bioconductor updated yet neoflow keeps showing update error

[jiwonhong95]

I have been trying the 2. Variant peptide identification step with my own data and I keep getting the error that bioconductor is not updated which I already have along with R.

When I check R, it runs in the version of R version 4.2.1 (2022-06-23) and Bioconductor is in the version of 3.15. > library(BiocManager) Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)

The error occurs in the last process and there were no issues during the example file run: Below, I have attached the full error message once the command was executed:

_[69/78f93c] process > msms_searching (PDAC102076... [100%] 24 of 24, cached:... [5c/bcddea] process > calculate_fdr (calculate_fdr) [100%] 1 of 1, cached: 1 ✔ [c8/3a5f19] process > prepare_pepquery_input (prep... [100%] 1 of 1, cached: 1 ✔ [55/8df182] process > run_pepquery (run_pepquery) [100%] 1 of 1, cached: 1 ✔ [55/4a2849] process > add_pepquery_validation (add... [100%] 1 of 1, failed: 1 ✘ Error executing process > 'add_pepquery_validation (add_pepquery_validation)'

Caused by: Process add_pepquery_validation (add_pepquery_validation) terminated with an error exit status (1)

Command executed:

!/usr/bin/env /usr/local/bin/Rscript

 library(dplyr)
 library(readr)
 library(stringr)

 psms <- read_tsv("novel_peptides_psm.tsv")

 psm_rank_file = "pepquery/psm_rank.txt"
 if(file.exists(psm_rank_file)){
     psm_rank <- read_tsv(psm_rank_file)

if("n_ptm" %in% names(psm_rank)){ psm_rank <- psm_rank %>% filter(pvalue<=0.01,n_ptm==0,rank==1) psms$pepquery <- ifelse(psms$peptide %in% psm_rank$peptide,1,0) }else{ psms$pepquery <- 0 } }else{ psms$pepquery <- 0 } psms %>% write_tsv("novel_peptides_psm_pepquery.tsv")

Command exit status: 1

Command output: (empty)

Command error: Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for help Bioconductor version '3.10' is out-of-date; the current release version '3.15' is available with R version '4.2'; see https://bioconductor.org/install

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

  filter, lag

The following objects are masked from ‘package:base’:

  intersect, setdiff, setequal, union

Parsed with column specification: cols( index = col_character(), evalue = col_character(), ion_score = col_character(), charge = col_character(), mass = col_character(), mz = col_character(), delta_da = col_character(), delta_ppm = col_character(), peptide = col_character(), isdecoy = col_character(), miss = col_character(), protein = col_character(), position = col_character(), rt = col_character(), isSAP = col_character(), mods = col_character(), FDR = col_character(), Qvalue = col_character(), is_novel = col_character() ) Error in $<-.data.frame(*tmp*, pepquery, value = 0) : replacement has 1 row, data has 0 Calls: $<- -> $<-.data.frame Execution halted

Would there be anything I may be missing?

Thank you again in advance

[wenbostar]

The error is not due to bioconductor version. Is that possible to share the input data and the command line you used for this step?

[jiwonhong95]

Yes will do Thank you. I have emailed you via your @bcm.edu email for the data as there were some data that we wish to stay confidential.

Thank you for your understanding

[wenbostar]

No problem.