR -#19 144.8 PKG_CFLAGS = -fopenmp -#19 144.8 PKG_LIBS = -fopenmp -lz -#19 144.8 if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi -#19 144.8 if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi -#19 144.8 installing to /usr/local/lib/R/site-library/00LOCK-data.table/00new/data.table/libs -#19 144.8 ** R -#19 144.8 ** inst -#19 144.8 ** byte-compile and prepare package for lazy loading -#19 147.7 ** help -#19 147.8 *** installing help indices -#19 147.9 ** building package indices -#19 148.1 ** installing vignettes -#19 148.1 ** testing if installed package can be loaded from temporary location -#19 148.3 ** checking absolute paths in shared objects and dynamic libraries -#19 148.3 ** testing if installed package can be loaded from final location -#19 148.5 ** testing if installed package keeps a record of temporary installation path -#19 148.6 * DONE (data.table) -#19 148.6 -#19 148.6 The downloaded source packages are in -#19 148.6 ‘/tmp/RtmpZsJzTy/downloaded_packages’ -#19 148.6 Installing package into ‘/usr/local/lib/R/site-library’ -#19 148.6 (as ‘lib’ is unspecified) -#19 148.8 trying URL 'http://ran.synapse.org/src/contrib/synapser_2.1.1.259.tar.gz' -#19 149.3 Content type 'application/x-tar' length 6046498 bytes (5.8 MB) -#19 149.6 ================================================== -#19 151.5 downloaded 5.8 MB -#19 151.5 -#19 151.8 * installing *source* package ‘synapser’ ... -#19 151.8 ** using staged installation -#19 152.8 [1] "*** Using Python Configuration:" -#19 153.5 python: /opt/venv/bin/python3 -#19 153.5 libpython: /usr/local/lib/libpython3.10.so -#19 153.5 pythonhome: /opt/venv:/opt/venv -#19 153.5 version: 3.10.12 (main, Oct 21 2024, 16:07:16) [GCC 14.2.0] -#19 153.5 numpy: /opt/venv/lib/python3.10/site-packages/numpy -#19 153.5 numpy_version: 1.24.4 -#19 153.5 -#19 153.5 NOTE: Python version was forced by RETICULATE_PYTHON -#19 153.5 Using virtual environment '/opt/venv' ... -#19 153.5 + /opt/venv/bin/python -m pip install --upgrade --no-user 'pandas>=1.5,<=2.0.3' jinja2 markupsafe 'numpy<=1.24.4' -#19 153.6 Requirement already satisfied: pandas<=2.0.3,>=1.5 in /opt/venv/lib/python3.10/site-packages (2.0.3) -#19 153.8 Requirement already satisfied: jinja2 in /opt/venv/lib/python3.10/site-packages (3.1.4) -#19 153.8 Requirement already satisfied: markupsafe in /opt/venv/lib/python3.10/site-packages (3.0.2) -#19 153.8 Requirement already satisfied: numpy<=1.24.4 in /opt/venv/lib/python3.10/site-packages (1.24.4) -#19 154.0 Requirement already satisfied: python-dateutil>=2.8.2 in /opt/venv/lib/python3.10/site-packages (from pandas<=2.0.3,>=1.5) (2.9.0.post0) -#19 154.0 Requirement already satisfied: pytz>=2020.1 in /opt/venv/lib/python3.10/site-packages (from pandas<=2.0.3,>=1.5) (2024.2) -#19 154.0 Requirement already satisfied: tzdata>=2022.1 in /opt/venv/lib/python3.10/site-packages (from pandas<=2.0.3,>=1.5) (2024.2) -#19 154.0 Requirement already satisfied: six>=1.5 in /opt/venv/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas<=2.0.3,>=1.5) (1.16.0) -#19 154.1 -#19 154.1 [notice] A new release of pip is available: 24.2 -> 24.3.1 -#19 154.1 [notice] To update, run: pip install --upgrade pip -#19 154.2 Using virtual environment '/opt/venv' ... -#19 154.3 + /opt/venv/bin/python -m pip install --upgrade --no-user 'synapseclient==4.4.0' -#19 154.4 Requirement already satisfied: synapseclient==4.4.0 in /opt/venv/lib/python3.10/site-packages (4.4.0) -#19 154.5 Requirement already satisfied: requests<3.0,>=2.22.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (2.32.3) -#19 154.5 Requirement already satisfied: urllib3<2,>=1.26.18 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.26.20) -#19 154.5 Requirement already satisfied: deprecated<2.0,>=1.2.4 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.2.15) -#19 154.5 Requirement already satisfied: opentelemetry-api~=1.21.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.21.0) -#19 154.5 Requirement already satisfied: opentelemetry-sdk~=1.21.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.21.0) -#19 154.5 Requirement already satisfied: opentelemetry-exporter-otlp-proto-http~=1.21.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.21.0) -#19 154.5 Requirement already satisfied: nest-asyncio~=1.6.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.6.0) -#19 154.5 Requirement already satisfied: asyncio-atexit~=1.0.1 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (1.0.1) -#19 154.5 Requirement already satisfied: httpx~=0.27.0 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (0.27.2) -#19 154.5 Requirement already satisfied: tqdm<5.0,>=4.66.2 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (4.67.0) -#19 154.5 Requirement already satisfied: async-lru~=2.0.4 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (2.0.4) -#19 154.5 Requirement already satisfied: psutil~=5.9.8 in /opt/venv/lib/python3.10/site-packages (from synapseclient==4.4.0) (5.9.8) -#19 154.5 Requirement already satisfied: typing-extensions>=4.0.0 in /opt/venv/lib/python3.10/site-packages (from async-lru~=2.0.4->synapseclient==4.4.0) (4.12.2) -#19 154.5 Requirement already satisfied: wrapt<2,>=1.10 in /opt/venv/lib/python3.10/site-packages (from deprecated<2.0,>=1.2.4->synapseclient==4.4.0) (1.16.0) -#19 154.5 Requirement already satisfied: anyio in /opt/venv/lib/python3.10/site-packages (from httpx~=0.27.0->synapseclient==4.4.0) (4.6.2.post1) -#19 154.5 Requirement already satisfied: certifi in /opt/venv/lib/python3.10/site-packages (from httpx~=0.27.0->synapseclient==4.4.0) (2024.8.30) -#19 154.5 Requirement already satisfied: httpcore==1.* in /opt/venv/lib/python3.10/site-packages (from httpx~=0.27.0->synapseclient==4.4.0) (1.0.7) -#19 154.5 Requirement already satisfied: idna in /opt/venv/lib/python3.10/site-packages (from httpx~=0.27.0->synapseclient==4.4.0) (3.10) -#19 154.5 Requirement already satisfied: sniffio in /opt/venv/lib/python3.10/site-packages (from httpx~=0.27.0->synapseclient==4.4.0) (1.3.1) -#19 154.5 Requirement already satisfied: h11<0.15,>=0.13 in /opt/venv/lib/python3.10/site-packages (from httpcore==1.*->httpx~=0.27.0->synapseclient==4.4.0) (0.14.0) -#19 154.5 Requirement already satisfied: importlib-metadata<7.0,>=6.0 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-api~=1.21.0->synapseclient==4.4.0) (6.11.0) -#19 154.5 Requirement already satisfied: backoff<3.0.0,>=1.10.0 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) (2.2.1) -#19 154.5 Requirement already satisfied: googleapis-common-protos~=1.52 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) (1.66.0) -#19 154.5 Requirement already satisfied: opentelemetry-exporter-otlp-proto-common==1.21.0 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) (1.21.0) -#19 154.5 Requirement already satisfied: opentelemetry-proto==1.21.0 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) (1.21.0) -#19 154.5 Requirement already satisfied: protobuf<5.0,>=3.19 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-proto==1.21.0->opentelemetry-exporter-otlp-proto-http~=1.21.0->synapseclient==4.4.0) (4.25.5) -#19 154.5 Requirement already satisfied: opentelemetry-semantic-conventions==0.42b0 in /opt/venv/lib/python3.10/site-packages (from opentelemetry-sdk~=1.21.0->synapseclient==4.4.0) (0.42b0) -#19 154.5 Requirement already satisfied: charset-normalizer<4,>=2 in /opt/venv/lib/python3.10/site-packages (from requests<3.0,>=2.22.0->synapseclient==4.4.0) (3.4.0) -#19 154.5 Requirement already satisfied: zipp>=0.5 in /opt/venv/lib/python3.10/site-packages (from importlib-metadata<7.0,>=6.0->opentelemetry-api~=1.21.0->synapseclient==4.4.0) (3.21.0) -#19 154.6 Requirement already satisfied: exceptiongroup>=1.0.2 in /opt/venv/lib/python3.10/site-packages (from anyio->httpx~=0.27.0->synapseclient==4.4.0) (1.2.2) -#19 154.6 -#19 154.6 [notice] A new release of pip is available: 24.2 -> 24.3.1 -#19 154.6 [notice] To update, run: pip install --upgrade pip -#19 155.8 ** R -#19 155.8 ** inst -#19 155.8 ** byte-compile and prepare package for lazy loading -#19 156.7 ** help -#19 156.8 *** installing help indices -#19 156.8 ** building package indices -#19 157.0 ** installing vignettes -#19 157.0 ** testing if installed package can be loaded from temporary location -#19 158.6 ** testing if installed package can be loaded from final location -#19 160.2 ** testing if installed package keeps a record of temporary installation path -#19 160.2 * DONE (synapser) -#19 160.2 -#19 160.2 The downloaded source packages are in -#19 160.2 ‘/tmp/RtmpZsJzTy/downloaded_packages’ -#19 160.2 Installing package into ‘/usr/local/lib/R/site-library’ -#19 160.2 (as ‘lib’ is unspecified) -#19 160.4 also installing the dependencies ‘R.oo’, ‘R.methodsS3’ -#19 160.4 -#19 160.4 trying URL 'https://cloud.r-project.org/src/contrib/R.oo_1.27.0.tar.gz' -#19 160.9 Content type 'application/x-gzip' length 384222 bytes (375 KB) -#19 160.9 ================================================== -#19 