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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1349/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsPTM 2.9.1  (landing page)
Devon Kohler
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/MSstatsPTM
git_branch: devel
git_last_commit: f1d70f4
git_last_commit_date: 2024-11-25 15:54:03 -0500 (Mon, 25 Nov 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for MSstatsPTM on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: MSstatsPTM
Version: 2.9.1
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_2.9.1.tar.gz
StartedAt: 2024-12-24 09:04:33 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 09:08:59 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 265.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsPTM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_2.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MSstatsPTM.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsPTM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsPTM’ version ‘2.9.1’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
groupComparisonPlotsPTM  16.439  0.128  16.598
dataSummarizationPTM_TMT  6.433  0.084   6.461
designSampleSizePTM       5.939  0.067   6.020
groupComparisonPTM        5.484  0.052   5.548
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MSstatsPTM.Rcheck/00check.log’
for details.


Installation output

MSstatsPTM.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘MSstatsPTM’ ...
** 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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/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)

Tests output

MSstatsPTM.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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 
  7.626   0.375   8.020 

MSstatsPTM.Rcheck/tests/tinytest.Rout


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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  [2024-12-24 09:08:15] ** Raw data from MaxQuant imported successfully.
INFO  [2024-12-24 09:08:15] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-12-24 09:08:15] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-12-24 09:08:15] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:15] ** Using provided annotation.
INFO  [2024-12-24 09:08:15] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:15] ** 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  [2024-12-24 09:08:15] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:15] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:15] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:15] ** PSMs have been aggregated to peptide ions.
INFO  [2024-12-24 09:08:15] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:15] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:15] ** Fractionation handled.
INFO  [2024-12-24 09:08:15] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:15] ** 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  [2024-12-24 09:08:16] ** Raw data from MaxQuant imported successfully.
INFO  [2024-12-24 09:08:16] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-12-24 09:08:16] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-12-24 09:08:16] ** Using provided annotation.
INFO  [2024-12-24 09:08:16] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:16] ** 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  [2024-12-24 09:08:16] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:16] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:16] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-24 09:08:16] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:16] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:16] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:16] ** Fractionation handled.
INFO  [2024-12-24 09:08:16] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:16] ** 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  [2024-12-24 09:08:19] ** Raw data from Spectronaut imported successfully.
INFO  [2024-12-24 09:08:19] ** Raw data from Spectronaut cleaned successfully.
INFO  [2024-12-24 09:08:19] ** Using provided annotation.
INFO  [2024-12-24 09:08:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:19] ** 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  [2024-12-24 09:08:19] ** PGQvalue not found in input columns.
WARN  [2024-12-24 09:08:19] ** EGQvalue not found in input columns.
INFO  [2024-12-24 09:08:19] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:19] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-24 09:08:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:19] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:19] ** Fractionation handled.
INFO  [2024-12-24 09:08:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:19] ** 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  [2024-12-24 09:08:21] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-24 09:08:21] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-24 09:08:21] ** Using provided annotation.
INFO  [2024-12-24 09:08:21] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:21] ** 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  [2024-12-24 09:08:21] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:21] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:21] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-24 09:08:21] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:21] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:21] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:21] ** Fractionation handled.
INFO  [2024-12-24 09:08:21] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:21] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   36 tests OK INFO: Extracting modifications
INFO  [2024-12-24 09:08:22] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-24 09:08:22] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-24 09:08:22] ** Using provided annotation.
INFO  [2024-12-24 09:08:22] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:22] ** 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  [2024-12-24 09:08:22] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:22] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:22] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-24 09:08:22] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:22] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:22] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:22] ** Fractionation handled.
INFO  [2024-12-24 09:08:22] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:22] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   37 tests OK INFO: Extracting modifications
INFO  [2024-12-24 09:08:24] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-24 09:08:24] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-24 09:08:24] ** Using provided annotation.
INFO  [2024-12-24 09:08:24] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:24] ** 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  [2024-12-24 09:08:24] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:24] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:24] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-24 09:08:24] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:24] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:24] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:24] ** Fractionation handled.
INFO  [2024-12-24 09:08:24] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:24] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   38 tests OK INFO  [2024-12-24 09:08:25] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-24 09:08:25] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-24 09:08:25] ** Using provided annotation.
INFO  [2024-12-24 09:08:25] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:25] ** 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  [2024-12-24 09:08:25] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:25] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:25] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-24 09:08:25] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:25] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:25] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:25] ** Fractionation handled.
