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This page was generated on 2024-04-17 11:36:09 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1347/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsPTM 2.4.4  (landing page)
Devon Kohler
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/MSstatsPTM
git_branch: RELEASE_3_18
git_last_commit: 3844aca
git_last_commit_date: 2024-02-13 09:08:14 -0400 (Tue, 13 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for MSstatsPTM on nebbiolo2


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: 2.4.4
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MSstatsPTM_2.4.4.tar.gz
StartedAt: 2024-04-16 01:18:48 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 01:23:28 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 280.4 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsPTM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MSstatsPTM_2.4.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MSstatsPTM.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MSstatsPTM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsPTM’ version ‘2.4.4’
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 R 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’
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 ... OK
* 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 11.24  0.104  11.334
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MSstatsPTM_LabelFree_Workflow.Rmd’ using ‘UTF-8’... OK
  ‘MSstatsPTM_TMT_Workflow.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/MSstatsPTM.Rcheck/00check.log’
for details.



Installation output

MSstatsPTM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MSstatsPTM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘MSstatsPTM’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c model_adjustment.cpp -o model_adjustment.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o MSstatsPTM.so RcppExports.o model_adjustment.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/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/tinytest.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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.............    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 
test_converters.R.............    5 tests OK 
test_converters.R.............    5 tests OK 
test_converters.R.............    6 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.............   10 tests OK 
test_converters.R.............   10 tests OK 
test_converters.R.............   11 tests OK 
test_converters.R.............   12 tests OK 
test_converters.R.............   13 tests OK 
test_converters.R.............   14 tests OK 
test_converters.R.............   14 tests OK 
test_converters.R.............   14 tests OK 
test_converters.R.............   14 tests OK INFO  [2024-04-16 01:21:33] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-04-16 01:21:33] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-04-16 01:21:33] ** Using provided annotation.
INFO  [2024-04-16 01:21:33] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-04-16 01:21:33] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2024-04-16 01:21:33] ** Features with all missing measurements across runs are removed.
INFO  [2024-04-16 01:21:33] ** Shared peptides are removed.
INFO  [2024-04-16 01:21:33] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-04-16 01:21:33] ** Features with one or two measurements across runs are removed.
INFO  [2024-04-16 01:21:33] ** Run annotation merged with quantification data.
INFO  [2024-04-16 01:21:33] ** Features with one or two measurements across runs are removed.
INFO  [2024-04-16 01:21:33] ** Fractionation handled.
INFO  [2024-04-16 01:21:33] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-04-16 01:21:33] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   15 tests OK INFO: Extracting modifications
INFO  [2024-04-16 01:21:34] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-04-16 01:21:34] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-04-16 01:21:34] ** Using provided annotation.
INFO  [2024-04-16 01:21:34] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-04-16 01:21:34] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2024-04-16 01:21:34] ** Features with all missing measurements across runs are removed.
INFO  [2024-04-16 01:21:34] ** Shared peptides are removed.
INFO  [2024-04-16 01:21:34] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-04-16 01:21:34] ** Features with one or two measurements across runs are removed.
INFO  [2024-04-16 01:21:34] ** Run annotation merged with quantification data.
INFO  [2024-04-16 01:21:34] ** Features with one or two measurements across runs are removed.
INFO  [2024-04-16 01:21:34] ** Fractionation handled.
INFO  [2024-04-16 01:21:34] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-04-16 01:21:34] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   16 tests OK INFO: Extracting modifications
INFO  [2024-04-16 01:21:34] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-04-16 01:21:34] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-04-16 01:21:34] ** Using provided annotation.
INFO  [2024-04-16 01:21:34] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-04-16 01:21:34] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2024-04-16 01:21:34] ** Features with all missing measurements across runs are removed.
INFO  [2024-04-16 01:21:34] ** Shared peptides are removed.
INFO  [2024-04-16 01:21:34] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-04-16 01:21:34] ** Features with one or two measurements across runs are removed.
INFO  [2024-04-16 01:21:34] ** Run annotation merged with quantification data.
INFO  [2024-04-16 01:21:34] ** Features with one or two measurements across runs are removed.
INFO  [2024-04-16 01:21:34] ** Fractionation handled.
INFO  [2024-04-16 01:21:34] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-04-16 01:21:34] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   17 tests OK INFO  [2024-04-16 01:21:35] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-04-16 01:21:35] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-04-16 01:21:35] ** Using provided annotation.
INFO  [2024-04-16 01:21:35] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-04-16 01:21:35] ** 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  [2024-04-16 01:21:35] ** Features with all missing measurements across runs are removed.
INFO  [2024-04-16 01:21:35] ** Shared peptides are removed.
INFO  [2024-04-16 01:21:35] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-04-16 01:21:35] ** Features with one or two measurements across runs are removed.
INFO  [2024-04-16 01:21:35] ** Run annotation merged with quantification data.
INFO  [2024-04-16 01:21:35] ** Features with one or two measurements across runs are removed.
INFO  [2024-04-16 01:21:35] ** Fractionation handled.
INFO  [2024-04-16 01:21:35] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-04-16 01:21:35] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   18 tests OK 
test_converters.R.............   19 tests OK INFO  [2024-04-16 01:21:36] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-04-16 01:21:36] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-04-16 01:21:36] ** Using provided annotation.
INFO  [2024-04-16 01:21:36] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-04-16 01:21:36] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2024-04-16 01:21:36] ** Features with all missing measurements across runs are removed.
INFO  [2024-04-16 01:21:36] ** Shared peptides are removed.
INFO  [2024-04-16 01:21:36] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-04-16 01:21:36] ** Features with one or two measurements across runs are removed.
INFO  [2024-04-16 01:21:36] ** Run annotation merged with quantification data.
INFO  [2024-04-16 01:21:36] ** Features with one or two measurements across runs are removed.
INFO  [2024-04-16 01:21:36] ** Fractionation handled.
INFO  [2024-04-16 01:21:36] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-04-16 01:21:36] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   20 tests OK 
test_converters.R.............   21 tests OK 
test_converters.R.............   22 tests OK 7.4s

