##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MSstatsPTM_2.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MSstatsPTM.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 loading without being on the library search path ... 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MSstatsPTM.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL MSstatsPTM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘MSstatsPTM’ ...
** this is package ‘MSstatsPTM’ version ‘2.10.1’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c model_adjustment.cpp -o model_adjustment.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o MSstatsPTM.so RcppExports.o model_adjustment.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-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)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
  7.568   0.364   7.939 

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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  [2025-08-19 11:45:28] ** Raw data from MaxQuant imported successfully.
INFO  [2025-08-19 11:45:28] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-08-19 11:45:28] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-08-19 11:45:28] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-08-19 11:45:28] ** Using provided annotation.
INFO  [2025-08-19 11:45:28] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-19 11:45:28] ** 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  [2025-08-19 11:45:28] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-08-19 11:45:28] ** Shared peptides are removed.
INFO  [2025-08-19 11:45:28] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-08-19 11:45:28] ** PSMs have been aggregated to peptide ions.
INFO  [2025-08-19 11:45:28] ** Run annotation merged with quantification data.
INFO  [2025-08-19 11:45:28] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-08-19 11:45:28] ** Fractionation handled.
INFO  [2025-08-19 11:45:28] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-19 11:45:28] ** 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  [2025-08-19 11:45:28] ** Raw data from MaxQuant imported successfully.
INFO  [2025-08-19 11:45:28] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2025-08-19 11:45:28] ** Rows with values of Reverse equal to + are removed 
INFO  [2025-08-19 11:45:28] ** Using provided annotation.
INFO  [2025-08-19 11:45:28] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-19 11:45:28] ** 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  [2025-08-19 11:45:28] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-19 11:45:28] ** Shared peptides are removed.
INFO  [2025-08-19 11:45:28] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-19 11:45:28] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:28] ** Run annotation merged with quantification data.
INFO  [2025-08-19 11:45:28] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:28] ** Fractionation handled.
INFO  [2025-08-19 11:45:28] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-19 11:45:28] ** 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  [2025-08-19 11:45:31] ** Raw data from Spectronaut imported successfully.
INFO  [2025-08-19 11:45:31] ** Raw data from Spectronaut cleaned successfully.
INFO  [2025-08-19 11:45:31] ** Using provided annotation.
INFO  [2025-08-19 11:45:31] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-19 11:45:31] ** 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  [2025-08-19 11:45:31] ** PGQvalue not found in input columns.
WARN  [2025-08-19 11:45:31] ** EGQvalue not found in input columns.
INFO  [2025-08-19 11:45:31] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-19 11:45:31] ** Shared peptides are removed.
INFO  [2025-08-19 11:45:31] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-19 11:45:31] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:31] ** Run annotation merged with quantification data.
INFO  [2025-08-19 11:45:31] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:31] ** Fractionation handled.
INFO  [2025-08-19 11:45:32] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-19 11:45:32] ** 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  [2025-08-19 11:45:33] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-19 11:45:33] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-19 11:45:33] ** Using provided annotation.
INFO  [2025-08-19 11:45:33] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-19 11:45:33] ** 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  [2025-08-19 11:45:33] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-19 11:45:33] ** Shared peptides are removed.
INFO  [2025-08-19 11:45:33] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-19 11:45:33] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:33] ** Run annotation merged with quantification data.
INFO  [2025-08-19 11:45:33] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:33] ** Fractionation handled.
INFO  [2025-08-19 11:45:33] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-19 11:45:33] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   36 tests OK INFO: Extracting modifications
INFO  [2025-08-19 11:45:34] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-19 11:45:34] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-19 11:45:34] ** Using provided annotation.
INFO  [2025-08-19 11:45:34] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-19 11:45:34] ** 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  [2025-08-19 11:45:34] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-19 11:45:34] ** Shared peptides are removed.
INFO  [2025-08-19 11:45:34] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-19 11:45:34] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:34] ** Run annotation merged with quantification data.
