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This page was generated on 2021-10-15 15:06:44 -0400 (Fri, 15 Oct 2021).

CHECK results for MSstatsTMT on machv2

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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstatsTMT_2.0.1.tar.gz
StartedAt: 2021-10-14 21:30:44 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 21:33:54 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 190.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsTMT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstatsTMT_2.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MSstatsTMT.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
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 ‘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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
dataProcessPlotsTMT  44.386  0.378  44.866
groupComparisonTMT   11.320  0.129  11.493
proteinSummarization  5.331  0.122   5.501
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/MSstatsTMT.Rcheck/00check.log’
for details.



Installation output

MSstatsTMT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MSstatsTMT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* 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
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstatsTMT)

Tests output

MSstatsTMT.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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  [2021-10-14 21:33:27] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2021-10-14 21:33:27] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2021-10-14 21:33:27] ** Using provided annotation.
INFO  [2021-10-14 21:33:27] ** Raw data from MaxQuant imported successfully.
INFO  [2021-10-14 21:33:27] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-14 21:33:27] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-14 21:33:27] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2021-10-14 21:33:27] ** Rows with values of Reverse equal to + are removed 
INFO  [2021-10-14 21:33:27] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2021-10-14 21:33:27] ** Features with all missing measurements across channels within each run are removed.
INFO  [2021-10-14 21:33:27] ** Raw data from MaxQuant cleaned successfully.
INFO  [2021-10-14 21:33:27] ** Using provided annotation.
INFO  [2021-10-14 21:33:27] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2021-10-14 21:33:27] ** 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  [2021-10-14 21:33:27] ** Features with all missing measurements across channels within each run are removed.
INFO  [2021-10-14 21:33:27] ** Shared peptides are removed.
INFO  [2021-10-14 21:33:27] ** Features with one or two measurements across channels within each run are removed.
INFO  [2021-10-14 21:33:27] ** PSMs have been aggregated to peptide ions.
INFO  [2021-10-14 21:33:27] ** Raw data from SpectroMine imported successfully.
INFO  [2021-10-14 21:33:27] ** Raw data from SpectroMine cleaned successfully.
INFO  [2021-10-14 21:33:27] ** Using provided annotation.
INFO  [2021-10-14 21:33:27] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2021-10-14 21:33:27] Model fitting for 10 proteins.

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INFO  [2021-10-14 21:33:28] Testing for 10 proteins:

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INFO  [2021-10-14 21:33:30] Model fitting for 10 proteins.

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INFO  [2021-10-14 21:33:32] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:32] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw ( 1  of  15 )

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INFO  [2021-10-14 21:33:32] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02.raw ( 2  of  15 )

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INFO  [2021-10-14 21:33:33] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01.raw ( 3  of  15 )

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INFO  [2021-10-14 21:33:33] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02.raw ( 4  of  15 )

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INFO  [2021-10-14 21:33:33] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_03.raw ( 5  of  15 )

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INFO  [2021-10-14 21:33:34] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_01.raw ( 6  of  15 )

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INFO  [2021-10-14 21:33:34] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_02.raw ( 7  of  15 )

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INFO  [2021-10-14 21:33:34] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_01.raw ( 8  of  15 )

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INFO  [2021-10-14 21:33:35] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02.raw ( 9  of  15 )

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INFO  [2021-10-14 21:33:35] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01.raw ( 10  of  15 )

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INFO  [2021-10-14 21:33:35] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02.raw ( 11  of  15 )

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INFO  [2021-10-14 21:33:36] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03.raw ( 12  of  15 )

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INFO  [2021-10-14 21:33:36] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03.raw ( 13  of  15 )

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INFO  [2021-10-14 21:33:36] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03.raw ( 14  of  15 )

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INFO  [2021-10-14 21:33:37] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_03.raw ( 15  of  15 )

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INFO  [2021-10-14 21:33:37] ** Protein-level summarization done by MSstats.
INFO  [2021-10-14 21:33:37] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:37] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:37] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:37] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:37] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:37] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:37] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:37] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:37] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:37] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:37] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:37] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:37] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:38] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:38] ** MSstatsTMT - proteinSummarization function
INFO  [2021-10-14 21:33:38] 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 
 15.891   0.585  16.587 

Example timings

MSstatsTMT.Rcheck/MSstatsTMT-Ex.timings

nameusersystemelapsed
MaxQtoMSstatsTMTFormat0.7430.0940.837
OpenMStoMSstatsTMTFormat0.2700.0120.283
PDtoMSstatsTMTFormat2.6940.1062.802
SpectroMinetoMSstatsTMTFormat0.4230.0160.440
annotation.mine0.0030.0010.003
annotation.mq0.0030.0010.004
annotation.pd0.0040.0010.004
dataProcessPlotsTMT44.386 0.37844.866
evidence0.0150.0130.028
groupComparisonTMT11.320 0.12911.493
input.pd0.0130.0020.016
proteinGroups0.1140.0590.174
proteinSummarization5.3310.1225.501
quant.pd.msstats0.0550.0040.059
raw.mine0.0100.0030.012
raw.om0.0060.0010.007
raw.pd0.0100.0040.014
test.pairwise0.0030.0010.003