Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:13 -0400 (Fri, 15 Oct 2021).

CHECK results for MSstatsTMT on tokay2

To the developers/maintainers of the MSstatsTMT package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsTMT.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1215/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsTMT 2.0.1  (landing page)
Ting Huang
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MSstatsTMT
git_branch: RELEASE_3_13
git_last_commit: 8d487f0
git_last_commit_date: 2021-06-14 15:10:42 -0400 (Mon, 14 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSstatsTMT
Version: 2.0.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsTMT.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MSstatsTMT_2.0.1.tar.gz
StartedAt: 2021-10-15 02:24:34 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 02:28:24 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 230.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsTMT.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsTMT.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MSstatsTMT_2.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MSstatsTMT.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSstatsTMT/DESCRIPTION' ... OK
* this is package 'MSstatsTMT' version '2.0.1'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'MSstatsTMT' can be installed ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.checkSingleSubject: no visible global function definition for '.'
.plotProfileTMT: no visible global function definition for '.'
Undefined global functions or variables:
  .
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
dataProcessPlotsTMT 29.00   0.23   29.39
groupComparisonTMT   7.47   0.31    7.81
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
dataProcessPlotsTMT 34.05   0.17   34.26
groupComparisonTMT   8.91   0.11    9.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/MSstatsTMT.Rcheck/00check.log'
for details.



Installation output

MSstatsTMT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MSstatsTMT_2.0.1.tar.gz && rm -rf MSstatsTMT.buildbin-libdir && mkdir MSstatsTMT.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSstatsTMT.buildbin-libdir MSstatsTMT_2.0.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MSstatsTMT_2.0.1.zip && rm MSstatsTMT_2.0.1.tar.gz MSstatsTMT_2.0.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 28 1524k   28  427k    0     0   952k      0  0:00:01 --:--:--  0:00:01  953k
100 1524k  100 1524k    0     0  1363k      0  0:00:01  0:00:01 --:--:-- 1364k

install for i386

* installing *source* package 'MSstatsTMT' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MSstatsTMT'
    finding HTML links ... done
    MSstatsComparisonModelSingleTMT         html  
    MSstatsFitComparisonModelsTMT           html  
    MSstatsGroupComparisonOutputTMT         html  
    MSstatsGroupComparisonTMT               html  
    MSstatsModerateTTest                    html  
    MSstatsNormalizeTMT                     html  
    MSstatsPrepareForGroupComparisonTMT     html  
    MSstatsPrepareForSummarizationTMT       html  
    MSstatsSummarizationOutputTMT           html  
    MSstatsSummarizeTMT                     html  
    MSstatsTMT                              html  
    MSstatsTestSingleProteinTMT             html  
    MaxQtoMSstatsTMTFormat                  html  
    OpenMStoMSstatsTMTFormat                html  
    PDtoMSstatsTMTFormat                    html  
    SpectroMinetoMSstatsTMTFormat           html  
    annotation.mine                         html  
    annotation.mq                           html  
    annotation.pd                           html  
    dataProcessPlotsTMT                     html  
    dot-checkContrastMatrix                 html  
    dot-checkSummarizationParams            html  
    dot-countRunsWithNorm                   html  
    dot-documentFunction                    html  
    dot-getNormalizationAbundance           html  
    dot-getRunsMedian                       html  
    dot-logSum                              html  
    dot-logSummarizationParams              html  
    dot-makeContrastSingleTMT               html  
    dot-makeFactorColumnsTMT                html  
    dot-medianPolish                        html  
    dot-normalizePeptides                   html  
    dot-normalizeProteins                   html  
    dot-prepareForSummarization             html  
    dot-removeRedundantChannels             html  
    dot-summarizeMSstats                    html  
    dot-summarizeSimpleStat                 html  
    dot-summarizeTMP                        html  
    dot-summarizeTMT                        html  
    evidence                                html  
    getProcessedTMT                         html  
    getSummarizedTMT                        html  
    groupComparisonTMT                      html  
    input.pd                                html  
    proteinGroups                           html  
    proteinSummarization                    html  
    quant.pd.msstats                        html  
    raw.mine                                html  
    raw.om                                  html  
    raw.pd                                  html  
    test.pairwise                           html  
** 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

install for x64

* installing *source* package 'MSstatsTMT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSstatsTMT' as MSstatsTMT_2.0.1.zip
* DONE (MSstatsTMT)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MSstatsTMT' successfully unpacked and MD5 sums checked

