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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1355/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsPTM 2.8.1  (landing page)
Devon Kohler
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/MSstatsPTM
git_branch: RELEASE_3_20
git_last_commit: 04cd9d1
git_last_commit_date: 2024-11-25 15:52:20 -0500 (Mon, 25 Nov 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for MSstatsPTM on palomino8

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: 2.8.1
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsPTM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MSstatsPTM_2.8.1.tar.gz
StartedAt: 2024-12-20 03:53:03 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 03:57:37 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 274.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsPTM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsPTM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MSstatsPTM_2.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/MSstatsPTM.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MSstatsPTM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsPTM' version '2.8.1'
* 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 whether package 'MSstatsPTM' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/MSstatsPTM/libs/x64/MSstatsPTM.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
groupComparisonPlotsPTM  15.14   0.13   15.27
groupComparisonPTM        6.18   0.15    6.34
designSampleSizePTM       5.98   0.11    6.11
dataSummarizationPTM_TMT  4.93   0.28    5.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
  Running 'tinytest.R'
 OK
* 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: 5 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/MSstatsPTM.Rcheck/00check.log'
for details.


Installation output

MSstatsPTM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MSstatsPTM
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'MSstatsPTM' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c model_adjustment.cpp -o model_adjustment.o
g++ -std=gnu++17 -shared -s -static-libgcc -o MSstatsPTM.dll tmp.def RcppExports.o model_adjustment.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-MSstatsPTM/00new/MSstatsPTM/libs/x64
** 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
** 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   6.62    0.64    7.26 

