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This page was generated on 2025-08-04 11:44 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1385/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsPTM 2.10.1  (landing page)
Devon Kohler
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/MSstatsPTM
git_branch: RELEASE_3_21
git_last_commit: 1171519
git_last_commit_date: 2025-07-11 19:13:47 -0400 (Fri, 11 Jul 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for MSstatsPTM on merida1

To the developers/maintainers of the MSstatsPTM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsPTM.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MSstatsPTM
Version: 2.10.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsPTM_2.10.1.tar.gz
StartedAt: 2025-08-01 06:52:10 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 06:57:36 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 325.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: MSstatsPTM.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsPTM_2.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MSstatsPTM.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsPTM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsPTM’ version ‘2.10.1’
* 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 hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsPTM’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘MSstats:::.getMedianSigmaSubject’ ‘MSstats:::.getVarComponent’
  ‘MSstatsConvert:::.filterFewMeasurements’
  ‘MSstatsConvert:::.filterManyColumns’
  ‘MSstatsConvert:::.getChannelColumns’
  ‘MSstatsConvert:::.standardizeColnames’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.extract_pd_mods: no visible binding for global variable
  ‘..sequence_col’
.format.data.process.plots: no visible binding for global variable
  ‘ABUNDANCE’
.pivotPS: no visible binding for global variable ‘..keep_cols’
.plot.model.volcano: no visible binding for global variable
  ‘text.angle’
.progensis.add.sites: no visible binding for global variable
  ‘..col_order’
.qc.all.plot.lf: no visible binding for global variable ‘text.angle’
.qc.single.plot.lf: no visible binding for global variable ‘text.angle’
.removeCutoffSites: no visible binding for global variable
  ‘..mod_pep_col’
.rmConfounded: no visible binding for global variable ‘..col_res’
DIANNtoMSstatsPTMFormat: no visible binding for global variable
  ‘..protein_id_col’
FragPipetoMSstatsPTMFormat: no visible binding for global variable
  ‘..msstats_cols’
MSstatsPTMSiteLocator: no visible binding for global variable
  ‘..mod_pep_col’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  ‘TMT.keyword’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  ‘ptm.keyword’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  ‘mod.num’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  ‘which.proteinid.ptm’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  ‘PeptideSequence’
MetamorpheusToMSstatsPTMFormat: no visible binding for global variable
  ‘..protein_id_col’
PStoMSstatsPTMFormat: no visible binding for global variable
  ‘Intensity’
ProgenesistoMSstatsPTMFormat: no visible binding for global variable
  ‘Type’
SkylinetoMSstatsPTMFormat: no visible binding for global variable
  ‘annotation_prot’
dataProcessPlotsPTM: no visible binding for global variable
  ‘PROTEINNAME’
dataProcessPlotsPTM: no visible binding for global variable
  ‘GLOBALPROTEIN’
dataSummarizationPTM: no visible binding for global variable ‘address’
locatePTM: no visible binding for global variable ‘..col_seq’
locatePTM: no visible binding for global variable ‘..col_fasta’
Undefined global functions or variables:
  ..col_fasta ..col_order ..col_res ..col_seq ..keep_cols ..mod_pep_col
  ..msstats_cols ..protein_id_col ..sequence_col ABUNDANCE
  GLOBALPROTEIN Intensity PROTEINNAME PeptideSequence TMT.keyword Type
  address annotation_prot mod.num ptm.keyword text.angle
  which.proteinid.ptm
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'dot-fixTerminus.Rd':
  ‘fasta_file’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MSstatsPTM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MetamorpheusToMSstatsPTMFormat
> ### Title: Import Metamorpheus files into PTM format
> ### Aliases: MetamorpheusToMSstatsPTMFormat
> 
> ### ** Examples
> 
> input = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv", 
+                                 package = "MSstatsPTM")
> input = data.table::fread(input)
> annot = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv", 
+                                 package = "MSstatsPTM")
> annot = data.table::fread(annot)
> input_protein = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaksGlobalProteome.tsv",
+                                 package = "MSstatsPTM")
> input_protein = data.table::fread(input_protein)
> annot_protein = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesignGlobalProteome.tsv", 
+                                 package = "MSstatsPTM")
> annot_protein = data.table::fread(annot_protein)
> fasta_path=system.file("extdata", "metamorpheus_fasta.fasta", 
+                                 package="MSstatsPTM")
> metamorpheus_imported = MetamorpheusToMSstatsPTMFormat(
+     input, 
+     annot, 
+     fasta_path=fasta_path,
+     input_protein=input_protein,
+     annotation_protein=annot_protein,
+     use_unmod_peptides=FALSE,
+     mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
+ )
[1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications."
Error in MSstatsConvert::MSstatsLogsSettings(use_log_file, append, verbose,  : 
  Assertion on 'append' failed: Must be of type 'logical', not 'NULL'.
Calls: MetamorpheusToMSstatsPTMFormat ... <Anonymous> -> <Anonymous> -> makeAssertion -> mstop
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
  Running ‘tinytest.R’
 ERROR
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  test_converters.R.............   50 tests OK 
  test_converters.R.............   50 tests OK 
  test_converters.R.............   50 tests OK 
  test_converters.R.............   50 tests OK 
  test_converters.R.............   50 tests OK 
  test_converters.R.............   51 tests 1 fails 
  test_converters.R.............   52 tests 2 fails 
  test_converters.R.............   53 tests 3 fails 
  test_converters.R.............   54 tests 3 fails 
  test_converters.R.............   55 tests 3 fails [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications."
  Error in MSstatsConvert::MSstatsLogsSettings(use_log_file, append, verbose,  : 
    Assertion on 'append' failed: Must be of type 'logical', not 'NULL'.
  Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> makeAssertion -> mstop
  In addition: There were 50 or more warnings (use warnings() to see the first 50)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/MSstatsPTM.Rcheck/00check.log’
for details.