Tests output

MSstatsTMT.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> library(testthat)
> library(MSstatsTMT)
> 
> test_check("MSstatsTMT")
INFO  [2021-10-15 02:27:53] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2021-10-15 02:27:54] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2021-10-15 02:27:54] ** Using provided annotation.
INFO  [2021-10-15 02:27:54] ** Raw data from MaxQuant imported successfully.
INFO  [2021-10-15 02:27:54] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:27:54] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:27:54] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:27:54] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:27:54] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-10-15 02:27:54] ** Features with all missing measurements across channels within each run are removed.
INFO  [2021-10-15 02:27:54] ** Raw data from MaxQuant cleaned successfully.
INFO  [2021-10-15 02:27:54] ** Using provided annotation.
INFO  [2021-10-15 02:27:54] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2021-10-15 02:27:54] ** 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  [2021-10-15 02:27:54] ** Features with all missing measurements across channels within each run are removed.
INFO  [2021-10-15 02:27:54] ** Shared peptides are removed.
INFO  [2021-10-15 02:27:54] ** Features with one or two measurements across channels within each run are removed.
INFO  [2021-10-15 02:27:54] ** PSMs have been aggregated to peptide ions.
INFO  [2021-10-15 02:27:54] ** Raw data from SpectroMine imported successfully.
INFO  [2021-10-15 02:27:54] ** Raw data from SpectroMine cleaned successfully.
INFO  [2021-10-15 02:27:54] ** Using provided annotation.
INFO  [2021-10-15 02:27:54] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2021-10-15 02:27:54] Model fitting for 10 proteins.

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INFO  [2021-10-15 02:27:55] Testing for 10 proteins:

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INFO  [2021-10-15 02:27:57] Model fitting for 10 proteins.

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INFO  [2021-10-15 02:27:58] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:27:58] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw ( 1  of  15 )

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INFO  [2021-10-15 02:27:58] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02.raw ( 2  of  15 )

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INFO  [2021-10-15 02:27:59] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01.raw ( 3  of  15 )

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INFO  [2021-10-15 02:27:59] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02.raw ( 4  of  15 )

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INFO  [2021-10-15 02:27:59] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_03.raw ( 5  of  15 )

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INFO  [2021-10-15 02:27:59] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_01.raw ( 6  of  15 )

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INFO  [2021-10-15 02:28:00] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_02.raw ( 7  of  15 )

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INFO  [2021-10-15 02:28:00] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_01.raw ( 8  of  15 )

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INFO  [2021-10-15 02:28:01] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02.raw ( 9  of  15 )

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INFO  [2021-10-15 02:28:01] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01.raw ( 10  of  15 )

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INFO  [2021-10-15 02:28:01] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02.raw ( 11  of  15 )

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INFO  [2021-10-15 02:28:02] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03.raw ( 12  of  15 )

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INFO  [2021-10-15 02:28:02] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03.raw ( 13  of  15 )

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INFO  [2021-10-15 02:28:02] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03.raw ( 14  of  15 )

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INFO  [2021-10-15 02:28:03] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_03.raw ( 15  of  15 )

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INFO  [2021-10-15 02:28:03] ** Protein-level summarization done by MSstats.
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:03] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw ( 1  of  15 )
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
  12.85    0.84   13.70 