MSstatsPTM.Rcheck/tests/tinytest.Rout


R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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  [2024-12-20 03:56:50] ** Raw data from MaxQuant imported successfully.
INFO  [2024-12-20 03:56:50] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-12-20 03:56:50] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-12-20 03:56:50] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-20 03:56:50] ** Using provided annotation.
INFO  [2024-12-20 03:56:50] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:56:50] ** 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  [2024-12-20 03:56:50] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-20 03:56:50] ** Shared peptides are removed.
INFO  [2024-12-20 03:56:50] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-20 03:56:50] ** PSMs have been aggregated to peptide ions.
INFO  [2024-12-20 03:56:50] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:56:50] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-20 03:56:50] ** Fractionation handled.
INFO  [2024-12-20 03:56:50] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:56:50] ** 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  [2024-12-20 03:56:51] ** Raw data from MaxQuant imported successfully.
INFO  [2024-12-20 03:56:51] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-12-20 03:56:51] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-12-20 03:56:51] ** Using provided annotation.
INFO  [2024-12-20 03:56:51] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:56:51] ** 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  [2024-12-20 03:56:51] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:56:51] ** Shared peptides are removed.
INFO  [2024-12-20 03:56:51] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-20 03:56:51] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:51] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:56:51] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:51] ** Fractionation handled.
INFO  [2024-12-20 03:56:51] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:56:51] ** 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  [2024-12-20 03:56:53] ** Raw data from Spectronaut imported successfully.
INFO  [2024-12-20 03:56:53] ** Raw data from Spectronaut cleaned successfully.
INFO  [2024-12-20 03:56:53] ** Using provided annotation.
INFO  [2024-12-20 03:56:53] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:56:53] ** 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  [2024-12-20 03:56:54] ** PGQvalue not found in input columns.
WARN  [2024-12-20 03:56:54] ** EGQvalue not found in input columns.
INFO  [2024-12-20 03:56:54] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:56:54] ** Shared peptides are removed.
INFO  [2024-12-20 03:56:54] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-20 03:56:54] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:54] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:56:54] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:54] ** Fractionation handled.
INFO  [2024-12-20 03:56:54] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:56:54] ** 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  [2024-12-20 03:56:55] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-20 03:56:55] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-20 03:56:55] ** Using provided annotation.
INFO  [2024-12-20 03:56:55] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:56:55] ** 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  [2024-12-20 03:56:55] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:56:55] ** Shared peptides are removed.
INFO  [2024-12-20 03:56:55] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-20 03:56:55] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:55] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:56:55] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:55] ** Fractionation handled.
INFO  [2024-12-20 03:56:55] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:56:55] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   36 tests OK INFO: Extracting modifications
INFO  [2024-12-20 03:56:56] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-20 03:56:56] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-20 03:56:56] ** Using provided annotation.
INFO  [2024-12-20 03:56:56] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:56:56] ** 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  [2024-12-20 03:56:56] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:56:56] ** Shared peptides are removed.
INFO  [2024-12-20 03:56:56] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-20 03:56:56] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:56] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:56:56] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:56] ** Fractionation handled.
INFO  [2024-12-20 03:56:56] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:56:56] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   37 tests OK INFO: Extracting modifications
INFO  [2024-12-20 03:56:57] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-20 03:56:57] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-20 03:56:57] ** Using provided annotation.
INFO  [2024-12-20 03:56:57] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:56:57] ** 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  [2024-12-20 03:56:57] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:56:57] ** Shared peptides are removed.
INFO  [2024-12-20 03:56:57] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-20 03:56:57] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:57] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:56:57] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:57] ** Fractionation handled.
INFO  [2024-12-20 03:56:57] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:56:57] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   38 tests OK INFO  [2024-12-20 03:56:58] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-20 03:56:58] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-20 03:56:58] ** Using provided annotation.
INFO  [2024-12-20 03:56:58] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:56:58] ** 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  [2024-12-20 03:56:58] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:56:58] ** Shared peptides are removed.
INFO  [2024-12-20 03:56:58] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-20 03:56:58] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:58] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:56:58] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:58] ** Fractionation handled.
INFO  [2024-12-20 03:56:58] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:56:58] ** 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  [2024-12-20 03:56:59] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-20 03:56:59] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-20 03:56:59] ** Using provided annotation.
INFO  [2024-12-20 03:56:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:56:59] ** 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  [2024-12-20 03:56:59] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:56:59] ** Shared peptides are removed.
INFO  [2024-12-20 03:56:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-20 03:56:59] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:59] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:56:59] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:56:59] ** Fractionation handled.
INFO  [2024-12-20 03:56:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:56:59] ** 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  [2024-12-20 03:57:00] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-20 03:57:00] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-20 03:57:00] ** Using provided annotation.
INFO  [2024-12-20 03:57:00] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:57:00] ** 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 removed.
INFO  [2024-12-20 03:57:00] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:00] ** Shared peptides are removed.
INFO  [2024-12-20 03:57:00] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:00] ** PSMs have been aggregated to peptide ions.
INFO  [2024-12-20 03:57:00] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:57:00] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:00] ** Fractionation handled.
INFO  [2024-12-20 03:57:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:57:00] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO  [2024-12-20 03:57:00] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-20 03:57:00] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-20 03:57:00] ** Using provided annotation.
INFO  [2024-12-20 03:57:00] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:57:00] ** 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 removed.
INFO  [2024-12-20 03:57:00] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:00] ** Shared peptides are removed.
INFO  [2024-12-20 03:57:00] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:00] ** PSMs have been aggregated to peptide ions.
INFO  [2024-12-20 03:57:00] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:57:00] ** For peptides overlapped between fractions of mixture1_1 use the fraction with maximal average abundance.
INFO  [2024-12-20 03:57:00] ** Fractions belonging to same mixture have been combined.
INFO  [2024-12-20 03:57:00] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:00] ** Fractionation handled.
INFO  [2024-12-20 03:57:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:57:00] ** 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 OK 
test_converters.R.............   52 tests OK 
test_converters.R.............   53 tests OK 
test_converters.R.............   54 tests OK 
test_converters.R.............   55 tests OK [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications."
INFO  [2024-12-20 03:57:00] ** Raw data from Metamorpheus imported successfully.
INFO  [2024-12-20 03:57:00] ** Raw data from Metamorpheus cleaned successfully.
INFO  [2024-12-20 03:57:00] ** Using provided annotation.
INFO  [2024-12-20 03:57:00] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:57:00] ** 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 across runs will be removed.
INFO  [2024-12-20 03:57:00] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:57:00] ** Shared peptides are removed.
INFO  [2024-12-20 03:57:00] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-20 03:57:00] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:57:00] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:57:00] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:57:00] ** Fractionation handled.
INFO  [2024-12-20 03:57:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:57:00] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
INFO  [2024-12-20 03:57:00] ** Raw data from Metamorpheus imported successfully.
INFO  [2024-12-20 03:57:00] ** Raw data from Metamorpheus cleaned successfully.
INFO  [2024-12-20 03:57:00] ** Using provided annotation.
INFO  [2024-12-20 03:57:00] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:57:00] ** 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 across runs will be removed.
INFO  [2024-12-20 03:57:00] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:57:00] ** Shared peptides are removed.
INFO  [2024-12-20 03:57:00] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-20 03:57:00] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:57:00] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:57:00] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:57:00] ** Fractionation handled.
INFO  [2024-12-20 03:57:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:57:00] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   55 tests OK 
test_converters.R.............   57 tests OK 
test_converters.R.............   58 tests OK 
test_converters.R.............   59 tests OK 
test_converters.R.............   60 tests OK 
test_converters.R.............   61 tests OK 
test_converters.R.............   62 tests OK [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications."
INFO  [2024-12-20 03:57:00] ** Raw data from Metamorpheus imported successfully.
INFO  [2024-12-20 03:57:00] ** Raw data from Metamorpheus cleaned successfully.
INFO  [2024-12-20 03:57:00] ** Using provided annotation.
INFO  [2024-12-20 03:57:00] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:57:00] ** 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 across runs will be removed.
INFO  [2024-12-20 03:57:01] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:57:01] ** Shared peptides are removed.
INFO  [2024-12-20 03:57:01] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-20 03:57:01] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:57:01] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:57:01] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:57:01] ** Fractionation handled.
INFO  [2024-12-20 03:57:01] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:57:01] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
INFO  [2024-12-20 03:57:01] ** Raw data from Metamorpheus imported successfully.
INFO  [2024-12-20 03:57:01] ** Raw data from Metamorpheus cleaned successfully.
INFO  [2024-12-20 03:57:01] ** Using provided annotation.
INFO  [2024-12-20 03:57:01] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:57:01] ** 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  [2024-12-20 03:57:01] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:57:01] ** Shared peptides are removed.
INFO  [2024-12-20 03:57:01] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-20 03:57:01] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:57:01] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:57:01] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:57:01] ** Fractionation handled.
INFO  [2024-12-20 03:57:01] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:57:01] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   62 tests OK 
test_converters.R.............   64 tests OK 
test_converters.R.............   65 tests OK 
test_converters.R.............   66 tests OK 
test_converters.R.............   67 tests OK 
test_converters.R.............   68 tests OK 
test_converters.R.............   69 tests OK 
test_converters.R.............   69 tests OK 
test_converters.R.............   69 tests OK 
test_converters.R.............   69 tests OK 
test_converters.R.............   69 tests OK 
test_converters.R.............   69 tests OK 
test_converters.R.............   69 tests OK 
test_converters.R.............   70 tests OK 
test_converters.R.............   71 tests OK INFO  [2024-12-20 03:57:01] ** Raw data from Progenesis imported successfully.
INFO  [2024-12-20 03:57:01] ** Raw data from Progenesis cleaned successfully.
INFO  [2024-12-20 03:57:01] ** Using provided annotation.
INFO  [2024-12-20 03:57:01] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:57:01] ** 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  [2024-12-20 03:57:01] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:57:01] ** Shared peptides are removed.
INFO  [2024-12-20 03:57:01] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-20 03:57:01] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:57:01] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:57:01] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-20 03:57:01] ** Fractionation handled.
INFO  [2024-12-20 03:57:01] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:57:01] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   71 tests OK 
test_converters.R.............   72 tests OK 
test_converters.R.............   73 tests OK 
test_converters.R.............   74 tests OK INFO  [2024-12-20 03:57:02] ** Raw data from Philosopher imported successfully.
INFO  [2024-12-20 03:57:02] ** Using provided annotation.
INFO  [2024-12-20 03:57:02] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:57:02] ** 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  [2024-12-20 03:57:02] ** Rows with values not greater than 0.6 in Purity are removed 
WARN  [2024-12-20 03:57:02] ** PeptideProphetProbability not found in input columns.
INFO  [2024-12-20 03:57:02] ** Sequences containing Oxidation are removed.
INFO  [2024-12-20 03:57:02] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:02] ** Shared peptides are removed.
INFO  [2024-12-20 03:57:02] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:02] ** PSMs have been aggregated to peptide ions.
INFO  [2024-12-20 03:57:02] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:57:02] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:02] ** Fractionation handled.
INFO  [2024-12-20 03:57:02] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:57:02] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO  [2024-12-20 03:57:02] ** Raw data from Philosopher imported successfully.