160.9 downloaded 375 KB -#19 160.9 -#19 160.9 trying URL 'https://cloud.r-project.org/src/contrib/R.methodsS3_1.8.2.tar.gz' -#19 161.3 Content type 'application/x-gzip' length 24131 bytes (23 KB) -#19 161.3 ================================================== -#19 161.3 downloaded 23 KB -#19 161.3 -#19 161.3 trying URL 'https://cloud.r-project.org/src/contrib/R.utils_2.12.3.tar.gz' -#19 161.9 Content type 'application/x-gzip' length 364188 bytes (355 KB) -#19 161.9 ================================================== -#19 161.9 downloaded 355 KB -#19 161.9 -#19 162.1 * installing *source* package ‘R.methodsS3’ ... -#19 162.1 ** package ‘R.methodsS3’ successfully unpacked and MD5 sums checked -#19 162.1 ** using staged installation -#19 162.1 ** R -#19 162.1 ** inst -#19 162.1 ** byte-compile and prepare package for lazy loading -#19 162.3 ** help -#19 162.3 *** installing help indices -#19 162.4 ** building package indices -#19 162.5 ** testing if installed package can be loaded from temporary location -#19 162.6 ** testing if installed package can be loaded from final location -#19 162.7 ** testing if installed package keeps a record of temporary installation path -#19 162.7 * DONE (R.methodsS3) -#19 162.9 * installing *source* package ‘R.oo’ ... -#19 163.0 ** package ‘R.oo’ successfully unpacked and MD5 sums checked -#19 163.0 ** using staged installation -#19 163.0 ** R -#19 163.0 ** inst -#19 163.0 ** byte-compile and prepare package for lazy loading -#19 164.2 Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : -#19 164.2 Renamed the preexisting function getMethods to getMethods.default, which was defined in environment R.oo. -#19 164.2 Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : -#19 164.2 Renamed the preexisting function getClasses to getClasses.default, which was defined in environment R.oo. -#19 164.2 ** help -#19 164.4 *** installing help indices -#19 164.6 ** building package indices -#19 164.8 ** testing if installed package can be loaded from temporary location -#19 165.0 ** testing if installed package can be loaded from final location -#19 165.1 ** testing if installed package keeps a record of temporary installation path -#19 165.1 * DONE (R.oo) -#19 165.4 * installing *source* package ‘R.utils’ ... -#19 165.4 ** package ‘R.utils’ successfully unpacked and MD5 sums checked -#19 165.4 ** using staged installation -#19 165.4 ** R -#19 165.4 ** inst -#19 165.4 ** byte-compile and prepare package for lazy loading -#19 167.9 Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : -#19 167.9 Renamed the preexisting function warnings to warnings.default, which was defined in environment R.utils. -#19 167.9 ** help -#19 168.3 *** installing help indices -#19 168.5 ** building package indices -#19 168.8 ** testing if installed package can be loaded from temporary location -#19 169.0 ** testing if installed package can be loaded from final location -#19 169.2 ** testing if installed package keeps a record of temporary installation path -#19 169.2 * DONE (R.utils) -#19 169.2 -#19 169.2 The downloaded source packages are in -#19 169.2 ‘/tmp/RtmpZsJzTy/downloaded_packages’ -#19 169.2 Installing package into ‘/usr/local/lib/R/site-library’ -#19 169.2 (as ‘lib’ is unspecified) -#19 169.4 also installing the dependency ‘stringi’ -#19 169.4 -#19 169.4 trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.8.4.tar.gz' -#19 169.9 Content type 'application/x-gzip' length 11917497 bytes (11.4 MB) -#19 169.9 ================================================== -#19 170.1 downloaded 11.4 MB -#19 170.1 -#19 170.1 trying URL 'https://cloud.r-project.org/src/contrib/stringr_1.5.1.tar.gz' -#19 170.6 Content type 'application/x-gzip' length 176599 bytes (172 KB) -#19 170.6 ================================================== -#19 170.7 downloaded 172 KB -#19 170.7 -#19 171.6 * installing *source* package ‘stringi’ ... -#19 171.6 ** package ‘stringi’ successfully unpacked and MD5 sums checked -#19 171.6 ** using staged installation -#19 171.7 checking for R_HOME... /usr/lib/R -#19 171.7 checking for R... /usr/lib/R/bin/R -#19 171.7 checking for endianness... little -#19 171.9 checking for cat... /usr/bin/cat -#19 171.9 checking whether the C++ compiler works... yes -#19 172.0 checking for C++ compiler default output file name... a.out -#19 172.0 checking for suffix of executables... -#19 172.0 checking whether we are cross compiling... no -#19 172.0 checking for suffix of object files... o -#19 172.0 checking whether the compiler supports GNU C++... yes -#19 172.0 checking whether g++ -std=gnu++17 accepts -g... yes -#19 172.1 checking for g++ -std=gnu++17 option to enable C++11 features... none needed -#19 172.1 checking whether the C++ compiler supports the 'long long' type... yes -#19 172.3 checking whether the compiler implements namespaces... yes -#19 172.4 checking whether the compiler supports the Standard Template Library... yes -#19 172.5 checking whether std::map is available... yes -#19 172.8 checking for pkg-config... /usr/bin/pkg-config -#19 172.8 checking with 'pkg-config' for the system ICU4C (icu-i18n icu-uc)... 72.1 -#19 172.8 checking for ICU4C >= 61... yes -#19 172.8 checking for additional CPPFLAGS, LDFLAGS, and LIBS required... done -#19 172.8 checking whether an ICU4C-based project can be built... yes -#19 173.0 checking programmatically for sufficient U_ICU_VERSION_MAJOR_NUM... yes -#19 173.0 checking the capabilities of the ICU data library (ucnv, uloc, utrans)... yes -#19 173.3 checking the capabilities of the ICU data library (ucol)... yes -#19 173.6 checking for stdio.h... yes -#19 173.6 checking for stdlib.h... yes -#19 173.6 checking for string.h... yes -#19 173.6 checking for inttypes.h... yes -#19 173.7 checking for stdint.h... yes -#19 173.7 checking for strings.h... yes -#19 173.7 checking for sys/stat.h... yes -#19 173.7 checking for sys/types.h... yes -#19 173.8 checking for unistd.h... yes -#19 173.8 checking for elf.h... yes -#19 173.8 configure: creating ./config.status -#19 173.9 config.status: creating src/Makevars -#19 173.9 config.status: creating src/uconfig_local.h -#19 173.9 config.status: creating src/install.libs.R -#19 173.9 -#19 173.9 *** stringi configure summary: -#19 173.9 ICU_FOUND=1 -#19 173.9 STRINGI_CXXSTD= -#19 173.9 STRINGI_CXXFLAGS= -fPIC -#19 173.9 STRINGI_CPPFLAGS=-I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -#19 173.9 STRINGI_LDFLAGS= -L/usr/lib/aarch64-linux-gnu -#19 173.9 STRINGI_LIBS= -licui18n -licuuc -licudata -#19 173.9 -#19 173.9 *** Compiler settings used: -#19 173.9 CXX=g++ -std=gnu++17 -#19 173.9 LD=g++ -std=gnu++17 -#19 173.9 CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -#19 173.9 CPPFLAGS= -#19 173.9 LDFLAGS= -#19 173.9 LIBS= -#19 173.9 -#19 173.9 ** libs -#19 173.9 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ -#19 173.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_brkiter.cpp -o stri_brkiter.o -#19 174.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_collator.cpp -o stri_collator.o -#19 174.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_common.cpp -o stri_common.o -#19 175.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_compare.cpp -o stri_compare.o -#19 175.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_base.cpp -o stri_container_base.o -#19 175.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_bytesearch.cpp -o stri_container_bytesearch.o -#19 176.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_listint.cpp -o stri_container_listint.o -#19 176.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_listraw.cpp -o stri_container_listraw.o -#19 176.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_listutf8.cpp -o stri_container_listutf8.o -#19 177.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_regex.cpp -o stri_container_regex.o -#19 177.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_usearch.cpp -o stri_container_usearch.o -#19 177.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_utf16.cpp -o stri_container_utf16.o -#19 178.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_utf8.cpp -o stri_container_utf8.o -#19 178.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_container_utf8_indexable.cpp -o stri_container_utf8_indexable.o -#19 178.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_encoding_conversion.cpp -o stri_encoding_conversion.o -#19 179.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_encoding_detection.cpp -o stri_encoding_detection.o -#19 180.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_encoding_management.cpp -o stri_encoding_management.o -#19 180.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_escape.cpp -o stri_escape.o -#19 181.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_exception.cpp -o stri_exception.o -#19 181.