MSstatsTMT.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> library(testthat)
> library(MSstatsTMT)
> 
> test_check("MSstatsTMT")
INFO  [2021-10-15 02:28:08] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2021-10-15 02:28:08] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2021-10-15 02:28:08] ** Using provided annotation.
INFO  [2021-10-15 02:28:08] ** Raw data from MaxQuant imported successfully.
INFO  [2021-10-15 02:28:08] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:28:08] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:28:08] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-15 02:28:08] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-15 02:28:08] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-10-15 02:28:08] ** Features with all missing measurements across channels within each run are removed.
INFO  [2021-10-15 02:28:08] ** Raw data from MaxQuant cleaned successfully.
INFO  [2021-10-15 02:28:08] ** Using provided annotation.
INFO  [2021-10-15 02:28:08] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2021-10-15 02:28:08] ** 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  [2021-10-15 02:28:08] ** Features with all missing measurements across channels within each run are removed.
INFO  [2021-10-15 02:28:08] ** Shared peptides are removed.
INFO  [2021-10-15 02:28:08] ** Features with one or two measurements across channels within each run are removed.
INFO  [2021-10-15 02:28:08] ** PSMs have been aggregated to peptide ions.
INFO  [2021-10-15 02:28:09] ** Raw data from SpectroMine imported successfully.
INFO  [2021-10-15 02:28:09] ** Raw data from SpectroMine cleaned successfully.
INFO  [2021-10-15 02:28:09] ** Using provided annotation.
INFO  [2021-10-15 02:28:09] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2021-10-15 02:28:09] Model fitting for 10 proteins.

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INFO  [2021-10-15 02:28:10] Testing for 10 proteins:

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INFO  [2021-10-15 02:28:11] Model fitting for 10 proteins.

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INFO  [2021-10-15 02:28:12] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:12] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw ( 1  of  15 )

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INFO  [2021-10-15 02:28:13] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02.raw ( 2  of  15 )

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INFO  [2021-10-15 02:28:13] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01.raw ( 3  of  15 )

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INFO  [2021-10-15 02:28:13] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02.raw ( 4  of  15 )

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INFO  [2021-10-15 02:28:14] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_03.raw ( 5  of  15 )

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INFO  [2021-10-15 02:28:14] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_01.raw ( 6  of  15 )

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INFO  [2021-10-15 02:28:14] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_02.raw ( 7  of  15 )

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INFO  [2021-10-15 02:28:15] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_01.raw ( 8  of  15 )

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INFO  [2021-10-15 02:28:15] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02.raw ( 9  of  15 )

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INFO  [2021-10-15 02:28:15] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01.raw ( 10  of  15 )

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INFO  [2021-10-15 02:28:15] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02.raw ( 11  of  15 )

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INFO  [2021-10-15 02:28:16] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03.raw ( 12  of  15 )

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INFO  [2021-10-15 02:28:16] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03.raw ( 13  of  15 )

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INFO  [2021-10-15 02:28:16] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03.raw ( 14  of  15 )

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INFO  [2021-10-15 02:28:17] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_03.raw ( 15  of  15 )

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INFO  [2021-10-15 02:28:17] ** Protein-level summarization done by MSstats.
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-15 02:28:17] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw ( 1  of  15 )
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
  12.78    0.56   13.34 

Example timings

MSstatsTMT.Rcheck/examples_i386/MSstatsTMT-Ex.timings

nameusersystemelapsed
MaxQtoMSstatsTMTFormat0.350.160.50
OpenMStoMSstatsTMTFormat0.150.010.17
PDtoMSstatsTMTFormat1.470.101.55
SpectroMinetoMSstatsTMTFormat0.360.000.35
annotation.mine000
annotation.mq000
annotation.pd0.010.000.02
dataProcessPlotsTMT29.00 0.2329.39
evidence0.020.000.02
groupComparisonTMT7.470.317.81
input.pd000
proteinGroups0.050.000.05
proteinSummarization4.340.244.55
quant.pd.msstats0.040.000.03
raw.mine0.010.000.02
raw.om000
raw.pd000
test.pairwise0.020.000.01

MSstatsTMT.Rcheck/examples_x64/MSstatsTMT-Ex.timings

nameusersystemelapsed
MaxQtoMSstatsTMTFormat0.640.130.74
OpenMStoMSstatsTMTFormat0.240.000.23
PDtoMSstatsTMTFormat2.250.112.34
SpectroMinetoMSstatsTMTFormat0.420.000.42
annotation.mine0.020.000.02
annotation.mq000
annotation.pd000
dataProcessPlotsTMT34.05 0.1734.26
evidence0.010.000.02
groupComparisonTMT8.910.119.02
input.pd000
proteinGroups0.050.010.06
proteinSummarization4.590.114.70
quant.pd.msstats0.080.000.08
raw.mine000
raw.om0.010.000.01
raw.pd000
test.pairwise000