INFO  [2025-08-19 11:45:34] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:34] ** Fractionation handled.
INFO  [2025-08-19 11:45:34] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-19 11:45:34] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   37 tests OK INFO: Extracting modifications
INFO  [2025-08-19 11:45:36] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-19 11:45:36] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-19 11:45:36] ** Using provided annotation.
INFO  [2025-08-19 11:45:36] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-19 11:45:36] ** 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  [2025-08-19 11:45:36] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-19 11:45:36] ** Shared peptides are removed.
INFO  [2025-08-19 11:45:36] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-19 11:45:36] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:36] ** Run annotation merged with quantification data.
INFO  [2025-08-19 11:45:36] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:36] ** Fractionation handled.
INFO  [2025-08-19 11:45:36] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-19 11:45:36] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   38 tests OK INFO  [2025-08-19 11:45:37] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-19 11:45:37] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-19 11:45:37] ** Using provided annotation.
INFO  [2025-08-19 11:45:37] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-19 11:45:37] ** 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  [2025-08-19 11:45:37] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-19 11:45:37] ** Shared peptides are removed.
INFO  [2025-08-19 11:45:37] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-19 11:45:37] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:37] ** Run annotation merged with quantification data.
INFO  [2025-08-19 11:45:37] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:37] ** Fractionation handled.
INFO  [2025-08-19 11:45:37] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-19 11:45:37] ** 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  [2025-08-19 11:45:39] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-19 11:45:39] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-19 11:45:39] ** Using provided annotation.
INFO  [2025-08-19 11:45:39] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-19 11:45:39] ** 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  [2025-08-19 11:45:39] ** Features with all missing measurements across runs are removed.
INFO  [2025-08-19 11:45:39] ** Shared peptides are removed.
INFO  [2025-08-19 11:45:39] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-08-19 11:45:39] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:39] ** Run annotation merged with quantification data.
INFO  [2025-08-19 11:45:39] ** Features with one or two measurements across runs are removed.
INFO  [2025-08-19 11:45:39] ** Fractionation handled.
INFO  [2025-08-19 11:45:39] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-19 11:45:39] ** 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  [2025-08-19 11:45:39] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-19 11:45:39] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-19 11:45:39] ** Using provided annotation.
INFO  [2025-08-19 11:45:39] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-19 11:45:39] ** 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  [2025-08-19 11:45:39] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-08-19 11:45:39] ** Shared peptides are removed.
INFO  [2025-08-19 11:45:39] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-08-19 11:45:39] ** PSMs have been aggregated to peptide ions.
INFO  [2025-08-19 11:45:39] ** Run annotation merged with quantification data.
INFO  [2025-08-19 11:45:39] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-08-19 11:45:39] ** Fractionation handled.
INFO  [2025-08-19 11:45:39] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-19 11:45:39] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO  [2025-08-19 11:45:39] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2025-08-19 11:45:39] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2025-08-19 11:45:39] ** Using provided annotation.
INFO  [2025-08-19 11:45:39] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-08-19 11:45:39] ** 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  [2025-08-19 11:45:39] ** Features with all missing measurements across channels within each run are removed.
INFO  [2025-08-19 11:45:39] ** Shared peptides are removed.
INFO  [2025-08-19 11:45:39] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-08-19 11:45:39] ** PSMs have been aggregated to peptide ions.
INFO  [2025-08-19 11:45:39] ** Run annotation merged with quantification data.
INFO  [2025-08-19 11:45:39] ** For peptides overlapped between fractions of mixture1_1 use the fraction with maximal average abundance.
INFO  [2025-08-19 11:45:39] ** Fractions belonging to same mixture have been combined.
INFO  [2025-08-19 11:45:39] ** Features with one or two measurements across channels within each run are removed.
INFO  [2025-08-19 11:45:39] ** Fractionation handled.
INFO  [2025-08-19 11:45:39] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-08-19 11:45:39] ** 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