Meena Choi
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/MSstats |
| git_branch: RELEASE_3_13 |
| git_last_commit: afa9e58 |
| git_last_commit_date: 2021-05-31 23:11:01 -0400 (Mon, 31 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:13 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the MSstats package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstats.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 1208/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstats 4.0.1 (landing page) Meena Choi
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MSstats |
| Version: 4.0.1 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MSstats_4.0.1.tar.gz |
| StartedAt: 2021-10-15 02:22:57 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 02:25:50 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 172.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstats.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MSstats_4.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MSstats.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 'MSstats/DESCRIPTION' ... OK * this is package 'MSstats' version '4.0.1' * 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 'MSstats' 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 .setCensoredByThreshold: no visible binding for global variable 'any_censored' Undefined global functions or variables: any_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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/MSstats/libs/i386/MSstats.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/MSstats/libs/x64/MSstats.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'tinytest.R' OK ** running tests for arch 'x64' ... Running 'tinytest.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 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MSstats.Rcheck/00check.log' for details.
MSstats.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MSstats_4.0.1.tar.gz && rm -rf MSstats.buildbin-libdir && mkdir MSstats.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSstats.buildbin-libdir MSstats_4.0.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MSstats_4.0.1.zip && rm MSstats_4.0.1.tar.gz MSstats_4.0.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 171k 100 171k 0 0 585k 0 --:--:-- --:--:-- --:--:-- 587k
install for i386
* installing *source* package 'MSstats' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c common.cpp -o common.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c comparison_contrasts.cpp -o comparison_contrasts.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c linear_summary.cpp -o linear_summary.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c median_polish.cpp -o median_polish.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o MSstats.dll tmp.def RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/MSstats.buildbin-libdir/00LOCK-MSstats/00new/MSstats/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MSstats'
finding HTML links ... done
DDARawData html
DDARawData.Skyline html
DIARawData html
DIAUmpiretoMSstatsFormat html
MSstatsContrastMatrix html
MSstatsGroupComparison html
MSstatsGroupComparisonOutput html
MSstatsGroupComparisonSingleProtein html
MSstatsHandleMissing html
MSstatsMergeFractions html
MSstatsNormalize html
MSstatsPrepareForDataProcess html
MSstatsPrepareForGroupComparison html
MSstatsPrepareForSummarization html
MSstatsSelectFeatures html
MSstatsSummarizationOutput html
MSstatsSummarize html
MSstatsSummarizeSingleLinear html
MSstatsSummarizeSingleTMP html
MaxQtoMSstatsFormat html
OpenMStoMSstatsFormat html
OpenSWATHtoMSstatsFormat html
PDtoMSstatsFormat html
ProgenesistoMSstatsFormat html
SRMRawData html
SkylinetoMSstatsFormat html
SpectronauttoMSstatsFormat html
checkRepeatedDesign html
dataProcess html
dataProcessPlots html
designSampleSize html
designSampleSizePlots html
dot-addCoverageInfo html
dot-addModelInformation html
dot-addModelVariances html
dot-addNInformativeInfo html
dot-addNoisyFlag html
dot-addOutlierCutoff html
dot-addOutlierInformation html
dot-addSurvivalPredictions html
dot-adjustLRuns html
dot-calculateOutlierCutoff html
dot-calculatePower html
dot-calculateProteinVariance html
dot-checkContrastMatrix html
dot-checkDataProcessParams html
dot-checkExperimentDesign html
dot-checkGCPlotsInput html
dot-checkGroupComparisonInput html
dot-checkSingleFeature html
dot-checkSingleLabelProteins html
dot-checkSingleSubject html
dot-checkTechReplicate html
dot-checkUnProcessedDataValidity html
dot-countInformative html
dot-countMissingPercentage html
dot-documentFunction html
dot-finalizeInput html
dot-finalizeLinear html
dot-finalizeTMP html
dot-fitHuber html
dot-fitLinearModel html
dot-fitModelForGroupComparison html
dot-fitModelSingleProtein html
dot-fitTukey html
dot-flagLowCoverage html
dot-flagUninformativeSingleLabel html
dot-getAllComparisons html
dot-getContrast html
dot-getContrastLabels html
dot-getEmptyComparison html
dot-getFeatureVariances html
dot-getMedian html
dot-getMedianSigmaSubject html
dot-getMin html
dot-getModelParameters html
dot-getNonMissingFilter html
dot-getNonMissingFilterStats html
dot-getNumSample html
dot-getSingleProteinForProfile html
dot-getVarComponent html
dot-getWideTable html
dot-getYaxis html
dot-handleEmptyConditions html
dot-handleSingleContrast html
dot-isSummarizable html
dot-logDatasetInformation html
dot-logMissingness html
dot-logSingleLabeledProteins html
dot-logSummaryStatistics html
dot-makeComparison html
dot-makeConditionPlot html
dot-makeFactorColumns html
dot-makeHeatmap html
dot-makeProfilePlot html
dot-makeQCPlot html
dot-makeSummaryProfilePlot html
dot-makeVolcano html
dot-nicePrint html
dot-normalizeGlobalStandards html
dot-normalizeMedian html
dot-normalizeQuantile html
dot-onLoad html
dot-plotComparison html
dot-plotHeatmap html
dot-plotVolcano html
dot-preProcessIntensities html
dot-prepareForDataProcess html
dot-prepareLinear html
dot-prepareSingleProteinForGC html
dot-prepareSummary html
dot-prepareTMP html
dot-quantileNormalizationSingleLabel html
dot-replaceZerosWithNA html
dot-runTukey html
dot-saveSessionInfo html
dot-saveTable html
dot-selectHighQualityFeatures html
dot-selectTopFeatures html
dot-setCensoredByThreshold html
dot-updateColumnsForProcessing html
dot-updateUnequalVariances html
getProcessed html
getSamplesInfo html
getSelectedProteins html
groupComparison html
groupComparisonPlots html
makePeptidesDictionary html
modelBasedQCPlots html
quantification html
savePlot html
theme_msstats 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 'MSstats' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c common.cpp -o common.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c comparison_contrasts.cpp -o comparison_contrasts.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c linear_summary.cpp -o linear_summary.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c median_polish.cpp -o median_polish.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o MSstats.dll tmp.def RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/MSstats.buildbin-libdir/MSstats/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSstats' as MSstats_4.0.1.zip
* DONE (MSstats)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MSstats' successfully unpacked and MD5 sums checked
|
MSstats.Rcheck/tests_i386/tinytest.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.
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+ tinytest::test_package("MSstats")
+ }
Attaching package: 'MSstats'
The following object is masked from 'package:grDevices':
savePlot
test_MSstatsdev.R............. 1 tests [0;32mOK[0m [0;36m47ms[0m
[0;36m0ms[0m
All ok, 1 results (63ms)
>
> proc.time()
user system elapsed
2.93 0.26 3.18
|
MSstats.Rcheck/tests_x64/tinytest.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.
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+ tinytest::test_package("MSstats")
+ }
Attaching package: 'MSstats'
The following object is masked from 'package:grDevices':
savePlot
test_MSstatsdev.R............. 1 tests [0;32mOK[0m [0;36m62ms[0m
[0;36m0ms[0m
All ok, 1 results (62ms)
>
> proc.time()
user system elapsed
3.42 0.18 3.59
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MSstats.Rcheck/examples_i386/MSstats-Ex.timings
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MSstats.Rcheck/examples_x64/MSstats-Ex.timings
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