test_converters.R.............   75 tests OK 
test_converters.R.............   76 tests OK INFO  [2024-12-20 03:57:03] ** Raw data from Philosopher imported successfully.
INFO  [2024-12-20 03:57:03] ** Using provided annotation.
INFO  [2024-12-20 03:57:03] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:57:03] ** 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  [2024-12-20 03:57:03] ** Rows with values not greater than 0.6 in Purity are removed 
WARN  [2024-12-20 03:57:03] ** PeptideProphetProbability not found in input columns.
INFO  [2024-12-20 03:57:03] ** Sequences containing Oxidation are removed.
INFO  [2024-12-20 03:57:03] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:03] ** Shared peptides are removed.
INFO  [2024-12-20 03:57:03] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:03] ** PSMs have been aggregated to peptide ions.
INFO  [2024-12-20 03:57:03] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:57:03] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:03] ** Fractionation handled.
INFO  [2024-12-20 03:57:03] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:57:03] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO  [2024-12-20 03:57:03] ** Raw data from Philosopher imported successfully.
INFO  [2024-12-20 03:57:03] ** Using provided annotation.
INFO  [2024-12-20 03:57:03] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:57:03] ** 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  [2024-12-20 03:57:03] ** Rows with values not greater than 0.6 in Purity are removed 
WARN  [2024-12-20 03:57:03] ** PeptideProphetProbability not found in input columns.
INFO  [2024-12-20 03:57:03] ** Sequences containing Oxidation are removed.
INFO  [2024-12-20 03:57:03] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:03] ** Shared peptides are removed.
INFO  [2024-12-20 03:57:03] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:03] ** PSMs have been aggregated to peptide ions.
INFO  [2024-12-20 03:57:03] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:57:03] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-20 03:57:03] ** Fractionation handled.
INFO  [2024-12-20 03:57:03] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:57:03] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.

