Problem with R version 4.2 #25
Description
I just updated R today to version 4.2 and I am trying to use the same script that I used before with the previous R version and the same excel file. When I want to use notame and import data I obtain the following error:
data_B11_notameA <- read_from_excel(file = "C:/Users/Usuario/Desktop/dataJhn_notame.xlsx", sheet = 1,
-
corner_row = 6, corner_column = "E", -
split_by = c("Column", "Ion Mode"))
INFO [2022-09-20 16:29:36] Corner detected correctly at row 6, column E
INFO [2022-09-20 16:29:36]
Extracting sample information from rows 1 to 6 and columns F to DK
INFO [2022-09-20 16:29:36] Replacing spaces in sample information column names with underscores ()
INFO [2022-09-20 16:29:36] Naming the last column of sample information "Datafile"
INFO [2022-09-20 16:29:36]
Extracting feature information from rows 7 to 1863 and columns A to E
INFO [2022-09-20 16:29:36] Creating Split column from Column, Ion Mode
INFO [2022-09-20 16:29:36] Feature_ID column not found, creating feature IDs
INFO [2022-09-20 16:29:36] Identified m/z column Mass and retention time column RT
INFO [2022-09-20 16:29:36] Creating feature IDs from Split, m/z and retention time
INFO [2022-09-20 16:29:36] Replacing dots (.) in feature information column names with underscores ()
INFO [2022-09-20 16:29:36]
Extracting feature abundances from rows 7 to 1863 and columns F to DK
INFO [2022-09-20 16:29:36]
Checking sample information
INFO [2022-09-20 16:29:36] Checking that feature abundances only contain numeric values
INFO [2022-09-20 16:29:36]
Checking feature information
INFO [2022-09-20 16:29:36] Checking that feature IDs are unique and not stored as numbers
INFO [2022-09-20 16:29:36] Checking that m/z and retention time values are reasonable
Error in check_feature_data(feature_data, mz_limits = mz_limits, rt_limits = rt_limits, :
Values in m/z or retention time columns are outside limits.
I have used the "skip_checks" but I have the same problem when I want to create the metaboset.
data_Jhn_Group_Filtered_notame <- construct_metabosets(exprs = data_Jhn_Group_Filtered$exprs, pheno_data = data_Jhn_Group_Filtered$pheno_data,
-
feature_data = data_Jhn_Group_Filtered$feature_data, -
group_col = "Group", time_col = "Time", subject_col ="Sample_name")
Initializing the object(s) with unflagged features
Error in check_feature_data(feature_data) :
Values in m/z or retention time columns are outside limits.