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_ICU_settings.cpp -o stri_ICU_settings.o -#19 181.6 In file included from stri_ICU_settings.cpp:37: -#19 181.6 uconfig_local.h:42:9: warning: "UCONFIG_USE_WINDOWS_LCID_MAPPING_API" redefined -#19 181.6 42 | #define UCONFIG_USE_WINDOWS_LCID_MAPPING_API 0 -#19 181.6 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -#19 181.6 In file included from /usr/include/unicode/platform.h:24, -#19 181.6 from /usr/include/unicode/ptypes.h:52, -#19 181.6 from stri_external.h:52, -#19 181.6 from stri_stringi.h:36, -#19 181.6 from stri_ICU_settings.cpp:33: -#19 181.6 /usr/include/unicode/uconfig.h:381:12: note: this is the location of the previous definition -#19 181.6 381 | # define UCONFIG_USE_WINDOWS_LCID_MAPPING_API 1 -#19 181.6 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -#19 181.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_join.cpp -o stri_join.o -#19 182.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_length.cpp -o stri_length.o -#19 182.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_pad.cpp -o stri_pad.o -#19 183.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_prepare_arg.cpp -o stri_prepare_arg.o -#19 183.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_random.cpp -o stri_random.o -#19 184.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_reverse.cpp -o stri_reverse.o -#19 184.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_count.cpp -o stri_search_class_count.o -#19 184.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_detect.cpp -o stri_search_class_detect.o -#19 185.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_extract.cpp -o stri_search_class_extract.o -#19 185.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_locate.cpp -o stri_search_class_locate.o -#19 186.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_replace.cpp -o stri_search_class_replace.o -#19 186.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_split.cpp -o stri_search_class_split.o -#19 187.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_startsendswith.cpp -o stri_search_class_startsendswith.o -#19 187.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_subset.cpp -o stri_search_class_subset.o -#19 187.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_class_trim.cpp -o stri_search_class_trim.o -#19 188.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_common.cpp -o stri_search_common.o -#19 188.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_count.cpp -o stri_search_coll_count.o -#19 188.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_detect.cpp -o stri_search_coll_detect.o -#19 189.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_extract.cpp -o stri_search_coll_extract.o -#19 189.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_locate.cpp -o stri_search_coll_locate.o -#19 190.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_replace.cpp -o stri_search_coll_replace.o -#19 190.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_split.cpp -o stri_search_coll_split.o -#19 191.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_startsendswith.cpp -o stri_search_coll_startsendswith.o -#19 191.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_coll_subset.cpp -o stri_search_coll_subset.o -#19 192.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_boundaries_count.cpp -o stri_search_boundaries_count.o -#19 192.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_boundaries_extract.cpp -o stri_search_boundaries_extract.o -#19 192.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_boundaries_locate.cpp -o stri_search_boundaries_locate.o -#19 193.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_boundaries_split.cpp -o stri_search_boundaries_split.o -#19 193.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_count.cpp -o stri_search_fixed_count.o -#19 193.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_detect.cpp -o stri_search_fixed_detect.o -#19 194.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_extract.cpp -o stri_search_fixed_extract.o -#19 194.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_locate.cpp -o stri_search_fixed_locate.o -#19 195.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_replace.cpp -o stri_search_fixed_replace.o -#19 195.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_split.cpp -o stri_search_fixed_split.o -#19 196.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_subset.cpp -o stri_search_fixed_subset.o -#19 196.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_fixed_startsendswith.cpp -o stri_search_fixed_startsendswith.o -#19 196.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_in.cpp -o stri_search_in.o -#19 196.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_other_split.cpp -o stri_search_other_split.o -#19 197.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_count.cpp -o stri_search_regex_count.o -#19 197.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_detect.cpp -o stri_search_regex_detect.o -#19 197.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_extract.cpp -o stri_search_regex_extract.o -#19 198.4 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_locate.cpp -o stri_search_regex_locate.o -#19 199.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_match.cpp -o stri_search_regex_match.o -#19 199.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_replace.cpp -o stri_search_regex_replace.o -#19 200.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_split.cpp -o stri_search_regex_split.o -#19 200.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_search_regex_subset.cpp -o stri_search_regex_subset.o -#19 200.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_sort.cpp -o stri_sort.o -#19 201.9 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_sprintf.cpp -o stri_sprintf.o -#19 202.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_stats.cpp -o stri_stats.o -#19 203.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_string8.cpp -o stri_string8.o -#19 203.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_stringi.cpp -o stri_stringi.o -#19 203.4 In file included from stri_stringi.cpp:39: -#19 203.4 uconfig_local.h:42:9: warning: "UCONFIG_USE_WINDOWS_LCID_MAPPING_API" redefined -#19 203.4 42 | #define UCONFIG_USE_WINDOWS_LCID_MAPPING_API 0 -#19 203.4 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -#19 203.4 In file included from /usr/include/unicode/platform.h:24, -#19 203.4 from /usr/include/unicode/ptypes.h:52, -#19 203.4 from stri_external.h:52, -#19 203.4 from stri_stringi.h:36, -#19 203.4 from stri_stringi.cpp:33: -#19 203.4 /usr/include/unicode/uconfig.h:381:12: note: this is the location of the previous definition -#19 203.4 381 | # define UCONFIG_USE_WINDOWS_LCID_MAPPING_API 1 -#19 203.4 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -#19 203.7 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_sub.cpp -o stri_sub.o -#19 204.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_test.cpp -o stri_test.o -#19 204.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_time_zone.cpp -o stri_time_zone.o -#19 204.8 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_time_calendar.cpp -o stri_time_calendar.o -#19 205.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_time_symbols.cpp -o stri_time_symbols.o -#19 205.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_time_format.cpp -o stri_time_format.o -#19 206.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_trans_casemap.cpp -o stri_trans_casemap.o -#19 206.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_trans_other.cpp -o stri_trans_other.o -#19 207.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_trans_normalization.cpp -o stri_trans_normalization.o -#19 207.3 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_trans_transliterate.cpp -o stri_trans_transliterate.o -#19 207.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_ucnv.cpp -o stri_ucnv.o -#19 208.0 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_uloc.cpp -o stri_uloc.o -#19 208.2 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_utils.cpp -o stri_utils.o -#19 208.