test_converters.R.............   76 tests OK 
test_converters.R.............   78 tests OK 
test_converters.R.............   79 tests OK 
test_converters.R.............   80 tests OK 
test_converters.R.............   81 tests OK 
test_converters.R.............   82 tests OK 
test_converters.R.............   83 tests OK 
test_converters.R.............   83 tests OK 
test_converters.R.............   83 tests OK 
test_converters.R.............   83 tests OK 
test_converters.R.............   83 tests OK 
test_converters.R.............   84 tests OK 
test_converters.R.............   85 tests OK INFO  [2024-12-20 03:57:03] ** Raw data from FragPipe imported successfully.
INFO  [2024-12-20 03:57:03] ** Using annotation extracted from quantification data.
INFO  [2024-12-20 03:57:03] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-20 03:57:03] ** 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 kept.
INFO  [2024-12-20 03:57:03] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:57:03] ** Shared peptides are removed.
INFO  [2024-12-20 03:57:03] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO  [2024-12-20 03:57:03] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:57:03] ** Run annotation merged with quantification data.
INFO  [2024-12-20 03:57:03] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-20 03:57:03] ** Fractionation handled.
INFO  [2024-12-20 03:57:03] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-20 03:57:03] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   85 tests OK 
test_converters.R.............   86 tests OK 
test_converters.R.............   87 tests OK 
test_converters.R.............   88 tests OK 14.7s