Installation output

MSstatsPTM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstatsPTM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘MSstatsPTM’ ...
** this is package ‘MSstatsPTM’ version ‘2.10.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c model_adjustment.cpp -o model_adjustment.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o MSstatsPTM.so RcppExports.o model_adjustment.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-MSstatsPTM/00new/MSstatsPTM/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstatsPTM)

Tests output

MSstatsPTM.Rcheck/tests/testthat.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(mockery)
> library(MSstatsPTM)
> 
> test_check("MSstatsPTM")
Drew the Quality Contol plot(boxplot) for all ptms/proteins.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
 12.760   0.836  13.870 

MSstatsPTM.Rcheck/tests/tinytest.Rout.fail


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+   tinytest::test_package("MSstatsPTM")
+ }

test_converters.R.............    0 tests    
test_converters.R.............    0 tests    
test_converters.R.............    0 tests    
test_converters.R.............    0 tests    
test_converters.R.............    0 tests    
test_converters.R.............    1 tests OK 
test_converters.R.............    2 tests OK 
test_converters.R.............    3 tests OK 
test_converters.R.............    4 tests OK 
test_converters.R.............    5 tests OK INFO  [2025-08-01 06:57:00] ** Raw data from MaxQuant imported successfully.
INFO  [2025-08-01 06:57:00] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-08-01 06:57:00] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-08-01 06:57:00] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-08-01 06:57:00] ** Using provided annotation.
INFO  [2025-08-01 06:57:00] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-01 06:57:00] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements within each run will be kept.
INFO  [2025-08-01 06:57:00] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-08-01 06:57:00] ** Shared peptides are removed.
INFO  [2025-08-01 06:57:00] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-08-01 06:57:00] ** PSMs have been aggregated to peptide ions.
INFO  [2025-08-01 06:57:00] ** Run annotation merged with quantification data.
INFO  [2025-08-01 06:57:00] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-08-01 06:57:00] ** Fractionation handled.
INFO  [2025-08-01 06:57:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-01 06:57:00] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.