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -fPIC -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c stri_wrap.cpp -o stri_wrap.o -#19 209.2 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o stringi.so stri_brkiter.o stri_collator.o stri_common.o stri_compare.o stri_container_base.o stri_container_bytesearch.o stri_container_listint.o stri_container_listraw.o stri_container_listutf8.o stri_container_regex.o stri_container_usearch.o stri_container_utf16.o stri_container_utf8.o stri_container_utf8_indexable.o stri_encoding_conversion.o stri_encoding_detection.o stri_encoding_management.o stri_escape.o stri_exception.o stri_ICU_settings.o stri_join.o stri_length.o stri_pad.o stri_prepare_arg.o stri_random.o stri_reverse.o stri_search_class_count.o stri_search_class_detect.o stri_search_class_extract.o stri_search_class_locate.o stri_search_class_replace.o stri_search_class_split.o stri_search_class_startsendswith.o stri_search_class_subset.o stri_search_class_trim.o stri_search_common.o stri_search_coll_count.o stri_search_coll_detect.o stri_search_coll_extract.o stri_search_coll_locate.o stri_search_coll_replace.o stri_search_coll_split.o stri_search_coll_startsendswith.o stri_search_coll_subset.o stri_search_boundaries_count.o stri_search_boundaries_extract.o stri_search_boundaries_locate.o stri_search_boundaries_split.o stri_search_fixed_count.o stri_search_fixed_detect.o stri_search_fixed_extract.o stri_search_fixed_locate.o stri_search_fixed_replace.o stri_search_fixed_split.o stri_search_fixed_subset.o stri_search_fixed_startsendswith.o stri_search_in.o stri_search_other_split.o stri_search_regex_count.o stri_search_regex_detect.o stri_search_regex_extract.o stri_search_regex_locate.o stri_search_regex_match.o stri_search_regex_replace.o stri_search_regex_split.o stri_search_regex_subset.o stri_sort.o stri_sprintf.o stri_stats.o stri_string8.o stri_stringi.o stri_sub.o stri_test.o stri_time_zone.o stri_time_calendar.o stri_time_symbols.o stri_time_format.o stri_trans_casemap.o stri_trans_other.o stri_trans_normalization.o stri_trans_transliterate.o stri_ucnv.o stri_uloc.o stri_utils.o stri_wrap.o -L/usr/lib/aarch64-linux-gnu -licui18n -licuuc -licudata -L/usr/lib/R/lib -lR -#19 209.4 installing via 'install.libs.R' to /usr/local/lib/R/site-library/00LOCK-stringi/00new/stringi -#19 209.4 ** R -#19 209.4 ** inst -#19 209.4 ** byte-compile and prepare package for lazy loading -#19 209.9 ** help -#19 210.3 *** installing help indices -#19 210.4 ** building package indices -#19 210.7 ** testing if installed package can be loaded from temporary location -#19 210.8 ** checking absolute paths in shared objects and dynamic libraries -#19 210.8 ** testing if installed package can be loaded from final location -#19 210.9 ** testing if installed package keeps a record of temporary installation path -#19 210.9 * DONE (stringi) -#19 211.1 * installing *source* package ‘stringr’ ... -#19 211.1 ** package ‘stringr’ successfully unpacked and MD5 sums checked -#19 211.1 ** using staged installation -#19 211.1 ** R -#19 211.1 ** data -#19 211.1 *** moving datasets to lazyload DB -#19 211.1 ** inst -#19 211.1 ** byte-compile and prepare package for lazy loading -#19 211.7 ** help -#19 211.7 *** installing help indices -#19 211.7 *** copying figures -#19 211.7 ** building package indices -#19 211.9 ** installing vignettes -#19 211.9 ** testing if installed package can be loaded from temporary location -#19 212.1 ** testing if installed package can be loaded from final location -#19 212.3 ** testing if installed package keeps a record of temporary installation path -#19 212.3 * DONE (stringr) -#19 212.3 -#19 212.3 The downloaded source packages are in -#19 212.3 ‘/tmp/RtmpZsJzTy/downloaded_packages’ -#19 212.3 Installing package into ‘/usr/local/lib/R/site-library’ -#19 212.3 (as ‘lib’ is unspecified) -#19 212.5 also installing the dependencies ‘purrr’, ‘cpp11’ -#19 212.5 -#19 212.5 trying URL 'https://cloud.r-project.org/src/contrib/purrr_1.0.2.tar.gz' -#19 213.2 Content type 'application/x-gzip' length 220868 bytes (215 KB) -#19 213.2 ================================================== -#19 213.2 downloaded 215 KB -#19 213.2 -#19 213.2 trying URL 'https://cloud.r-project.org/src/contrib/cpp11_0.5.0.tar.gz' -#19 213.7 Content type 'application/x-gzip' length 275693 bytes (269 KB) -#19 213.7 ================================================== -#19 213.7 downloaded 269 KB -#19 213.7 -#19 213.7 trying URL 'https://cloud.r-project.org/src/contrib/tidyr_1.3.1.tar.gz' -#19 214.2 Content type 'application/x-gzip' length 809058 bytes (790 KB) -#19 214.2 ================================================== -#19 214.2 downloaded 790 KB -#19 214.2 -#19 214.5 * installing *source* package ‘purrr’ ... -#19 214.5 ** package ‘purrr’ successfully unpacked and MD5 sums checked -#19 214.5 ** using staged installation -#19 214.7 ** libs -#19 214.7 using C compiler: ‘gcc (Debian 14.2.0-6) 14.2.0’ -#19 214.7 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c backports.c -o backports.o -#19 214.7 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cleancall.c -o cleancall.o -#19 214.8 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c coerce.c -o coerce.o -#19 214.8 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c conditions.c -o conditions.o -#19 214.9 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c flatten.c -o flatten.o -#19 215.1 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o -#19 215.1 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c map.c -o map.o -#19 215.2 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c pluck.c -o pluck.o -#19 215.3 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c transpose.c -o transpose.o -#19 215.3 gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cli/include' -fvisibility=hidden -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o -#19 215.4 gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o purrr.so backports.o cleancall.o coerce.o conditions.o flatten.o init.o map.o pluck.o transpose.o utils.o -L/usr/lib/R/lib -lR -#19 215.4 installing to /usr/local/lib/R/site-library/00LOCK-purrr/00new/purrr/libs -#19 215.4 ** R -#19 215.4 ** inst -#19 215.4 ** byte-compile and prepare package for lazy loading -#19 216.2 ** help -#19 216.3 *** installing help indices -#19 216.4 *** copying figures -#19 216.4 ** building package indices -#19 216.6 ** installing vignettes -#19 216.6 ** testing if installed package can be loaded from temporary location -#19 216.8 ** checking absolute paths in shared objects and dynamic libraries -#19 216.8 ** testing if installed package can be loaded from final location -#19 217.0 ** testing if installed package keeps a record of temporary installation path -#19 217.0 * DONE (purrr) -#19 217.2 * installing *source* package ‘cpp11’ ... -#19 217.2 ** package ‘cpp11’ successfully unpacked and MD5 sums checked -#19 217.2 ** using staged installation -#19 217.2 ** R -#19 217.2 ** inst -#19 217.2 ** byte-compile and prepare package for lazy loading -#19 217.4 ** help -#19 217.4 *** installing help indices -#19 217.4 ** building package indices -#19 217.6 ** installing vignettes -#19 217.6 ** testing if installed package can be loaded from temporary location -#19 217.7 ** testing if installed package can be loaded from final location -#19 217.8 ** testing if installed package keeps a record of temporary installation path -#19 217.8 * DONE (cpp11) -#19 218.1 * installing *source* package ‘tidyr’ ... -#19 218.1 ** package ‘tidyr’ successfully unpacked and MD5 sums checked -#19 218.1 ** using staged installation -#19 218.1 ** libs -#19 218.1 using C++ compiler: ‘g++ (Debian 14.2.0-6) 14.2.0’ -#19 218.1 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cpp11/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c cpp11.cpp -o cpp11.o -#19 218.6 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cpp11/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c melt.cpp -o melt.o -#19 219.5 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/cpp11/include' -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c simplifyPieces.cpp -o simplifyPieces.o -#19 220.2 g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o tidyr.so cpp11.o melt.o simplifyPieces.o -L/usr/lib/R/lib -lR -#19 220.2 installing to /usr/local/lib/R/site-library/00LOCK-tidyr/00new/tidyr/libs -#19 220.2 ** R -#19 220.2 ** data -#19 220.2 *** moving datasets to lazyload DB -#19 220.6 ** inst -#19 220.6 ** byte-compile and prepare package for lazy loading -#19 221.7 ** help -#19 221.8 *** installing help indices -#19 221.9 *** copying figures -#19 221.9 ** building package indices -#19 222.0 ** installing vignettes -#19 222.0 ** testing if installed package can be loaded from temporary location -#19 222.4 ** checking absolute paths in shared objects and dynamic libraries -#19 222.4 ** testing if installed package can be loaded from final location -#19 222.7 ** testing if installed package keeps a record of temporary installation path -#19 222.7 * DONE (tidyr) -#19 222.7 -#19 222.7 The downloaded source packages are in -#19 222.7 ‘/tmp/RtmpZsJzTy/downloaded_packages’ -#19 DONE 222.9s - -#20 exporting to image -#20 exporting layers -#20 exporting layers 2.6s done -#20 writing image sha256:3812c88e7d3f4e4bbcc71ca3d6d1c53c4601dab50a410c8579086533a58b83d2 done -#20 naming to docker.io/library/mpnstpdx done -#20 DONE 2.6s - - 1 warning found (use --debug to expand): - - UndefinedVar: Usage of undefined variable '$PYTHONPATH' (line 34) - -View build details: docker-desktop://dashboard/build/desktop-linux/desktop-linux/rjrwxqzbvz2qr9uxna8wl95zm - -What's next: - View a summary of image vulnerabilities and recommendations → docker scout quickview  diff --git a/build/docker/Dockerfile.mpnstPDX b/build/docker/Dockerfile.mpnstPDX index 88e4ff53..86a3c02e 100755 --- a/build/docker/Dockerfile.mpnstPDX +++ b/build/docker/Dockerfile.mpnstPDX @@ -39,9 +39,9 @@ ENV MPLCONFIGDIR=/app/tmp/matplotlib RUN mkdir -p /app/tmp/matplotlib # Add necessary files to the container -ADD build/mpnstPDX/requirements.txt . -ADD build/mpnstPDX/requirements.r . -ADD build/mpnstPDX/* ./ +ADD build/mpnstpdx/requirements.txt . +ADD build/mpnstpdx/requirements.r . +ADD build/mpnstpdx/* ./ ADD build/utils/* ./ # installing python libraries diff --git a/build/docker/docker-compose.yml b/build/docker/docker-compose.yml index bf28ef65..373eb5d6 100644 --- a/build/docker/docker-compose.yml +++ b/build/docker/docker-compose.yml @@ -44,6 +44,7 @@ services: HTTPS_PROXY: ${HTTPS_PROXY} platform: linux/amd64 image: mpnst:latest + mpnstpdx: build: context: ../../ diff --git a/build/mpnst/build_drugs.sh b/build/mpnst/build_drugs.sh index 8512222f..3b969d2b 100644 --- a/build/mpnst/build_drugs.sh +++ b/build/mpnst/build_drugs.sh @@ -1,2 +1,10 @@ -Rscript 02_get_drug_data.R $SYNAPSE_AUTH_TOKEN $1 /tmp/mpnst_drugs.tsv +#!