* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mpwR.Rcheck’ * using R Under development (unstable) (2025-02-23 r87804) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘mpwR/DESCRIPTION’ ... OK * this is package ‘mpwR’ version ‘0.1.5’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘mpwR’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/mpwR-00install.html' for details. * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [1s/2s] OK * checking whether the package can be unloaded cleanly ... [1s/3s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/2s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [19s/27s] OK * checking Rd files ... [0s/1s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [8s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [33s/46s] ERROR Running ‘testthat.R’ [32s/45s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(mpwR) > > test_check("mpwR") For DIA-NN no quantitative LFQ data on peptide-level. For PD no quantitative LFQ data on peptide-level. For DIA-NN no quantitative LFQ data on peptide-level. For PD no quantitative LFQ data on proteingroup-level. Protein-level not available for Spectronaut. For MaxQuant evidence.txt - the following column need to be present: Raw file For MaxQuant evidence.txt - the following column need to be present: Proteins For MaxQuant evidence.txt - the following column need to be present: Modified sequence For MaxQuant evidence.txt - the following column need to be present: Sequence For MaxQuant evidence.txt - the following column need to be present: Missed cleavages For MaxQuant evidence.txt - the following column need to be present: Charge For MaxQuant evidence.txt - the following column need to be present: Retention time For MaxQuant evidence.txt - the following column need to be present: Potential contaminant For MaxQuant evidence.txt - the following column need to be present: Reverse For DIA-NN input - the following column need to be present: Run For DIA-NN input - the following column need to be present: Protein.Group For DIA-NN input - the following column need to be present: Protein.Ids For DIA-NN input - the following column need to be present: Modified.Sequence For DIA-NN input - the following column need to be present: Stripped.Sequence For DIA-NN input - the following column need to be present: Precursor.Id For DIA-NN input - the following column need to be present: Precursor.Charge For DIA-NN input - the following column need to be present: RT For DIA-NN input - the following column need to be present: PG.MaxLFQ For DIA-NN input - the following column need to be present: Run For DIA-NN input - the following column need to be present: Protein.Group For DIA-NN input - the following column need to be present: Protein.Ids For DIA-NN input - the following column need to be present: Modified.Sequence For DIA-NN input - the following column need to be present: Stripped.Sequence For DIA-NN input - the following column need to be present: Precursor.Id For DIA-NN input - the following column need to be present: Precursor.Charge For DIA-NN input - the following column need to be present: RT For DIA-NN input - the following column need to be present: PG.MaxLFQ For PD PSMs.txt - the following column need to be present: Confidence For PD PSMs.txt - the following column need to be present: Spectrum File For PD PSMs.txt - the following column need to be present: Protein Accessions For PD PSMs.txt - the following column need to be present: Annotated Sequence For PD PSMs.txt - the following column need to be present: Modifications For PD PSMs.txt - the following column need to be present: Number of Missed Cleavages For PD PSMs.txt - the following column need to be present: Charge For PD PSMs.txt - the following column need to be present: RT in min For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample For PD PeptideGroups.txt - the following column need to be present: Number of Protein Groups For PD PeptideGroups.txt - the following column need to be present: Number of Proteins For PD PeptideGroups.txt - the following column need to be present: Number of PSMs For PD PeptideGroups.txt - the following column need to be present: Confidence For PD PeptideGroups.txt - the following column need to be present: Sequence For PD PeptideGroups.txt - the following column need to be present: Modifications For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages For PD PeptideGroups.txt - the following column(s) need to be present: Found in Sample For PD PeptideGroups.txt - the following column need to be present: Number of Protein Groups For PD PeptideGroups.txt - the following column need to be present: Number of Proteins For PD PeptideGroups.txt - the following column need to be present: Number of PSMs For PD PeptideGroups.txt - the following column need to be present: Confidence For PD PeptideGroups.txt - the following column need to be present: Sequence For PD PeptideGroups.txt - the following column need to be present: Modifications For PD PeptideGroups.txt - the following column need to be present: Number of Missed Cleavages For PD Proteins.txt - the following column(s) need to be present: Found in Sample For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID For PD Proteins.txt - the following column need to be present: Accession For PD Proteins.txt - the following column need to be present: Description For PD Proteins.txt - the following column(s) need to be present: Found in Sample For PD Proteins.txt - the following column need to be present: Proteins Unique Sequence ID For PD Proteins.txt - the following column need to be present: Accession For PD Proteins.txt - the following column need to be present: Description For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID For PD ProteinGroups.txt - the following column need to be present: Group Description For PD ProteinGroups.txt - the following column need to be present: Number of Proteins For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides For PD ProteinGroups.txt - the following column(s) need to be present: Found in Sample For PD ProteinGroups.txt - the following column need to be present: Protein Groups Protein Group ID For PD ProteinGroups.txt - the following column need to be present: Group Description For PD ProteinGroups.txt - the following column need to be present: Number of Proteins For PD ProteinGroups.txt - the following column need to be present: Number of Unique Peptides For plotting density: CV_Retention.time_mpwR is not detected in submitted data. For plotting density: CV_Peptide_LFQ_mpwR is not detected in submitted data. For plotting density: CV_ProteinGroup_LFQ_mpwR is not detected in submitted data. For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation. For plotting stacked barplot: Only NA detected for Protein.IDs! Not included in vizualisation. For plotting barplot: Only NA detected for Protein.IDs! Not included in vizualisation. For plotting boxplot: Only NA detected for Protein.IDs! Not included in vizualisation. [ FAIL 1 | WARN 123 | SKIP 0 | PASS 633 ] â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• ── Error ('test_utils_helpers.R:691:4'): prepare_Upset works ─────────────────── Error in `unlist(., .data, use.names = FALSE)`: 'recursive' must be a length-1 vector Backtrace: â–† 1. ├─mpwR:::prepare_Upset(...) at test_utils_helpers.R:691:4 2. │ └─flowTraceR::convert_proteingroups(input_df = input_df, software = software) 3. │ └─flowTraceR:::sort_string_pg(...) 4. │ └─input_df %>% dplyr::select(!!as.symbol(sort_column)) %>% ... 5. └─base::unlist(., .data, use.names = FALSE) [ FAIL 1 | WARN 123 | SKIP 0 | PASS 633 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [25s/36s] OK * checking PDF version of manual ... [5s/8s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR