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This page was generated on 2024-12-24 11:45 -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 1353/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsTMT 2.15.1  (landing page)
Devon Kohler
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/MSstatsTMT
git_branch: devel
git_last_commit: 6bf3322
git_last_commit_date: 2024-11-14 16:00:18 -0500 (Thu, 14 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 MSstatsTMT on kjohnson3

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: 2.15.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsTMT_2.15.1.tar.gz
StartedAt: 2024-12-23 20:23:31 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 20:24:23 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 52.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsTMT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsTMT_2.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MSstatsTMT.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsTMT/DESCRIPTION’ ... OK
* this is package ‘MSstatsTMT’ version ‘2.15.1’
* 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 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 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 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’
.getVarComponentTMT : <anonymous>: no visible global function
  definition for ‘is’
.handleSingleContrastTMT: no visible global function definition for
  ‘.mygrad’
.plotProfileTMT: no visible global function definition for ‘.’
.plotProfileTMT: no visible binding for global variable ‘censored’
.savePlotlyPlotHTML: no visible global function definition for ‘zip’
Undefined global functions or variables:
  . .mygrad Condition censored is zip
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "zip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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-documentFunction.Rd':
  ‘removeProtein_with1Peptide’ ‘use_log_file’ ‘append’ ‘verbose’
  ‘log_file_path’

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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
dataProcessPlotsTMT 9.276  0.107   9.494
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/MSstatsTMT.Rcheck/00check.log’
for details.


Installation output

MSstatsTMT.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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  [2024-12-23 20:24:17] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-12-23 20:24:17] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-12-23 20:24:17] ** Using provided annotation.
INFO  [2024-12-23 20:24:17] ** Raw data from MaxQuant imported successfully.
INFO  [2024-12-23 20:24:17] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-12-23 20:24:17] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-12-23 20:24:17] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-12-23 20:24:17] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-12-23 20:24:17] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2024-12-23 20:24:17] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-23 20:24:17] ** Raw data from MaxQuant cleaned successfully.
INFO  [2024-12-23 20:24:17] ** Using provided annotation.
INFO  [2024-12-23 20:24:17] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-23 20:24:17] ** 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  [2024-12-23 20:24:17] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-12-23 20:24:17] ** Shared peptides are removed.
INFO  [2024-12-23 20:24:17] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-12-23 20:24:17] ** PSMs have been aggregated to peptide ions.
INFO  [2024-12-23 20:24:17] ** Raw data from SpectroMine imported successfully.
INFO  [2024-12-23 20:24:17] ** Raw data from SpectroMine cleaned successfully.
INFO  [2024-12-23 20:24:17] ** Using provided annotation.
INFO  [2024-12-23 20:24:17] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-12-23 20:24:17] Design: 5 mixtures.
INFO  [2024-12-23 20:24:17] Design: 3 technical replicated MS runs per mixture.
INFO  [2024-12-23 20:24:17] Design: 1 subject per condition (No biological variation).
INFO  [2024-12-23 20:24:17] Model fitting for 10 proteins.

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INFO  [2024-12-23 20:24:17] Testing for 10 proteins:

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INFO  [2024-12-23 20:24:17] Design: 5 mixtures.
INFO  [2024-12-23 20:24:17] Design: 3 technical replicated MS runs per mixture.
INFO  [2024-12-23 20:24:17] Design: 1 subject per condition (No biological variation).
INFO  [2024-12-23 20:24:17] Model fitting for 10 proteins.

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INFO  [2024-12-23 20:24:17] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:17] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01raw ( 1  of  15 )

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INFO  [2024-12-23 20:24:18] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02raw ( 2  of  15 )

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INFO  [2024-12-23 20:24:18] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01raw ( 3  of  15 )

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INFO  [2024-12-23 20:24:18] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02raw ( 4  of  15 )

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INFO  [2024-12-23 20:24:18] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_03raw ( 5  of  15 )

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INFO  [2024-12-23 20:24:18] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_01raw ( 6  of  15 )

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INFO  [2024-12-23 20:24:18] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_02raw ( 7  of  15 )

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INFO  [2024-12-23 20:24:18] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_01raw ( 8  of  15 )

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INFO  [2024-12-23 20:24:18] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02raw ( 9  of  15 )

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INFO  [2024-12-23 20:24:18] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01raw ( 10  of  15 )

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INFO  [2024-12-23 20:24:18] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02raw ( 11  of  15 )

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INFO  [2024-12-23 20:24:18] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03raw ( 12  of  15 )

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INFO  [2024-12-23 20:24:18] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03raw ( 13  of  15 )

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INFO  [2024-12-23 20:24:19] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03raw ( 14  of  15 )

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INFO  [2024-12-23 20:24:19] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_03raw ( 15  of  15 )

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INFO  [2024-12-23 20:24:19] ** Protein-level summarization done by MSstats.
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] ** MSstatsTMT - proteinSummarization function
INFO  [2024-12-23 20:24:19] 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 
  3.273   0.175   3.518 

Example timings

MSstatsTMT.Rcheck/MSstatsTMT-Ex.timings

nameusersystemelapsed
MaxQtoMSstatsTMTFormat0.1560.0290.187
OpenMStoMSstatsTMTFormat0.0440.0030.048
PDtoMSstatsTMTFormat0.5140.0270.541
SpectroMinetoMSstatsTMTFormat0.0830.0030.086
annotation.mine0.0010.0000.001
annotation.mq000
annotation.pd0.0010.0010.000
dataProcessPlotsTMT9.2760.1079.494
designSampleSizeTMT1.6310.0531.684
evidence0.0070.0010.008
groupComparisonTMT1.5620.0331.612
input.pd0.0140.0020.021
proteinGroups0.0390.0090.048
proteinSummarization1.0950.0481.207
quant.pd.msstats0.0120.0010.013
raw.mine0.0030.0000.003
raw.om0.0010.0000.001
raw.pd0.0030.0010.005
test.pairwise0.0000.0000.001