test_dataSummarizationPTM.R...    0 tests    
test_dataSummarizationPTM.R...    1 tests OK 
test_dataSummarizationPTM.R...    2 tests OK 
test_dataSummarizationPTM.R...    3 tests OK 
test_dataSummarizationPTM.R...    4 tests OK 
test_dataSummarizationPTM.R...    5 tests OK 
test_dataSummarizationPTM.R...    6 tests OK 
test_dataSummarizationPTM.R...    7 tests OK 
test_dataSummarizationPTM.R...    8 tests OK 
test_dataSummarizationPTM.R...    9 tests OK 
test_dataSummarizationPTM.R...   10 tests OK 
test_dataSummarizationPTM.R...   11 tests OK 
test_dataSummarizationPTM.R...   12 tests OK 
test_dataSummarizationPTM.R...   13 tests OK 
test_dataSummarizationPTM.R...   14 tests OK 
test_dataSummarizationPTM.R...   15 tests OK 
test_dataSummarizationPTM.R...   16 tests OK 
test_dataSummarizationPTM.R...   17 tests OK 
test_dataSummarizationPTM.R...   18 tests OK 
test_dataSummarizationPTM.R...   19 tests OK 
test_dataSummarizationPTM.R...   20 tests OK 
test_dataSummarizationPTM.R...   21 tests OK 
test_dataSummarizationPTM.R...   22 tests OK 
test_dataSummarizationPTM.R...   23 tests OK 
test_dataSummarizationPTM.R...   24 tests OK 
test_dataSummarizationPTM.R...   25 tests OK 
test_dataSummarizationPTM.R...   26 tests OK 
test_dataSummarizationPTM.R...   27 tests OK 
test_dataSummarizationPTM.R...   28 tests OK 
test_dataSummarizationPTM.R...   29 tests OK 
test_dataSummarizationPTM.R...   30 tests OK Starting PTM summarization...

test_dataSummarizationPTM.R...   31 tests OK 0.2s

test_dataSummarizationPTM_TMT.R    0 tests    
test_dataSummarizationPTM_TMT.R    1 tests OK 
test_dataSummarizationPTM_TMT.R    2 tests OK 
test_dataSummarizationPTM_TMT.R    3 tests OK 
test_dataSummarizationPTM_TMT.R    4 tests OK 
test_dataSummarizationPTM_TMT.R    5 tests OK 
test_dataSummarizationPTM_TMT.R    6 tests OK 
test_dataSummarizationPTM_TMT.R    7 tests OK 
test_dataSummarizationPTM_TMT.R    8 tests OK 
test_dataSummarizationPTM_TMT.R    9 tests OK 
test_dataSummarizationPTM_TMT.R   10 tests OK 
test_dataSummarizationPTM_TMT.R   11 tests OK 
test_dataSummarizationPTM_TMT.R   12 tests OK 
test_dataSummarizationPTM_TMT.R   13 tests OK 
test_dataSummarizationPTM_TMT.R   14 tests OK 
test_dataSummarizationPTM_TMT.R   15 tests OK 
test_dataSummarizationPTM_TMT.R   16 tests OK 
test_dataSummarizationPTM_TMT.R   17 tests OK 
test_dataSummarizationPTM_TMT.R   18 tests OK 
test_dataSummarizationPTM_TMT.R   19 tests OK 
test_dataSummarizationPTM_TMT.R   20 tests OK 
test_dataSummarizationPTM_TMT.R   21 tests OK 
test_dataSummarizationPTM_TMT.R   22 tests OK 
test_dataSummarizationPTM_TMT.R   23 tests OK 
test_dataSummarizationPTM_TMT.R   24 tests OK 
test_dataSummarizationPTM_TMT.R   25 tests OK 
test_dataSummarizationPTM_TMT.R   26 tests OK 
test_dataSummarizationPTM_TMT.R   27 tests OK 
test_dataSummarizationPTM_TMT.R   28 tests OK 
test_dataSummarizationPTM_TMT.R   29 tests OK 
test_dataSummarizationPTM_TMT.R   30 tests OK 
test_dataSummarizationPTM_TMT.R   31 tests OK 0.2s

test_groupComparisonPTM.R.....    0 tests    
test_groupComparisonPTM.R.....    0 tests    
test_groupComparisonPTM.R.....    1 tests OK 
test_groupComparisonPTM.R.....    2 tests OK Starting PTM modeling...

test_groupComparisonPTM.R.....    3 tests OK Starting PTM modeling...
INFO  [2024-12-20 03:57:08]  == Start to test and get inference in whole plot ...

