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This page was generated on 2023-10-16 11:36:23 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1323/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsTMT 2.8.0  (landing page)
Ting Huang
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/MSstatsTMT
git_branch: RELEASE_3_17
git_last_commit: c6c55a8
git_last_commit_date: 2023-04-25 11:05:11 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for MSstatsTMT on palomino3


To the developers/maintainers of the MSstatsTMT package:
- 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 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: MSstatsTMT
Version: 2.8.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsTMT.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MSstatsTMT_2.8.0.tar.gz
StartedAt: 2023-10-16 04:30:31 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 04:32:44 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 132.9 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsTMT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsTMT.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MSstatsTMT_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/MSstatsTMT.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MSstatsTMT/DESCRIPTION' ... OK
* this is package 'MSstatsTMT' version '2.8.0'
* 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
* 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
.checkRepeatedMeasures: no visible global function definition for '.'
.checkSingleSubject: no visible global function definition for '.'
.checkTechReplicate: no visible global function definition for '.'
.getGroupLabel: no visible binding for global variable 'Condition'
.handleSingleContrastTMT: no visible global function definition for
  '.mygrad'
.plotProfileTMT: no visible global function definition for '.'
.plotProfileTMT: no visible binding for global variable 'censored'
Undefined global functions or variables:
  . .mygrad Condition censored
* 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 33.86   0.69   34.69
groupComparisonTMT   5.44   0.23    5.80
* 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc/meat/MSstatsTMT.Rcheck/00check.log'
for details.



Installation output

MSstatsTMT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL MSstatsTMT
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 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  [2023-10-16 04:32:28] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2023-10-16 04:32:28] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2023-10-16 04:32:28] ** Using provided annotation.
INFO  [2023-10-16 04:32:28] ** Raw data from MaxQuant imported successfully.
INFO  [2023-10-16 04:32:28] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2023-10-16 04:32:29] ** Rows with values of Reverse equal to + are removed 
INFO  [2023-10-16 04:32:29] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2023-10-16 04:32:29] ** Rows with values of Reverse equal to + are removed 
INFO  [2023-10-16 04:32:29] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2023-10-16 04:32:29] ** Features with all missing measurements across channels within each run are removed.
INFO  [2023-10-16 04:32:29] ** Raw data from MaxQuant cleaned successfully.
INFO  [2023-10-16 04:32:29] ** Using provided annotation.
INFO  [2023-10-16 04:32:29] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2023-10-16 04:32:29] ** 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 removed.
INFO  [2023-10-16 04:32:29] ** Features with all missing measurements across channels within each run are removed.
INFO  [2023-10-16 04:32:29] ** Shared peptides are removed.
INFO  [2023-10-16 04:32:29] ** Features with one or two measurements across channels within each run are removed.
INFO  [2023-10-16 04:32:29] ** PSMs have been aggregated to peptide ions.
INFO  [2023-10-16 04:32:29] ** Raw data from SpectroMine imported successfully.
INFO  [2023-10-16 04:32:29] ** Raw data from SpectroMine cleaned successfully.
INFO  [2023-10-16 04:32:29] ** Using provided annotation.
INFO  [2023-10-16 04:32:29] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2023-10-16 04:32:29] Design: 5 mixtures.
INFO  [2023-10-16 04:32:29] Design: 3 technical replicated MS runs per mixture.
INFO  [2023-10-16 04:32:29] Design: 1 subject per condition (No biological variation).
INFO  [2023-10-16 04:32:29] Model fitting for 10 proteins.

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INFO  [2023-10-16 04:32:30] Testing for 10 proteins:

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INFO  [2023-10-16 04:32:30] Design: 5 mixtures.
INFO  [2023-10-16 04:32:30] Design: 3 technical replicated MS runs per mixture.
INFO  [2023-10-16 04:32:30] Design: 1 subject per condition (No biological variation).
INFO  [2023-10-16 04:32:30] Model fitting for 10 proteins.

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INFO  [2023-10-16 04:32:30] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:31] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01raw ( 1  of  15 )

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INFO  [2023-10-16 04:32:31] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02raw ( 2  of  15 )

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INFO  [2023-10-16 04:32:31] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01raw ( 3  of  15 )

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INFO  [2023-10-16 04:32:32] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02raw ( 4  of  15 )

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INFO  [2023-10-16 04:32:32] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_03raw ( 5  of  15 )

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INFO  [2023-10-16 04:32:32] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_01raw ( 6  of  15 )

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INFO  [2023-10-16 04:32:32] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_02raw ( 7  of  15 )

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INFO  [2023-10-16 04:32:32] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_01raw ( 8  of  15 )

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INFO  [2023-10-16 04:32:33] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02raw ( 9  of  15 )

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INFO  [2023-10-16 04:32:33] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01raw ( 10  of  15 )

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INFO  [2023-10-16 04:32:33] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02raw ( 11  of  15 )

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INFO  [2023-10-16 04:32:33] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03raw ( 12  of  15 )

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INFO  [2023-10-16 04:32:34] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03raw ( 13  of  15 )

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INFO  [2023-10-16 04:32:34] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03raw ( 14  of  15 )

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INFO  [2023-10-16 04:32:34] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_03raw ( 15  of  15 )

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  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2023-10-16 04:32:34] ** Protein-level summarization done by MSstats.
INFO  [2023-10-16 04:32:34] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:34] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:34] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:34] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:34] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:34] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:34] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:34] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:34] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:35] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:35] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:35] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:35] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:35] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:35] ** MSstatsTMT - proteinSummarization function
INFO  [2023-10-16 04:32:35] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01raw ( 1  of  15 )
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
   8.70    0.65    9.53 

Example timings

MSstatsTMT.Rcheck/MSstatsTMT-Ex.timings

nameusersystemelapsed
MaxQtoMSstatsTMTFormat0.420.160.59
OpenMStoMSstatsTMTFormat0.150.000.16
PDtoMSstatsTMTFormat1.670.071.77
SpectroMinetoMSstatsTMTFormat0.270.000.26
annotation.mine000
annotation.mq000
annotation.pd0.010.000.02
dataProcessPlotsTMT33.86 0.6934.69
evidence0.000.020.01
groupComparisonTMT5.440.235.80
input.pd0.030.000.03
proteinGroups0.060.020.08
proteinSummarization3.550.153.84
quant.pd.msstats0.030.000.03
raw.mine000
raw.om000
raw.pd0.020.000.02
test.pairwise000