test_converters.R.............    5 tests OK 
test_converters.R.............    7 tests OK 
test_converters.R.............    8 tests OK 
test_converters.R.............    9 tests OK 
test_converters.R.............   10 tests OK 
test_converters.R.............   11 tests OK 
test_converters.R.............   12 tests OK 
test_converters.R.............   12 tests OK 
test_converters.R.............   12 tests OK 
test_converters.R.............   13 tests OK 
test_converters.R.............   14 tests OK 
test_converters.R.............   15 tests OK 
test_converters.R.............   16 tests OK 
test_converters.R.............   17 tests OK INFO  [2025-08-01 06:57:01] ** Raw data from MaxQuant imported successfully.
INFO  [2025-08-01 06:57:01] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-08-01 06:57:01] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-08-01 06:57:01] ** Using provided annotation.
INFO  [2025-08-01 06:57:01] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-01 06:57:01] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-08-01 06:57:01] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-01 06:57:01] ** Shared peptides are removed.
INFO  [2025-08-01 06:57:01] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-01 06:57:01] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:01] ** Run annotation merged with quantification data.
INFO  [2025-08-01 06:57:01] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:01] ** Fractionation handled.
INFO  [2025-08-01 06:57:01] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-01 06:57:01] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   17 tests OK 
test_converters.R.............   19 tests OK 
test_converters.R.............   20 tests OK 
test_converters.R.............   21 tests OK 
test_converters.R.............   22 tests OK 
test_converters.R.............   23 tests OK 
test_converters.R.............   24 tests OK 
test_converters.R.............   24 tests OK 
test_converters.R.............   24 tests OK 
test_converters.R.............   25 tests OK 
test_converters.R.............   26 tests OK 
test_converters.R.............   27 tests OK 
test_converters.R.............   28 tests OK INFO  [2025-08-01 06:57:07] ** Raw data from Spectronaut imported successfully.
INFO  [2025-08-01 06:57:07] ** Raw data from Spectronaut cleaned successfully.
INFO  [2025-08-01 06:57:07] ** Using provided annotation.
INFO  [2025-08-01 06:57:07] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-01 06:57:07] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
WARN  [2025-08-01 06:57:07] ** PGQvalue not found in input columns.
WARN  [2025-08-01 06:57:07] ** EGQvalue not found in input columns.
INFO  [2025-08-01 06:57:07] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-01 06:57:07] ** Shared peptides are removed.
INFO  [2025-08-01 06:57:07] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-01 06:57:07] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:07] ** Run annotation merged with quantification data.
INFO  [2025-08-01 06:57:07] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:07] ** Fractionation handled.
INFO  [2025-08-01 06:57:07] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-01 06:57:07] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   28 tests OK 
test_converters.R.............   30 tests OK 
test_converters.R.............   31 tests OK 
test_converters.R.............   32 tests OK 
test_converters.R.............   33 tests OK 
test_converters.R.............   34 tests OK 
test_converters.R.............   35 tests OK 
test_converters.R.............   35 tests OK 
test_converters.R.............   35 tests OK 
test_converters.R.............   35 tests OK INFO  [2025-08-01 06:57:09] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-01 06:57:09] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-01 06:57:09] ** Using provided annotation.
INFO  [2025-08-01 06:57:09] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-01 06:57:09] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-08-01 06:57:09] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-01 06:57:09] ** Shared peptides are removed.
INFO  [2025-08-01 06:57:09] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-01 06:57:09] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:09] ** Run annotation merged with quantification data.
INFO  [2025-08-01 06:57:09] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:09] ** Fractionation handled.
INFO  [2025-08-01 06:57:09] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-01 06:57:09] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   36 tests OK INFO: Extracting modifications
INFO  [2025-08-01 06:57:11] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-01 06:57:11] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-01 06:57:11] ** Using provided annotation.
INFO  [2025-08-01 06:57:11] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-01 06:57:11] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-08-01 06:57:11] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-01 06:57:11] ** Shared peptides are removed.
INFO  [2025-08-01 06:57:11] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-01 06:57:12] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:12] ** Run annotation merged with quantification data.
INFO  [2025-08-01 06:57:12] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:12] ** Fractionation handled.
INFO  [2025-08-01 06:57:12] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-01 06:57:12] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   37 tests OK INFO: Extracting modifications
INFO  [2025-08-01 06:57:14] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-01 06:57:14] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-01 06:57:14] ** Using provided annotation.
INFO  [2025-08-01 06:57:14] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-01 06:57:14] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-08-01 06:57:14] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-01 06:57:14] ** Shared peptides are removed.
INFO  [2025-08-01 06:57:14] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-01 06:57:14] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:14] ** Run annotation merged with quantification data.
INFO  [2025-08-01 06:57:14] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:14] ** Fractionation handled.
INFO  [2025-08-01 06:57:14] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-01 06:57:14] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   38 tests OK INFO  [2025-08-01 06:57:16] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-01 06:57:16] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-01 06:57:16] ** Using provided annotation.
INFO  [2025-08-01 06:57:16] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-01 06:57:16] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-08-01 06:57:16] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-01 06:57:16] ** Shared peptides are removed.
INFO  [2025-08-01 06:57:16] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-01 06:57:16] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:16] ** Run annotation merged with quantification data.
INFO  [2025-08-01 06:57:16] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:16] ** Fractionation handled.
INFO  [2025-08-01 06:57:16] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-01 06:57:16] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   39 tests OK 
test_converters.R.............   40 tests OK INFO  [2025-08-01 06:57:19] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-01 06:57:19] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-01 06:57:19] ** Using provided annotation.
INFO  [2025-08-01 06:57:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-01 06:57:19] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2025-08-01 06:57:19] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-01 06:57:19] ** Shared peptides are removed.
INFO  [2025-08-01 06:57:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-01 06:57:19] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:19] ** Run annotation merged with quantification data.
INFO  [2025-08-01 06:57:19] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-01 06:57:19] ** Fractionation handled.
INFO  [2025-08-01 06:57:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-01 06:57:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   41 tests OK 
test_converters.R.............   42 tests OK 
test_converters.R.............   43 tests OK 
test_converters.R.............   43 tests OK 
test_converters.R.............   43 tests OK 
test_converters.R.............   43 tests OK 
test_converters.R.............   43 tests OK 
test_converters.R.............   43 tests OK 
test_converters.R.............   43 tests OK 
test_converters.R.............   43 tests OK 
test_converters.R.............   43 tests OK 
test_converters.R.............   43 tests OK INFO: Extracting modifications
INFO  [2025-08-01 06:57:19] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-01 06:57:19] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-01 06:57:19] ** Using provided annotation.
INFO  [2025-08-01 06:57:19] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-01 06:57:19] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements within each run will be removed.
INFO  [2025-08-01 06:57:19] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-08-01 06:57:19] ** Shared peptides are removed.
INFO  [2025-08-01 06:57:19] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-08-01 06:57:19] ** PSMs have been aggregated to peptide ions.
INFO  [2025-08-01 06:57:19] ** Run annotation merged with quantification data.
INFO  [2025-08-01 06:57:19] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-08-01 06:57:19] ** Fractionation handled.
INFO  [2025-08-01 06:57:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-01 06:57:19] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO  [2025-08-01 06:57:19] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-01 06:57:19] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-01 06:57:19] ** Using provided annotation.
INFO  [2025-08-01 06:57:19] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-01 06:57:19] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements within each run will be removed.
INFO  [2025-08-01 06:57:19] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-08-01 06:57:19] ** Shared peptides are removed.
INFO  [2025-08-01 06:57:19] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-08-01 06:57:19] ** PSMs have been aggregated to peptide ions.
INFO  [2025-08-01 06:57:19] ** Run annotation merged with quantification data.
INFO  [2025-08-01 06:57:19] ** For peptides overlapped between fractions of mixture1_1 use the fraction with maximal average abundance.
INFO  [2025-08-01 06:57:19] ** Fractions belonging to same mixture have been combined.
INFO  [2025-08-01 06:57:19] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-08-01 06:57:19] ** Fractionation handled.
INFO  [2025-08-01 06:57:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-01 06:57:19] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.

