RuleException during execution of snakemake

[LucaCappelletti94]

During the execution of snakemake, after having fixed all the errors of the previous issue, I now receive this error:

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	all
	1	append_sequence
	1	create_design_matrix
	1	create_extended_design_matrix
	1	process_raw_data
	20	train_exclude_features
	12	train_predictive_models
	37

[Fri Nov  2 19:18:36 2018]
rule process_raw_data:
    input: data/eclip/raw/metadata.tsv, fasta/gencode.v25.annotation.gtf.rds, fasta/GRCh38.p7.genome.fa, Scripts/RBP/Eclip/0_match_peaks_genes.R
    output: data/eclip/processed/protein_peak_overlaps.rds, data/eclip/processed/peak_center-gene_mapping.rds
    jobid: 36

Loading packages and configuration from src/r/config.R...
Error in library(tictoc) : there is no package called 'tictoc'
Calls: suppressMessages ... withCallingHandlers -> source -> withVisible -> eval -> eval -> library
Execution halted
[Fri Nov  2 19:18:37 2018]
Error in rule process_raw_data:
    jobid: 36
    output: data/eclip/processed/protein_peak_overlaps.rds, data/eclip/processed/peak_center-gene_mapping.rds

RuleException:
CalledProcessError in line 58 of /data/Avsec/Manuscript_Avsec_Bioinformatics_2017/Scripts/RBP/Eclip/Snakefile:
Command ' set -euo pipefail;  Rscript /data/Avsec/Manuscript_Avsec_Bioinformatics_2017/.snakemake/scripts/tmpgvq7njle.0_match_peaks_genes.R ' returned non-zero exit status 1.
  File "/data/Avsec/Manuscript_Avsec_Bioinformatics_2017/Scripts/RBP/Eclip/Snakefile", line 58, in __rule_process_raw_data
  File "/usr/local/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

What can I do to proceed? Thank you.

[Avsecz]

You are missing the tictic R package. You can install it with install.packages('tictoc')

https://cran.r-project.org/package=tictoc

[LucaCappelletti94]

Is there a list of required R packages?

[Avsecz]

https://github.com/gagneurlab/Manuscript_Avsec_Bioinformatics_2017#r

[LucaCappelletti94]

I thought I had it installed, but now I can see that when I try to install it I get the following error:

Loading packages and configuration from src/r/config.R...
Error in library(tictoc) : there is no package called 'tictoc'
Calls: suppressMessages ... withCallingHandlers -> source -> withVisible -> eval -> eval -> library
Execution halted

Do you now what can be done of it? Thanks!

[Avsecz]

you should make sure all the packages are installed before starting R from the root of the repo. Start R with R --vanilla and then install the packages. This will prevent loading the .Rprofile