INFO  [2024-12-24 09:08:25] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:25] ** 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  [2024-12-24 09:08:27] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-24 09:08:27] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-24 09:08:27] ** Using provided annotation.
INFO  [2024-12-24 09:08:27] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:27] ** 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  [2024-12-24 09:08:27] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:27] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:27] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-24 09:08:27] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:27] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:27] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:27] ** Fractionation handled.
INFO  [2024-12-24 09:08:27] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:27] ** 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  [2024-12-24 09:08:27] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-24 09:08:27] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-24 09:08:27] ** Using provided annotation.
INFO  [2024-12-24 09:08:27] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:27] ** 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  [2024-12-24 09:08:27] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:27] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:27] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:27] ** PSMs have been aggregated to peptide ions.
INFO  [2024-12-24 09:08:27] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:27] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:27] ** Fractionation handled.
INFO  [2024-12-24 09:08:27] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:27] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO  [2024-12-24 09:08:27] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-24 09:08:27] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-24 09:08:27] ** Using provided annotation.
INFO  [2024-12-24 09:08:27] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:27] ** 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  [2024-12-24 09:08:27] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:27] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:27] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:27] ** PSMs have been aggregated to peptide ions.
INFO  [2024-12-24 09:08:27] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:27] ** For peptides overlapped between fractions of mixture1_1 use the fraction with maximal average abundance.
INFO  [2024-12-24 09:08:27] ** Fractions belonging to same mixture have been combined.
INFO  [2024-12-24 09:08:27] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:27] ** Fractionation handled.
INFO  [2024-12-24 09:08:27] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:27] ** 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  [2024-12-24 09:08:28] ** Raw data from Metamorpheus imported successfully.
INFO  [2024-12-24 09:08:28] ** Raw data from Metamorpheus cleaned successfully.
INFO  [2024-12-24 09:08:28] ** Using provided annotation.
INFO  [2024-12-24 09:08:28] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:28] ** 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  [2024-12-24 09:08:28] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:28] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-24 09:08:28] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:28] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Fractionation handled.
INFO  [2024-12-24 09:08:28] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:28] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
INFO  [2024-12-24 09:08:28] ** Raw data from Metamorpheus imported successfully.
INFO  [2024-12-24 09:08:28] ** Raw data from Metamorpheus cleaned successfully.
INFO  [2024-12-24 09:08:28] ** Using provided annotation.
INFO  [2024-12-24 09:08:28] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:28] ** 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  [2024-12-24 09:08:28] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:28] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-24 09:08:28] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:28] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Fractionation handled.
INFO  [2024-12-24 09:08:28] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:28] ** 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  [2024-12-24 09:08:28] ** Raw data from Metamorpheus imported successfully.
INFO  [2024-12-24 09:08:28] ** Raw data from Metamorpheus cleaned successfully.
INFO  [2024-12-24 09:08:28] ** Using provided annotation.
INFO  [2024-12-24 09:08:28] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:28] ** 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  [2024-12-24 09:08:28] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:28] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-24 09:08:28] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:28] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Fractionation handled.
INFO  [2024-12-24 09:08:28] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:28] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
INFO  [2024-12-24 09:08:28] ** Raw data from Metamorpheus imported successfully.
INFO  [2024-12-24 09:08:28] ** Raw data from Metamorpheus cleaned successfully.
INFO  [2024-12-24 09:08:28] ** Using provided annotation.
INFO  [2024-12-24 09:08:28] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:28] ** 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  [2024-12-24 09:08:28] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:28] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-24 09:08:28] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:28] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Fractionation handled.
INFO  [2024-12-24 09:08:28] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:28] ** 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  [2024-12-24 09:08:28] ** Raw data from Progenesis imported successfully.
INFO  [2024-12-24 09:08:28] ** Raw data from Progenesis cleaned successfully.
INFO  [2024-12-24 09:08:28] ** Using provided annotation.
INFO  [2024-12-24 09:08:28] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:28] ** 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  [2024-12-24 09:08:28] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:28] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-12-24 09:08:28] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:28] ** Features with one or two measurements across runs are removed.
INFO  [2024-12-24 09:08:28] ** Fractionation handled.
INFO  [2024-12-24 09:08:28] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:28] ** 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  [2024-12-24 09:08:29] ** Raw data from Philosopher imported successfully.
INFO  [2024-12-24 09:08:29] ** Using provided annotation.
INFO  [2024-12-24 09:08:29] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:29] ** 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  [2024-12-24 09:08:29] ** Rows with values not greater than 0.6 in Purity are removed 
WARN  [2024-12-24 09:08:29] ** PeptideProphetProbability not found in input columns.
INFO  [2024-12-24 09:08:29] ** Sequences containing Oxidation are removed.
INFO  [2024-12-24 09:08:29] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:29] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:29] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:30] ** PSMs have been aggregated to peptide ions.
INFO  [2024-12-24 09:08:30] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:30] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:30] ** Fractionation handled.
INFO  [2024-12-24 09:08:30] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:30] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO  [2024-12-24 09:08:30] ** Raw data from Philosopher imported successfully.