/bin/bash +set -euo pipefail + +trap 'echo "Error on or near line $LINENO while executing: $BASH_COMMAND"; exit 1' ERR + +echo "Running 02_get_drug_data.R with /tmp/mpnst_drugs.tsv and $1." +Rscript 02_get_drug_data.R /tmp/mpnst_drugs.tsv $1 + +echo "Running build_drug_desc.py." /opt/venv/bin/python3 build_drug_desc.py --drugtable /tmp/mpnst_drugs.tsv --desctable /tmp/mpnst_drug_descriptors.tsv.gz diff --git a/build/mpnstPDX/01_mpnst_get_omics.R b/build/mpnstPDX/01_mpnst_get_omics.R index 776ea41c..86e3cbb8 100755 --- a/build/mpnstPDX/01_mpnst_get_omics.R +++ b/build/mpnstPDX/01_mpnst_get_omics.R @@ -30,7 +30,7 @@ synLogin(authToken = PAT) # Read the sample mapping CSV and genes.csv samples_df <- fread(patients)|> dplyr::select(improve_sample_id,common_name,model_type)|> - distinct()#"mpnst/synapse_NF-MPNSTPDX_samples.csv") + distinct()#"mpnst/synapse_NF-MPNSTpdx_samples.csv") pdx_samps<-subset(samples_df,model_type=='patient derived xenograft') tumor_samps<-subset(samples_df,model_type=='tumor') @@ -41,7 +41,7 @@ manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|> dplyr::rename(common_name='Sample') -##for now we only have tumor and PDX data +##for now we only have tumor and pdx data ##they each get their own sample identifier pdx_data<-manifest|>dplyr::select(common_name,starts_with("PDX"))|> left_join(pdx_samps)|> @@ -83,7 +83,7 @@ proteomics<-do.call('rbind',lapply(setdiff(pdx_data$Proteomics,c('',NA,"NA")),fu # } })) -fwrite(proteomics,'/tmp/mpnstPDX_proteomics.csv.gz') +fwrite(proteomics,'/tmp/mpnstpdx_proteomics.csv.gz') #### FIRST WE GET RNASeq Data @@ -108,7 +108,7 @@ rnaseq<-do.call('rbind',lapply(setdiff(pdx_data$RNASeq,c(NA,"NA")),function(x){ # } })) -fwrite(rnaseq,'/tmp/mpnstPDX_transcriptomics.csv.gz') +fwrite(rnaseq,'/tmp/mpnstpdx_transcriptomics.csv.gz') @@ -136,7 +136,7 @@ wes<-do.call(rbind,lapply(setdiff(pdx_data$`Mutations`,c(NA,"NA")),function(x){ # } })) -fwrite(wes,'/tmp/mpnstPDX_mutations.csv.gz') +fwrite(wes,'/tmp/mpnstpdx_mutations.csv.gz') print(paste("getting CNV")) @@ -190,6 +190,6 @@ cnv<-do.call(rbind,lapply(setdiff(pdx_data$CopyNumber,c(NA,"NA")),function(x){ # } })) -fwrite(cnv,'/tmp/mpnstPDX_copy_number.csv.gz') +fwrite(cnv,'/tmp/mpnstpdx_copy_number.csv.gz') ##TODO: get proteomics!!! diff --git a/build/mpnstPDX/03_get_drug_response_data.R b/build/mpnstPDX/03_get_drug_response_data.R index 7f3eabb9..095dba34 100644 --- a/build/mpnstPDX/03_get_drug_response_data.R +++ b/build/mpnstPDX/03_get_drug_response_data.R @@ -162,7 +162,7 @@ pdx_data<-rbind(old_data,new_data) fwrite(pdx_data,'/tmp/curve_data.tsv',sep='\t') ##TODO: create new curve fitting script in python -pycmd = '/opt/venv/bin/python calc_pdx_metrics.py --input /tmp/curve_data.tsv --outprefix /tmp/mpnstPDX' +pycmd = '/opt/venv/bin/python calc_pdx_metrics.py --input /tmp/curve_data.tsv --outprefix /tmp/mpnstpdx' print('running curve fitting') #system(pycmd) diff --git a/build/mpnstPDX/build_samples.sh b/build/mpnstPDX/build_samples.sh index 13066a85..76d743d9 100644 --- a/build/mpnstPDX/build_samples.sh +++ b/build/mpnstPDX/build_samples.sh @@ -1 +1 @@ -cp $1 /tmp/mpnstPDX_samples.csv +cp $1 /tmp/mpnstpdx_samples.csv diff --git a/build/mpnstPDX/requirements.r b/build/mpnstPDX/requirements.r index 72dd457d..e6139cd4 100755 --- a/build/mpnstPDX/requirements.r +++ b/build/mpnstPDX/requirements.r @@ -8,4 +8,6 @@ install.packages("data.table") install.packages("synapser", repos = c("http://ran.synapse.org", "https://cloud.r-project.org")) install.packages("R.utils") install.packages("stringr") -install.packages("tidyr") \ No newline at end of file +install.packages("tidyr") +install.packages('readr') +install.packages("readxl") From 1680f41af4b2692d1cdff92e8192e2460cd068f9 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Fri, 22 Nov 2024 11:10:53 -0800 Subject: [PATCH 07/17] updated --- build/mpnstPDX/build_drugs.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/build/mpnstPDX/build_drugs.sh b/build/mpnstPDX/build_drugs.sh index 0a92e3e5..be87c3c3 100644 --- a/build/mpnstPDX/build_drugs.sh +++ b/build/mpnstPDX/build_drugs.sh @@ -1,2 +1,4 @@ +##get drug data Rscript 02_get_drug_data.R $SYNAPSE_AUTH_TOKEN $1 /tmp/mpnstpdx_drugs.tsv +##get drug descriptors /opt/venv/bin/python3 build_drug_desc.py --drugtable /tmp/mpnstpdx_drugs.tsv --desctable /tmp/mpnstpdx_drug_descriptors.tsv.gz From 8a0fe2203d01ad0ff98ffafa9f9238496ccc31f5 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Fri, 22 Nov 2024 16:35:19 -0800 Subject: [PATCH 08/17] fixed #251 --- build/mpnst/00_sample_gen.R | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/build/mpnst/00_sample_gen.R b/build/mpnst/00_sample_gen.R index 299aa10f..ccd3f853 100755 --- a/build/mpnst/00_sample_gen.R +++ b/build/mpnst/00_sample_gen.R @@ -42,8 +42,13 @@ sampTable<-manifest|> tidyr::unite(col='other_id',c('common_name','model_type'),sep=' ',remove=FALSE) +pdxmt<-manifest|> + dplyr::select(common_name='Sample',MicroTissueDrugFolder)|> + dplyr::mutate(other_id_source='NF Data Portal',other_names='',cancer_type="Malignant peripheral nerve sheath tumor",species='Human',model_type='organoid')|> + tidyr::unite(col='other_id',c('common_name','model_type'),sep=' ',remove=FALSE) + ##third, generate a sample for the MTs if they were generated -pdxmt<-subset(sampTable,!is.na(MicroTissueDrugFolder)) +#pdxmt<-subset(sampTable,!is.na(MicroTissueDrugFolder)) pdxmt$model_type=rep('organoid',nrow(pdxmt)) print(pdxmt) From b46234a3802543ecdcb94e5baec0fe2958cc56bf Mon Sep 17 00:00:00 2001 From: Jeremy Date: Sat, 23 Nov 2024 08:42:55 -0800 Subject: [PATCH 09/17] GDC Tool Moved. Replaced URLs. --- build/hcmi/02-getHCMIData.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/build/hcmi/02-getHCMIData.py b/build/hcmi/02-getHCMIData.py index a7e3e74a..f2cebd9a 100644 --- a/build/hcmi/02-getHCMIData.py +++ b/build/hcmi/02-getHCMIData.py @@ -71,10 +71,11 @@ def ensure_gdc_client(): if not is_tool(tool_name): print("Downloading gdc-client") urls = { - "Darwin": 'https://gdc.cancer.gov/files/public/file/gdc-client_v1.6.1_OSX_x64.zip', - "Windows": 'https://gdc.cancer.gov/files/public/file/gdc-client_v1.6.1_Windows_x64.zip', - "Linux": 'https://gdc.cancer.gov/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip' + "Darwin": 'https://gdc.cancer.gov/system/files/public/file/gdc-client_2.3_OSX_x64-py3.8-macos-14.zip', + "Windows": 'https://gdc.cancer.gov/system/files/public/file/gdc-client_2.3_Windows_x64-py3.8-windows-2019.zip', + "Linux": 'https://gdc.cancer.gov/system/files/public/file/gdc-client_2.3_Ubuntu_x64-py3.8-ubuntu-20.04.zip' } + download_tool(urls.get(platform.system())) else: print("gdc-client already installed") From fa1b22522f91efd5a690a8caaaa79e39db0a633c Mon Sep 17 00:00:00 2001 From: Jeremy Date: Sun, 24 Nov 2024 02:25:37 -0800 Subject: [PATCH 10/17] GDC Client was updated. Working on quick fix. This will need more work in future --- build/hcmi/02-getHCMIData.py | 23 +++++++++++++++++------ 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/build/hcmi/02-getHCMIData.py b/build/hcmi/02-getHCMIData.py index f2cebd9a..ab876bcf 100644 --- a/build/hcmi/02-getHCMIData.py +++ b/build/hcmi/02-getHCMIData.py @@ -35,12 +35,23 @@ def download_tool(url): filename = wget.download(url) files_before = os.listdir() - shutil.unpack_archive(filename) - files_after = os.listdir() - new_file = str(next(iter((set(files_after) - set(files_before))))) - st = os.stat(new_file) - os.chmod(new_file, st.st_mode | stat.S_IEXEC) - return filename + # shutil.unpack_archive(filename) + + #This is just set for AWS to debug. This will have to be mapped to OS. They changed their file structure. This should be updated. + shutil.unpack_archive("gdc-client_2.3_Ubuntu_x64.zip") + if not os.path.exists('gdc-client'): + raise FileNotFoundError("gdc-client executable not found after extraction.") + # Ensure 'gdc-client' is executable + st = os.stat('gdc-client') + os.chmod('gdc-client', st.st_mode | stat.S_IEXEC) + # Return the path to the executable + return './gdc-client' + + # files_after = os.listdir() + # new_file = str(next(iter((set(files_after) - set(files_before))))) + # st = os.stat(new_file) + # os.chmod(new_file, st.st_mode | stat.S_IEXEC) + # return filename def is_tool(name): """ From d0dc5ed968e1cfcc73865674424cdb0801c2cb52 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Tue, 26 Nov 2024 18:32:18 -0800 Subject: [PATCH 11/17] addresses the issues in #251 mPnst and mpnstpdx code now build. --- build/docker/Dockerfile.mpnst | 2 +- build/mpnst/00_sample_gen.R | 40 +++++++++++++++++-------- build/mpnst/03_get_drug_response_data.R | 2 +- build/mpnst/README.md | 2 +- build/mpnst/build_drugs.sh | 4 +-- build/mpnst/requirements.r | 4 +-- build/utils/build_drug_desc.py | 3 +- 7 files changed, 36 insertions(+), 21 deletions(-) diff --git a/build/docker/Dockerfile.mpnst b/build/docker/Dockerfile.mpnst index 92fe9c6d..94e04e87 100755 --- a/build/docker/Dockerfile.mpnst +++ b/build/docker/Dockerfile.mpnst @@ -1,4 +1,4 @@ -FROM r-base:4.3.2 +FROM r-base:4.3.3 # Set environment to noninteractive ENV DEBIAN_FRONTEND=noninteractive diff --git a/build/mpnst/00_sample_gen.R b/build/mpnst/00_sample_gen.R index 0d009853..ae45826c 100755 --- a/build/mpnst/00_sample_gen.R +++ b/build/mpnst/00_sample_gen.R @@ -7,14 +7,25 @@ library(dplyr) ##adding a command line argument args = commandArgs(trailingOnly=TRUE) -if(length(args)!=2){ - stop("Need a sample file and synapse token as argument. Rscript 00_sample_gen.R [samplefile] [synapse token]") +if(length(args) > 1 ){ + stop("Up to one argument is allowed. This is the filepath to the previously run samples file.") +} + +if (length(args) == 0 || is.na(args[1]) || args[1] == "" || !file.exists(args[1])) { + orig_samples <- "" +} else { + orig_samples <- fread(args[1]) } -orig_samples<-fread(args[1]) -synapser::synLogin(authToken=args[2]) +# Check if Synapse token is available from the environment +synapse_token <- Sys.getenv("SYNAPSE_AUTH_TOKEN") +if (synapse_token == "") { + stop("Error: SYNAPSE_AUTH_TOKEN environment variable is not set.") +} + +synapser::synLogin(authToken=synapse_token) manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|> as.data.frame() @@ -32,23 +43,18 @@ manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|> ##first create samples for the original tumors tumorTable<-manifest|> dplyr::select(common_name='Sample')|> - dplyr::mutate(other_id_source='NF Data Portal',other_names='',cancer_type="Malignant peripheral nerve sheath tumor",species='Human',model_type='tumor')|> + dplyr::mutate(other_id_source='NF Data Portal',other_names='',cancer_type="Malignant peripheral nerve sheath tumor",species='Homo sapiens (Human)',model_type='tumor')|> tidyr::unite(col='other_id',c('common_name','model_type'),sep=' ',remove=FALSE) ##then create samples for the PDX sampTable<-manifest|> dplyr::select(common_name='Sample',MicroTissueDrugFolder)|> - dplyr::mutate(other_id_source='NF Data Portal',other_names='',cancer_type="Malignant peripheral nerve sheath tumor",species='Human',model_type='patient derived xenograft')|> + dplyr::mutate(other_id_source='NF Data Portal',other_names='',cancer_type="Malignant peripheral nerve sheath tumor",species='Homo sapiens (Human)',model_type='patient derived xenograft')|> tidyr::unite(col='other_id',c('common_name','model_type'),sep=' ',remove=FALSE) -pdxmt<-manifest|> - dplyr::select(common_name='Sample',MicroTissueDrugFolder)|> - dplyr::mutate(other_id_source='NF Data Portal',other_names='',cancer_type="Malignant peripheral nerve sheath tumor",species='Human',model_type='organoid')|> - tidyr::unite(col='other_id',c('common_name','model_type'),sep=' ',remove=FALSE) - ##third, generate a sample for the MTs if they were generated -#pdxmt<-subset(sampTable,!is.na(MicroTissueDrugFolder)) +pdxmt<-subset(sampTable,!is.na(MicroTissueDrugFolder)) pdxmt$model_type=rep('organoid',nrow(pdxmt)) print(pdxmt) @@ -58,7 +64,15 @@ main<-rbind(sampTable,pdxmt)|> #main <- fread("mpnst/NF_MPNST_samples.csv") #previous_aml <- fread(args[1])#"beatAML/beataml_samples.csv") -max_id <- max(orig_samples$improve_sample_id) + +# If there is no previous samples file - start at 1, else, continue where the previous one left off. +if (identical(orig_samples, "")) { + max_id <- 1 +} else { + max_id <- max(orig_samples$improve_sample_id, na.rm = TRUE) +} + + main$improve_sample_id <- seq(from = max_id + 1, length.out = nrow(main)) #synapse_main <- fread("mpnst/synapse_NF-MPNST_samples.csv") diff --git a/build/mpnst/03_get_drug_response_data.R b/build/mpnst/03_get_drug_response_data.R index 8f02ca80..9bbb6f00 100644 --- a/build/mpnst/03_get_drug_response_data.R +++ b/build/mpnst/03_get_drug_response_data.R @@ -32,7 +32,7 @@ org_samps<-subset(samples_df,model_type=='organoid') ##now get the manifest from synapse manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|> - as.data.frame()|> + as.data.table()|> dplyr::rename(common_name='Sample') diff --git a/build/mpnst/README.md b/build/mpnst/README.md index 10d0bcd9..13c08454 100755 --- a/build/mpnst/README.md +++ b/build/mpnst/README.md @@ -12,7 +12,7 @@ directory. Currently using the test files as input. `mpnst_samples.csv` file. This pulls from the latest synapse project metadata table. ``` - docker run -v $PWD:/tmp -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN mpnst sh build_samples.sh /tmp/build/build_test/test_samples.csv + docker run -v $PWD:/tmp -e -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN mpnst sh build_samples.sh /tmp/build/build_test/test_samples.csv ``` 3. Pull the data and map it to the samples. This uses the metadata diff --git a/build/mpnst/build_drugs.sh b/build/mpnst/build_drugs.sh index 3b969d2b..821bc46c 100644 --- a/build/mpnst/build_drugs.sh +++ b/build/mpnst/build_drugs.sh @@ -1,7 +1,7 @@ #!/bin/bash -set -euo pipefail +#set -euo pipefail -trap 'echo "Error on or near line $LINENO while executing: $BASH_COMMAND"; exit 1' ERR +#trap 'echo "Error on or near line $LINENO while executing: $BASH_COMMAND"; exit 1' ERR echo "Running 02_get_drug_data.R with /tmp/mpnst_drugs.tsv and $1." Rscript 02_get_drug_data.R /tmp/mpnst_drugs.tsv $1 diff --git a/build/mpnst/requirements.r b/build/mpnst/requirements.r index 72dd457d..7796236d 100755 --- a/build/mpnst/requirements.r +++ b/build/mpnst/requirements.r @@ -4,8 +4,8 @@ install.packages('remotes') remotes::install_version('rjson', version = '0.2.21', repos = 'https://cloud.r-project.org') install.packages('synapser', repos = c('http://ran.synapse.org', 'https://cloud.r-project.org')) install.packages("dplyr") -install.packages("data.table") install.packages("synapser", repos = c("http://ran.synapse.org", "https://cloud.r-project.org")) +install.packages("data.table") install.packages("R.utils") install.packages("stringr") -install.packages("tidyr") \ No newline at end of file +install.packages("tidyr") diff --git a/build/utils/build_drug_desc.py b/build/utils/build_drug_desc.py index 7e25212e..f119bc77 100644 --- a/build/utils/build_drug_desc.py +++ b/build/utils/build_drug_desc.py @@ -82,8 +82,9 @@ def main(): cansmiles = [a for a in set(tab.canSMILES) if str(a)!='nan'] # isosmiles = list(set(tab.isoSMILES)) morgs = smiles_to_fingerprint(cansmiles) - +# print(morgs) ids = pd.DataFrame(tab[['improve_drug_id','canSMILES']]).drop_duplicates() +# print(ids) id_morg = ids.rename({"canSMILES":'smile'},axis=1).merge(morgs)[['improve_drug_id','structural_descriptor','descriptor_value']] mords = smiles_to_mordred(cansmiles,nproc=ncors) From 54227fc9c9e8811961cc3b0fddab97fbe90adaa9 Mon Sep 17 00:00:00 2001 From: Jeremy Date: Mon, 2 Dec 2024 14:23:34 -0800 Subject: [PATCH 12/17] Update for NCI60, bug fixes, and HCMI GDC tool --- build/broad_sanger/04b-nci60-updated.py | 5 +- build/build_dataset.py | 4 +- build/hcmi/02-getHCMIData.py | 88 ++++++++++++++----------- schema/expected_files.yaml | 2 +- 4 files changed, 57 insertions(+), 42 deletions(-) diff --git a/build/broad_sanger/04b-nci60-updated.py b/build/broad_sanger/04b-nci60-updated.py index b6a82001..c515f59d 100644 --- a/build/broad_sanger/04b-nci60-updated.py +++ b/build/broad_sanger/04b-nci60-updated.py @@ -107,10 +107,11 @@ def main(): finaldf = pl.DataFrame( { - 'source':['NCI60' for a in molar['improve_drug_id']], ##2024 build + 'source':['NCI60_24' for a in molar['improve_drug_id']], ##2024 build 'improve_sample_id':molar['improve_sample_id'], 'Drug':molar['improve_drug_id'], - 'study': molar['EXPID'],#['NCI60' for a in nonulls['improve_drug_id']], + # 'study': molar['EXPID'],#['NCI60' for a in nonulls['improve_drug_id']], + 'study': "NCI60", 'time':molar['time'], 'time_unit':molar['time_unit'], 'DOSE': [(10**a)*1000000 for a in molar['CONCENTRATION']], ##move from molar to uM to match pharmacoDB diff --git a/build/build_dataset.py b/build/build_dataset.py index 88863090..dd585604 100644 --- a/build/build_dataset.py +++ b/build/build_dataset.py @@ -218,7 +218,7 @@ def run_docker_validate_cmd(cmd_arr, all_files_dir, name): Wrapper for 'docker run' command used during validation and uploads. ''' env = os.environ.copy() - docker_run = ['docker', 'run', '-v', f"{env['PWD']}/local/{all_files_dir}:/tmp"] + docker_run = ['docker', 'run', '-v', f"{env['PWD']}/local/{all_files_dir}:/tmp", '--platform=linux/amd64'] docker_run.extend(['upload']) docker_run.extend(cmd_arr) print('Executing:', ' '.join(docker_run)) @@ -258,7 +258,7 @@ def run_schema_checker(dataset): decompress_file(os.path.join('local', all_files_dir, file)) # Run schema checker - schema_check_command = ['python3', 'scripts/check_schema.py', '--datasets'] + datasets + schema_check_command = ['python3', 'check_schema.py', '--datasets'] + datasets run_docker_validate_cmd(schema_check_command, all_files_dir, 'Validation') def main(): diff --git a/build/hcmi/02-getHCMIData.py b/build/hcmi/02-getHCMIData.py index ab876bcf..b329a68a 100644 --- a/build/hcmi/02-getHCMIData.py +++ b/build/hcmi/02-getHCMIData.py @@ -17,79 +17,93 @@ import polars as pl import gc import hashlib +from pathlib import Path def download_tool(url): """ - Download, extract, and make a tool (GDC Client) executable from the provided URL. + Download, extract, and prepare the GDC client tool. Parameters ---------- url : str - The URL from where the tool needs to be downloaded. + The URL to download the tool from. Returns ------- str - Name of the downloaded file. + The path to the `gdc-client` executable. """ - + # Download the file + print("Downloading tool...") filename = wget.download(url) - files_before = os.listdir() - # shutil.unpack_archive(filename) - - #This is just set for AWS to debug. This will have to be mapped to OS. They changed their file structure. This should be updated. - shutil.unpack_archive("gdc-client_2.3_Ubuntu_x64.zip") - if not os.path.exists('gdc-client'): - raise FileNotFoundError("gdc-client executable not found after extraction.") - # Ensure 'gdc-client' is executable - st = os.stat('gdc-client') - os.chmod('gdc-client', st.st_mode | stat.S_IEXEC) - # Return the path to the executable - return './gdc-client' - - # files_after = os.listdir() - # new_file = str(next(iter((set(files_after) - set(files_before))))) - # st = os.stat(new_file) - # os.chmod(new_file, st.st_mode | stat.S_IEXEC) - # return filename + + # First extraction + print(f"\nExtracting {filename}...") + shutil.unpack_archive(filename) + os.remove(filename) + + # Check for a nested zip file and extract again + extracted_files = [f for f in os.listdir() if os.path.isfile(f) and f.endswith(".zip")] + for zip_file in extracted_files: + print(f"Extracting nested archive: {zip_file}...") + shutil.unpack_archive(zip_file) + os.remove(zip_file) + + gdc_client_path = None + for root, dirs, files in os.walk("."): + if "gdc-client" in files: + gdc_client_path = os.path.join(root, "gdc-client") + break + + if not gdc_client_path: + raise FileNotFoundError("`gdc-client` executable not found after extraction.") + + # Ensure `gdc-client` is executable + print(f"Making {gdc_client_path} executable...") + st = os.stat(gdc_client_path) + os.chmod(gdc_client_path, st.st_mode | stat.S_IEXEC) + + return gdc_client_path def is_tool(name): """ - Check if a specific tool is available on the system or in the current directory. + Check if a specific tool is available on the system. Parameters ---------- name : str - The name of the tool to check. + The name of the tool. Returns ------- bool True if the tool is found, otherwise False. """ - - return which(name) is not None or name in os.listdir() + return shutil.which(name) is not None or name in os.listdir() def ensure_gdc_client(): """ - Ensure that the gdc-client is available on the system. + Ensure that the GDC client tool is available on the system. - If the gdc-client tool isn't found, this function will automatically - download the appropriate version based on the operating system. + If the tool isn't found, this function downloads and prepares it. """ - tool_name = "gdc-client" if not is_tool(tool_name): - print("Downloading gdc-client") + print("GDC client not found. Downloading...") urls = { - "Darwin": 'https://gdc.cancer.gov/system/files/public/file/gdc-client_2.3_OSX_x64-py3.8-macos-14.zip', - "Windows": 'https://gdc.cancer.gov/system/files/public/file/gdc-client_2.3_Windows_x64-py3.8-windows-2019.zip', - "Linux": 'https://gdc.cancer.gov/system/files/public/file/gdc-client_2.3_Ubuntu_x64-py3.8-ubuntu-20.04.zip' + "Darwin": "https://gdc.cancer.gov/system/files/public/file/gdc-client_2.3_OSX_x64-py3.8-macos-14.zip", + "Windows": "https://gdc.cancer.gov/system/files/public/file/gdc-client_2.3_Windows_x64-py3.8-windows-2019.zip", + "Linux": "https://gdc.cancer.gov/system/files/public/file/gdc-client_2.3_Ubuntu_x64-py3.8-ubuntu-20.04.zip" } - - download_tool(urls.get(platform.system())) + os_type = platform.system() + url = urls.get(os_type) + if not url: + raise ValueError(f"Unsupported OS: {os_type}") + gdc_client_path = download_tool(url) + print(f"`gdc-client` downloaded and available at {gdc_client_path}") else: - print("gdc-client already installed") + print("`gdc-client` is already installed.") + def extract_uuids_from_manifest(manifest_data): """ diff --git a/schema/expected_files.yaml b/schema/expected_files.yaml index 7567fa58..91f9770e 100644 --- a/schema/expected_files.yaml +++ b/schema/expected_files.yaml @@ -39,7 +39,7 @@ datasets: - target_class: Drug file: /tmp/mpnst_drugs.tsv - mpnst: + mpnstpdx: - target_class: Sample file: /tmp/mpnstpdx_samples.csv - target_class: Transcriptomics From f144edb8b162362d534338fb092a67399d22c1ba Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Mon, 2 Dec 2024 15:52:34 -0800 Subject: [PATCH 13/17] removed --- mpnstpdx_ignore_chems.txt | 130 -------------------------------------- 1 file changed, 130 deletions(-) delete mode 100644 mpnstpdx_ignore_chems.txt diff --git a/mpnstpdx_ignore_chems.txt b/mpnstpdx_ignore_chems.txt deleted file mode 100644 index eac569e9..00000000 --- a/mpnstpdx_ignore_chems.txt +++ /dev/null @@ -1,130 +0,0 @@ -vks -tno 155 [who-dd] -bdbm50553783 -(3s,4s)-8-[6-amino-5-(2-amino-3-chloropyridin-4-yl)sulfanylpyrazin-2-yl]-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine -nsc825523 -(3s,4s)-8-{6-amino-5-[(2-amino-3-chloropyridin-4- yl)sulfanyl]pyrazin-2-yl}-3-methyl-2-oxa-8- azaspiro[4.5]decan-4-amine -batoprotafib [inn] -ptpn11 inhibitor tno155 -(3s,4s)-8-{6-amino-5-[(2-amino-3-chloropyridin-4-yl)sulfanyl]pyrazin-2-yl}-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine -schembl16914359 -(3s,4s)-8-[6-amino-5-[(2-amino-3-chloro-4-pyridinyl)thio]-2-pyrazinyl]-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine -1801765-04-7 -compound 1 (pmid: 32910655) -tno 155 -nsc-825523 -ac-36494 -ms-27407 -d81634 -cs-0120271 -(3s,4s)-8-(6-amino-5-((2-amino-3-chloropyridin-4-yl)sulfanyl)pyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro(4.5)decan-4-amine -2-oxa-8-azaspiro[4.5]decan-4-amine, 8-[6-amino-5-[(2-amino-3-chloro-4-pyridinyl)thio]-2-pyrazinyl]-3-methyl-, (3s,4s)- -(3s,4s)-8-(6-amino-5-((2-amino-3-chloropyridin-4-yl)thio)pyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine -fpjworqegi -gtpl12068 -batoprotafib -unii-fpjworqegi -tno-155; tno 155 -akos040740434 -tno-155 -tno155 -compound 1 [pmid: 32910655] -tno155? -ex-a3645 -hy-136173 -bcp33299 -db-130941 -(3s,4s)-8-(6-amino-5-(2-amino-3-chloropyridin-4-ylthio)pyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine -mfcd32693919 -chembl4650521 -shp2 inhibitor tno155 -(3s,4s)-8-(6-amino-5-(2-amino-3-chloropyridin-4-yl)sulfanylpyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro(4.5)decan-4-amine -brd-k13514097-001-01-2 -(1r,9s,12s,15r,16e,18r,19r,21r,23s,24e,26e,28e,30s,32s,35r)-1,18-dihydroxy-12-((1r)-2-((1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl)-1-methylethyl)-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo(30.3.1.0(sup 4,9))hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentaone -(3s,6r,7e,9r,10r,12r,14s,15e,17e,19e,21s,23s,26r,27r,34as)-9,10,12,13,14,21,22,23,24,25,26,27,32,33,34,34a-hexadecahydro-9,27-dihydroxy-3-((1r)-2-((1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl)-1-methylethyl)-10,21-dimethoxy-6,8,12,14,20,26-hexamethyl-23,27-epoxy-3h-pyrido(2,1-c)(1,4)oxaazacyclohentriacontine-1,5,11,28,29(4h,6h,31h)-pentone -42-o-(2-hydroxy)ethyl rapamycin -xience v -bdbm50088378 -everolimus [ema epar] -everolimus, analytical standard -everolimus (mart.) -everolimus [vandf] -dihydroxy-[(1r)-2-[(1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxy-cyclohexyl]-1-methyl-ethyl]-dimethoxy-hexamethyl-[?]pentone -rad 001 -everolimus (rad001) -ncgc00167512-01 -everolimus [ep monograph] -159351-69-6 -brd-k13514097-001-05-3 -votubia -rapamycin, 42-o-(2-hydroxyethyl)- -(1r,9s,12s,15r,16e,18r,19r,21r,23s,24e,26e,28e,30s,35r)-1,18-dihydroxy-12-{(2r)-1-[(1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl]propan-2-yl}-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo[30.3.1.0(4,9)]hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentone -40-o-(2-hydroxyethyl)-rapamycin -everolimus (inn) -rad-001c -l04aa18 -everolimus [mi] -rad, sdz -q421052 -db01590 -everolimus [usan:inn:ban] -gtpl5889 -42-o-(2-hydroxyethyl)-rapamycin -zortress -rad001 -sdz-rad -(3s,6r,7e,9r,10r,12r,14s,15e,17e,19e,21s,23s,26r,27r,34as)-9,27-dihydroxy-3-((2r)-1-((1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl)propan-2-yl)-10,21-dimethoxy-6,8,12,14,20,26-hexamethyl-9,10,12,13,14,21,22,23,24,25,26,27,32,33,34,34a-hexadecahydro-3h-23,27-epoxypyrido(2,1-c)(1,4)oxazacyclohentriacontine-1,5,11,28,29(4h,6h,31h)-pentone -everolimus [usp-rs] -(1r,9s,12s,15r,16e,18r,19r,21r,23s,24e,26e,28e,30s,35r)-1,18-dihydroxy-12-((2r)-1-((1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl)propan-2-yl)-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo(30.3.1.0(4,9))hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentone -afinitordisperz -everolimus tablets -001, rad -everolimus (ep monograph) -tox21_112510 -dtxsid0040599 -everolimus [inn] -everolimus [orange book] -(1r,9s,12s,15r,16e,18r,19r,21r,23s,24e,26e,28e,30s,32s,35r)-1,18-dihydroxy-12-[(2r)-1-[(1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl]propan-2-yl]-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo[30.3.1.04,9]hexatriaconta-16,24,2 -everolimus (rad-001, sdz-rad) -everolimus -eve - everolimus -(3s,6r,7e,9r,10r,12r,14s,15e,17e,19e,21s,23s,26r,27r,34as)-9,27-dihydroxy-3-{(2r)-1-[(1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl]propan-2-yl}-10,21-dimethoxy-6,8,12,14,20,26-hexamethyl-9,10,12,13,14,21,22,23,24,25,26,27,32,33,34,34a-hexadecahydro-3h-23,27-epoxypyrido[2,1-c][1,4]oxazacyclohentriacontine-1,5,11,28,29(4h,6h,31h)-pentone -dtxcid8020599 -everolimusum -ex-a2057 -hy-10218r -everolimus [mart.] -afinitor -unii-9hw64q8g6g -rad-001 -chembl1908360 -cas-159351-69-6 -everolimus (~90% pure) -rad -akos015850977 -9hw64q8g6g -(1r,9s,12s,15r,16e,18r,19r,21r,23s,24e,26e,28e,30s,32s,35r)-1,18-dihydroxy-12-((1r)-2-((1s,3r,4r)-4-(2-hydroxyethoxy)-3-methoxycyclohexyl)-1-methylethyl)-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo(30.3.1.04,9)hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentaone -everolimus (usp-rs) -everolimus? -chebi:68478 -everolimus (standard) -as-16971 -q-101413 -nsc733504 -everolimus; rad001; sdz-rad -hsdb 8255 -everolimus [who-dd] -sdz rad -schembl4378 -afinitor disperz -42-o-(2-hydroxyethyl)rapamycin -40-o-(2-hydroxyethyl)rapamycin -certican -hy-10218 -rad-666 -rad 666 -everolimus [jan] -nvp-rad-001 -l01xe10 -cs-0064 -everolimus [usan] From 11d28d209530c8366b8f6cdb9072390902cacfd5 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Thu, 5 Dec 2024 08:46:59 -0800 Subject: [PATCH 14/17] closes #256 Only change is needed for BeatAML - MPNST issue handed on synapse. --- build/beatAML/GetBeatAML.py | 1 + 1 file changed, 1 insertion(+) diff --git a/build/beatAML/GetBeatAML.py b/build/beatAML/GetBeatAML.py index 5bf94233..4ea0ca8c 100755 --- a/build/beatAML/GetBeatAML.py +++ b/build/beatAML/GetBeatAML.py @@ -468,6 +468,7 @@ def map_and_combine(df, data_type, entrez_map_file, improve_map_file, map_file=N mapped_df.insert(0, 'improve_sample_id', mapped_df.pop('improve_sample_id')) mapped_df['source'] = 'synapse' mapped_df['study'] = 'BeatAML' + mapped_df =mapped_df.drop_duplicates() final_dataframe = mapped_df.dropna() return final_dataframe From 65c2570376aef705a9b47852637f351b46a330cf Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Fri, 6 Dec 2024 09:10:08 -0800 Subject: [PATCH 15/17] fixed issue with MPNST MT sample mapping --- build/mpnst/01_mpnst_get_omics.R | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/build/mpnst/01_mpnst_get_omics.R b/build/mpnst/01_mpnst_get_omics.R index 173ca71e..b12d3335 100755 --- a/build/mpnst/01_mpnst_get_omics.R +++ b/build/mpnst/01_mpnst_get_omics.R @@ -46,21 +46,25 @@ manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|> ##they each get their own sample identifier pdx_data<-manifest|>dplyr::select(common_name,starts_with("PDX"))|> left_join(pdx_samps)|> - dplyr::select(improve_sample_id,common_name,model_type,RNASeq='PDX_RNASeq',Mutations='PDX_Somatic_Mutations',CopyNumber='PDX_CNV',Proteomics='PDX_Proteomics') + dplyr::select(improve_sample_id,common_name,model_type,RNASeq='PDX_RNASeq',Mutations='PDX_Somatic_Mutations',CopyNumber='PDX_CNV',Proteomics='PDX_Proteomics')|> + subset(!is.na(improve_sample_id) tumor_data<- manifest|>dplyr::select(common_name,starts_with("Tumor"))|> left_join(tumor_samps)|> dplyr::select(improve_sample_id,common_name,model_type,RNASeq='Tumor_RNASeq',Mutations='Tumor_Somatic_Mutations',CopyNumber='Tumor_CNV')|> - mutate(Proteomics='') ##we dont have tumor proteomics from these samples + mutate(Proteomics='')|> + subset(!is.na(improve_sample_id) + ##we dont have tumor proteomics from these samples #print(tumor_data) mt_data<- manifest|>dplyr::select(common_name,starts_with("PDX"))|> left_join(mt_samps)|> - dplyr::select(improve_sample_id,common_name,model_type, RNASeq='PDX_RNASeq',Mutations='PDX_Somatic_Mutations',CopyNumber='PDX_CNV',Proteomics='PDX_Proteomics')##we dont have mt data yet, so collecting PDX instead + dplyr::select(improve_sample_id,common_name,model_type, RNASeq='PDX_RNASeq',Mutations='PDX_Somatic_Mutations',CopyNumber='PDX_CNV',Proteomics='PDX_Proteomics')|>##we dont have mt data yet, so collecting PDX instead + subset(!is.na(improve_sample_id) #print(tumor_data) -combined<-rbind(pdx_data,tumor_data)|>distinct() +combined<-rbind(pdx_data,tumor_data,mt_data)|>distinct() # gene mapping table genes_df <- fread(genefile) From 56b8ea89ed630e84c2167f2cc963e2b8410c1895 Mon Sep 17 00:00:00 2001 From: Jeremy Date: Fri, 6 Dec 2024 11:08:32 -0800 Subject: [PATCH 16/17] fixed float to int --- build/beatAML/GetBeatAML.py | 5 +++++ build/cptac/getCptacData.py | 4 ++++ 2 files changed, 9 insertions(+) diff --git a/build/beatAML/GetBeatAML.py b/build/beatAML/GetBeatAML.py index 5bf94233..9a1a55b1 100755 --- a/build/beatAML/GetBeatAML.py +++ b/build/beatAML/GetBeatAML.py @@ -466,6 +466,11 @@ def map_and_combine(df, data_type, entrez_map_file, improve_map_file, map_file=N right_on='other_id', how='left') mapped_df.insert(0, 'improve_sample_id', mapped_df.pop('improve_sample_id')) + + print(mapped_df.to_string()) + mapped_df['improve_sample_id'] = mapped_df['improve_sample_id'].astype(int) + mapped_df['entrez_id'] = mapped_df['entrez_id'].fillna(0) + mapped_df['entrez_id'] = mapped_df['entrez_id'].astype(int) mapped_df['source'] = 'synapse' mapped_df['study'] = 'BeatAML' diff --git a/build/cptac/getCptacData.py b/build/cptac/getCptacData.py index 527ff700..c3c401a2 100755 --- a/build/cptac/getCptacData.py +++ b/build/cptac/getCptacData.py @@ -380,11 +380,15 @@ def main(): dat_files[dtype_key] = fdf2 else: dat_files[dtype_key] = fdf.dropna() + print(dtype_key) # Now concatenate all the cancers into a single file for dtype_key, df in dat_files.items(): print('Saving ' + "cptac_" + dtype_key + '.csv.gz' + ' file') + print(df.to_string()) + df['entrez_id'] = df['entrez_id'].fillna(0) + df['entrez_id'] = df['entrez_id'].astype(int) df.to_csv("/tmp/" + "cptac_" + dtype_key + '.csv.gz', sep=',', index=False, compression='gzip') if __name__ == '__main__': From 76be15170c787aefc76b88600771c21fca90942d Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Fri, 6 Dec 2024 12:02:40 -0800 Subject: [PATCH 17/17] final change --- build/mpnst/01_mpnst_get_omics.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/build/mpnst/01_mpnst_get_omics.R b/build/mpnst/01_mpnst_get_omics.R index b12d3335..a1276eff 100755 --- a/build/mpnst/01_mpnst_get_omics.R +++ b/build/mpnst/01_mpnst_get_omics.R @@ -47,20 +47,20 @@ manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|> pdx_data<-manifest|>dplyr::select(common_name,starts_with("PDX"))|> left_join(pdx_samps)|> dplyr::select(improve_sample_id,common_name,model_type,RNASeq='PDX_RNASeq',Mutations='PDX_Somatic_Mutations',CopyNumber='PDX_CNV',Proteomics='PDX_Proteomics')|> - subset(!is.na(improve_sample_id) + subset(!is.na(improve_sample_id)) tumor_data<- manifest|>dplyr::select(common_name,starts_with("Tumor"))|> left_join(tumor_samps)|> dplyr::select(improve_sample_id,common_name,model_type,RNASeq='Tumor_RNASeq',Mutations='Tumor_Somatic_Mutations',CopyNumber='Tumor_CNV')|> mutate(Proteomics='')|> - subset(!is.na(improve_sample_id) + subset(!is.na(improve_sample_id)) ##we dont have tumor proteomics from these samples #print(tumor_data) mt_data<- manifest|>dplyr::select(common_name,starts_with("PDX"))|> left_join(mt_samps)|> dplyr::select(improve_sample_id,common_name,model_type, RNASeq='PDX_RNASeq',Mutations='PDX_Somatic_Mutations',CopyNumber='PDX_CNV',Proteomics='PDX_Proteomics')|>##we dont have mt data yet, so collecting PDX instead - subset(!is.na(improve_sample_id) + subset(!is.na(improve_sample_id)) #print(tumor_data)