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INFO  [2024-12-20 03:57:12]  == Comparisons for all proteins are done.
Starting Protein modeling...
INFO  [2024-12-20 03:57:12]  == Start to test and get inference in whole plot ...

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INFO  [2024-12-20 03:57:13]  == Comparisons for all proteins are done.
Starting adjustment...

test_groupComparisonPTM.R.....    3 tests OK 
test_groupComparisonPTM.R.....    4 tests OK 
test_groupComparisonPTM.R.....    5 tests OK 
test_groupComparisonPTM.R.....    6 tests OK 
test_groupComparisonPTM.R.....    7 tests OK 
test_groupComparisonPTM.R.....    8 tests OK 
test_groupComparisonPTM.R.....    9 tests OK 
test_groupComparisonPTM.R.....   10 tests OK Starting PTM modeling...
INFO  [2024-12-20 03:57:13] Design: 2 mixtures.
INFO  [2024-12-20 03:57:13] Design: 1 MS run per mixture.
INFO  [2024-12-20 03:57:13] Design: group comparison design (Different conditions contains different biological subjects).
INFO  [2024-12-20 03:57:13] Model fitting for 90 proteins.

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INFO  [2024-12-20 03:57:16] Testing for 90 proteins:

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Starting Protein modeling...
INFO  [2024-12-20 03:57:17] Design: 2 mixtures.
INFO  [2024-12-20 03:57:17] Design: 1 MS run per mixture.
INFO  [2024-12-20 03:57:17] Design: group comparison design (Different conditions contains different biological subjects).
INFO  [2024-12-20 03:57:17] Model fitting for 85 proteins.

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INFO  [2024-12-20 03:57:23] Testing for 85 proteins:

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Starting adjustment...

test_groupComparisonPTM.R.....   10 tests OK 
test_groupComparisonPTM.R.....   11 tests OK 
test_groupComparisonPTM.R.....   12 tests OK 
test_groupComparisonPTM.R.....   13 tests OK 
test_groupComparisonPTM.R.....   14 tests OK 
test_groupComparisonPTM.R.....   15 tests OK 
test_groupComparisonPTM.R.....   16 tests OK 
test_groupComparisonPTM.R.....   17 tests OK 20.7s
All ok, 167 results (35.9s)
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
  40.26    1.79   42.40 

Example timings

MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings

nameusersystemelapsed
DIANNtoMSstatsPTMFormat000
FragPipetoMSstatsPTMFormat0.820.030.85
MSstatsPTMSiteLocator000
MaxQtoMSstatsPTMFormat1.010.001.03
MetamorpheusToMSstatsPTMFormat0.240.000.25
PDtoMSstatsPTMFormat1.390.201.61
PStoMSstatsPTMFormat0.050.020.06
ProgenesistoMSstatsPTMFormat0.060.010.08
SkylinetoMSstatsPTMFormat0.070.000.07
SpectronauttoMSstatsPTMFormat0.840.070.92
annotSite000
dataProcessPlotsPTM2.660.012.67
dataSummarizationPTM2.820.082.92
dataSummarizationPTM_TMT4.930.285.27
designSampleSizePTM5.980.116.11
fragpipe_annotation000
fragpipe_annotation_protein000
fragpipe_input0.020.000.01
fragpipe_input_protein0.000.020.02
groupComparisonPTM6.180.156.34
groupComparisonPlotsPTM15.14 0.1315.27
locateMod000
locatePTM0.030.000.03
maxq_lf_annotation000
maxq_lf_evidence0.020.000.01
maxq_tmt_annotation0.020.000.02
maxq_tmt_evidence0.010.000.01
pd_annotation000
pd_psm_input0.000.010.02
pd_testing_output0.420.050.46
raw.input0.080.000.08
raw.input.tmt0.000.020.02
spectronaut_annotation000
spectronaut_input000
summary.data0.700.260.97
summary.data.tmt1.230.581.81
tidyFasta0.020.000.02