- 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 the install log 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 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── 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:
▆
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