test_converters.R.............   75 tests OK 
test_converters.R.............   76 tests OK INFO  [2024-12-24 09:08:30] ** Raw data from Philosopher imported successfully.
INFO  [2024-12-24 09:08:30] ** Using provided annotation.
INFO  [2024-12-24 09:08:30] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:30] ** 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  [2024-12-24 09:08:30] ** Rows with values not greater than 0.6 in Purity are removed 
WARN  [2024-12-24 09:08:30] ** PeptideProphetProbability not found in input columns.
INFO  [2024-12-24 09:08:30] ** Sequences containing Oxidation are removed.
INFO  [2024-12-24 09:08:30] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:30] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:30] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:30] ** PSMs have been aggregated to peptide ions.
INFO  [2024-12-24 09:08:30] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:30] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:30] ** Fractionation handled.
INFO  [2024-12-24 09:08:30] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:30] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO  [2024-12-24 09:08:30] ** Raw data from Philosopher imported successfully.
INFO  [2024-12-24 09:08:30] ** Using provided annotation.
INFO  [2024-12-24 09:08:30] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:30] ** 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  [2024-12-24 09:08:30] ** Rows with values not greater than 0.6 in Purity are removed 
WARN  [2024-12-24 09:08:30] ** PeptideProphetProbability not found in input columns.
INFO  [2024-12-24 09:08:30] ** Sequences containing Oxidation are removed.
INFO  [2024-12-24 09:08:30] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:30] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:30] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:30] ** PSMs have been aggregated to peptide ions.
INFO  [2024-12-24 09:08:30] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:30] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-24 09:08:30] ** Fractionation handled.
INFO  [2024-12-24 09:08:30] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:30] ** 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  [2024-12-24 09:08:30] ** Raw data from FragPipe imported successfully.
INFO  [2024-12-24 09:08:30] ** Using annotation extracted from quantification data.
INFO  [2024-12-24 09:08:30] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-24 09:08:30] ** 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  [2024-12-24 09:08:30] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:30] ** Shared peptides are removed.
INFO  [2024-12-24 09:08:30] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO  [2024-12-24 09:08:30] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:30] ** Run annotation merged with quantification data.
INFO  [2024-12-24 09:08:30] ** Features with all missing measurements across runs are removed.
INFO  [2024-12-24 09:08:30] ** Fractionation handled.
INFO  [2024-12-24 09:08:30] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-12-24 09:08:30] ** 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 16.7s

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 0.3s

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 0.3s

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  [2024-12-24 09:08:36]  == Start to test and get inference in whole plot ...

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INFO  [2024-12-24 09:08:41]  == Comparisons for all proteins are done.
Starting Protein modeling...
INFO  [2024-12-24 09:08:41]  == Start to test and get inference in whole plot ...

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INFO  [2024-12-24 09:08:42]  == 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  [2024-12-24 09:08:43] Design: 2 mixtures.
INFO  [2024-12-24 09:08:43] Design: 1 MS run per mixture.
INFO  [2024-12-24 09:08:43] Design: group comparison design (Different conditions contains different biological subjects).
INFO  [2024-12-24 09:08:43] Model fitting for 90 proteins.

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INFO  [2024-12-24 09:08:45] Testing for 90 proteins:

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Starting Protein modeling...
INFO  [2024-12-24 09:08:46] Design: 2 mixtures.
INFO  [2024-12-24 09:08:46] Design: 1 MS run per mixture.
INFO  [2024-12-24 09:08:46] Design: group comparison design (Different conditions contains different biological subjects).
INFO  [2024-12-24 09:08:46] Model fitting 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 22.2s
All ok, 167 results (39.5s)
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
 46.209   0.893  47.103 

Example timings

MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings

nameusersystemelapsed
DIANNtoMSstatsPTMFormat000
FragPipetoMSstatsPTMFormat1.2500.0321.276
MSstatsPTMSiteLocator000
MaxQtoMSstatsPTMFormat0.4830.0200.498
MetamorpheusToMSstatsPTMFormat0.1650.0080.178
PDtoMSstatsPTMFormat1.5650.0881.648
PStoMSstatsPTMFormat0.1010.0000.101
ProgenesistoMSstatsPTMFormat0.0790.0000.081
SkylinetoMSstatsPTMFormat0.0620.0040.066
SpectronauttoMSstatsPTMFormat0.7050.0240.718
annotSite0.0000.0000.001
dataProcessPlotsPTM3.2100.0843.296
dataSummarizationPTM3.1280.0443.161
dataSummarizationPTM_TMT6.4330.0846.461
designSampleSizePTM5.9390.0676.020
fragpipe_annotation0.0020.0000.002
fragpipe_annotation_protein0.0020.0000.002
fragpipe_input0.0060.0000.006
fragpipe_input_protein0.0060.0000.006
groupComparisonPTM5.4840.0525.548
groupComparisonPlotsPTM16.439 0.12816.598
locateMod0.0010.0000.000
locatePTM0.0210.0080.029
maxq_lf_annotation0.0020.0000.001
maxq_lf_evidence0.0080.0040.013
maxq_tmt_annotation0.0020.0000.002
maxq_tmt_evidence0.0160.0040.019
pd_annotation0.0020.0000.001
pd_psm_input0.0090.0040.013
pd_testing_output0.0760.0320.114
raw.input0.0730.0000.074
raw.input.tmt0.0060.0000.006
spectronaut_annotation0.0020.0000.002
spectronaut_input0.0060.0000.006
summary.data0.1600.0800.241
summary.data.tmt0.3450.1440.490
tidyFasta0.010.000.01