test_converters.R.............   43 tests OK 
test_converters.R.............   45 tests OK 
test_converters.R.............   46 tests OK 
test_converters.R.............   47 tests OK 
test_converters.R.............   48 tests OK 
test_converters.R.............   49 tests OK 
test_converters.R.............   50 tests OK 
test_converters.R.............   50 tests OK 
test_converters.R.............   50 tests OK 
test_converters.R.............   50 tests OK 
test_converters.R.............   50 tests OK 
test_converters.R.............   50 tests OK 
test_converters.R.............   50 tests OK 
test_converters.R.............   50 tests OK 
test_converters.R.............   50 tests OK 
test_converters.R.............   50 tests OK 
test_converters.R.............   51 tests 1 fails 
test_converters.R.............   52 tests 2 fails 
test_converters.R.............   53 tests 3 fails 
test_converters.R.............   54 tests 3 fails 
test_converters.R.............   55 tests 3 fails [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications."
Error in MSstatsConvert::MSstatsLogsSettings(use_log_file, append, verbose,  : 
  Assertion on 'append' failed: Must be of type 'logical', not 'NULL'.
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> makeAssertion -> mstop
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

Example timings

MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings

nameusersystemelapsed
DIANNtoMSstatsPTMFormat0.0000.0010.001
FragPipetoMSstatsPTMFormat1.8450.0632.051
MSstatsPTMSiteLocator000
MaxQtoMSstatsPTMFormat0.8630.0730.990