Ting Huang
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/MSstatsTMT |
| git_branch: master |
| git_last_commit: 3648ead |
| git_last_commit_date: 2022-02-18 13:33:24 -0400 (Fri, 18 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:07 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 1241/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsTMT 2.3.7 (landing page) Ting Huang
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MSstatsTMT |
| Version: 2.3.7 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsTMT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MSstatsTMT_2.3.7.tar.gz |
| StartedAt: 2022-03-17 19:41:01 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:43:15 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 133.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsTMT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsTMT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MSstatsTMT_2.3.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MSstatsTMT.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '2.3.7'
* 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 29.18 0.38 29.69
groupComparisonTMT 4.26 0.22 5.51
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/MSstatsTMT.Rcheck/00check.log'
for details.
MSstatsTMT.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MSstatsTMT
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
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
PhilosophertoMSstatsTMTFormat 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-handleSingleContrastTMT 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
* DONE (MSstatsTMT)
Making 'packages.html' ... done
MSstatsTMT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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 [2022-03-17 19:42:54] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2022-03-17 19:42:54] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2022-03-17 19:42:54] ** Using provided annotation.
INFO [2022-03-17 19:42:54] ** Raw data from MaxQuant imported successfully.
INFO [2022-03-17 19:42:54] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-03-17 19:42:54] ** Rows with values of Reverse equal to + are removed
INFO [2022-03-17 19:42:54] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-03-17 19:42:54] ** Rows with values of Reverse equal to + are removed
INFO [2022-03-17 19:42:54] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO [2022-03-17 19:42:54] ** Features with all missing measurements across channels within each run are removed.
INFO [2022-03-17 19:42:54] ** Raw data from MaxQuant cleaned successfully.
INFO [2022-03-17 19:42:54] ** Using provided annotation.
INFO [2022-03-17 19:42:54] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2022-03-17 19:42:54] ** 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 [2022-03-17 19:42:54] ** Features with all missing measurements across channels within each run are removed.
INFO [2022-03-17 19:42:54] ** Shared peptides are removed.
INFO [2022-03-17 19:42:54] ** Features with one or two measurements across channels within each run are removed.
INFO [2022-03-17 19:42:54] ** PSMs have been aggregated to peptide ions.
INFO [2022-03-17 19:42:54] ** Raw data from SpectroMine imported successfully.
INFO [2022-03-17 19:42:54] ** Raw data from SpectroMine cleaned successfully.
INFO [2022-03-17 19:42:54] ** Using provided annotation.
INFO [2022-03-17 19:42:54] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2022-03-17 19:42:55] Design: 5 mixtures.
INFO [2022-03-17 19:42:55] Design: 3 technical replicated MS runs per mixture.
INFO [2022-03-17 19:42:55] Design: 1 subject per condition (No biological variation).
INFO [2022-03-17 19:42:55] Model fitting for 10 proteins.
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:55] Testing for 10 proteins:
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:56] Design: 5 mixtures.
INFO [2022-03-17 19:42:56] Design: 3 technical replicated MS runs per mixture.
INFO [2022-03-17 19:42:56] Design: 1 subject per condition (No biological variation).
INFO [2022-03-17 19:42:56] Model fitting for 10 proteins.
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:56] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:56] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01raw ( 1 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:56] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02raw ( 2 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:57] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01raw ( 3 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:57] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02raw ( 4 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:57] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_03raw ( 5 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:57] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_01raw ( 6 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:57] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_02raw ( 7 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:57] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_01raw ( 8 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:58] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02raw ( 9 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:58] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01raw ( 10 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:58] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02raw ( 11 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:58] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03raw ( 12 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:58] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03raw ( 13 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:59] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03raw ( 14 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:59] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_03raw ( 15 of 15 )
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
INFO [2022-03-17 19:42:59] ** Protein-level summarization done by MSstats.
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2022-03-17 19:42:59] 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
7.18 0.64 8.39
MSstatsTMT.Rcheck/MSstatsTMT-Ex.timings
| name | user | system | elapsed | |
| MaxQtoMSstatsTMTFormat | 0.55 | 0.04 | 0.56 | |
| OpenMStoMSstatsTMTFormat | 0.11 | 0.03 | 0.14 | |
| PDtoMSstatsTMTFormat | 1.64 | 0.14 | 1.76 | |
| SpectroMinetoMSstatsTMTFormat | 0.23 | 0.00 | 0.24 | |
| annotation.mine | 0 | 0 | 0 | |
| annotation.mq | 0 | 0 | 0 | |
| annotation.pd | 0 | 0 | 0 | |
| dataProcessPlotsTMT | 29.18 | 0.38 | 29.69 | |
| evidence | 0 | 0 | 0 | |
| groupComparisonTMT | 4.26 | 0.22 | 5.51 | |
| input.pd | 0.03 | 0.00 | 0.03 | |
| proteinGroups | 0.03 | 0.01 | 0.05 | |
| proteinSummarization | 2.75 | 0.13 | 3.32 | |
| quant.pd.msstats | 0.04 | 0.00 | 0.04 | |
| raw.mine | 0 | 0 | 0 | |
| raw.om | 0.01 | 0.00 | 0.01 | |
| raw.pd | 0 | 0 | 0 | |
| test.pairwise | 0 | 0 | 0 | |