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  [2024-04-16 01:21:40]  == Start to test and get inference in whole plot ...

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INFO  [2024-04-16 01:21:43]  == Comparisons for all proteins are done.
Starting Protein modeling...
INFO  [2024-04-16 01:21:43]  == Start to test and get inference in whole plot ...

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INFO  [2024-04-16 01:21:44]  == 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  [2024-04-16 01:21:44] Design: 2 mixtures.
INFO  [2024-04-16 01:21:44] Design: 1 MS run per mixture.
INFO  [2024-04-16 01:21:44] Design: group comparison design (Different conditions contains different biological subjects).
INFO  [2024-04-16 01:21:44] Model fitting for 90 proteins.

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INFO  [2024-04-16 01:21:46] Testing for 90 proteins:

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Starting Protein modeling...
INFO  [2024-04-16 01:21:47] Design: 2 mixtures.
INFO  [2024-04-16 01:21:47] Design: 1 MS run per mixture.
INFO  [2024-04-16 01:21:47] Design: group comparison design (Different conditions contains different biological subjects).
INFO  [2024-04-16 01:21:47] Model fitting for 85 proteins.

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INFO  [2024-04-16 01:21:51] 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 15.4s
All ok, 101 results (23.2s)
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
 29.228   0.809  29.112 

Example timings

MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings

nameusersystemelapsed
DIANNtoMSstatsPTMFormat0.0010.0000.000
FragPipetoMSstatsPTMFormat0.4760.0440.455
MSstatsPTMSiteLocator000
MaxQtoMSstatsPTMFormat0.8580.0400.820
PDtoMSstatsPTMFormat0.7610.0600.763
PStoMSstatsPTMFormat0.0690.0000.069
ProgenesistoMSstatsPTMFormat0.0470.0000.047
SkylinetoMSstatsPTMFormat0.0470.0000.047
SpectronauttoMSstatsPTMFormat0.5990.0350.552
annotSite0.0010.0000.000
dataProcessPlotsPTM2.1140.0372.109
dataSummarizationPTM2.2720.0122.133
dataSummarizationPTM_TMT4.6190.1204.200
designSampleSizePTM4.4830.0564.534
fragpipe_annotation0.0020.0000.002
fragpipe_annotation_protein0.0020.0000.002
fragpipe_input0.0040.0000.004
fragpipe_input_protein0.0040.0000.004
groupComparisonPTM3.9030.0643.958
groupComparisonPlotsPTM11.240 0.10411.334
locateMod0.0010.0000.000
locatePTM0.0140.0000.014
maxq_lf_annotation0.0010.0000.002
maxq_lf_evidence0.0080.0000.008
maxq_tmt_annotation0.0010.0000.001
maxq_tmt_evidence0.0090.0040.012
pd_annotation0.0010.0000.001
pd_psm_input0.0080.0000.008
pd_testing_output0.0680.0480.116
raw.input0.0650.0000.065
raw.input.tmt0.0050.0000.005
spectronaut_annotation0.0010.0000.002
spectronaut_input0.0040.0000.004
summary.data0.150.120.27
summary.data.tmt0.3200.2080.528
tidyFasta0.010.000.01