Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:33 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 1331/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSstats 4.11.1 (landing page) Meena Choi
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the MSstats package: - 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 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. |
Package: MSstats |
Version: 4.11.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstats_4.11.1.tar.gz |
StartedAt: 2024-03-02 07:21:41 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 07:26:32 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 291.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MSstats.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstats_4.11.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MSstats.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSstats/DESCRIPTION’ ... OK * this is package ‘MSstats’ version ‘4.11.1’ * 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 ‘MSstats’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘statmod’ All declared Imports should be used. Unexported object imported by a ':::' call: ‘MSstatsConvert:::.standardizeColnames’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .plotHeatmap : <anonymous>: no visible global function definition for ‘col2rgb’ .plotProfile: no visible binding for global variable ‘newABUNDANCE’ .savePlotlyPlotHTML: no visible global function definition for ‘zip’ .setCensoredByThreshold: no visible binding for global variable ‘any_censored’ DIANNtoMSstatsFormat: no visible binding for global variable ‘DetectionQValue’ DIANNtoMSstatsFormat: no visible binding for global variable ‘LibPGQValue’ DIANNtoMSstatsFormat: no visible binding for global variable ‘LibQValue’ DIANNtoMSstatsFormat: no visible binding for global variable ‘GlobalPGQValue’ DIANNtoMSstatsFormat: no visible binding for global variable ‘GlobalQValue’ MSstatsPrepareForSummarization: no visible binding for global variable ‘ref’ MSstatsPrepareForSummarization: no visible binding for global variable ‘LABEL’ MSstatsPrepareForSummarization: no visible binding for global variable ‘RUN’ SDRFtoAnnotation: no visible binding for global variable ‘..extract_cols’ extractSDRF: no visible binding for global variable ‘..extract_cols’ Undefined global functions or variables: ..extract_cols DetectionQValue GlobalPGQValue GlobalQValue LABEL LibPGQValue LibQValue RUN any_censored col2rgb newABUNDANCE ref zip Consider adding importFrom("grDevices", "col2rgb") importFrom("utils", "zip") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘example_SDRF’ Undocumented data sets: ‘example_SDRF’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'dot-documentFunction.Rd': ‘removeFewMeasurements’ ‘useUniquePeptide’ ‘summaryforMultipleRows’ ‘removeProtein_with1Feature’ ‘removeProtein_with1Peptide’ ‘removeOxidationMpeptides’ ‘removeMpeptides’ ‘use_log_file’ ‘append’ ‘verbose’ ‘log_file_path’ Documented arguments not in \usage in Rd file 'dot-getContrast.Rd': ‘contrast_matrix’ Documented arguments not in \usage in Rd file 'dot-getSingleProteinForProfile.Rd': ‘dataProcess’ Documented arguments not in \usage in Rd file 'dot-getWideTable.Rd': ‘vector’ 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 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed dataProcessPlots 13.173 0.128 15.419 dot-makeQCPlot 12.016 0.113 14.118 groupComparisonPlots 5.957 0.083 6.913 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tinytest.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: 1 WARNING, 5 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/MSstats.Rcheck/00check.log’ for details.
MSstats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstats ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MSstats’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c common.cpp -o common.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c comparison_contrasts.cpp -o comparison_contrasts.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c linear_summary.cpp -o linear_summary.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c median_polish.cpp -o median_polish.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o MSstats.so RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-MSstats/00new/MSstats/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MSstats)
MSstats.Rcheck/tests/tinytest.Rout
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > 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;34m0.4s[0m [0;34m0.2s[0m All ok, 1 results (1.1s) > > proc.time() user system elapsed 6.205 0.575 8.086
MSstats.Rcheck/MSstats-Ex.timings
name | user | system | elapsed | |
DDARawData | 0.011 | 0.004 | 0.016 | |
DDARawData.Skyline | 0.008 | 0.003 | 0.014 | |
DIANNtoMSstatsFormat | 0 | 0 | 0 | |
DIARawData | 0.006 | 0.001 | 0.008 | |
DIAUmpiretoMSstatsFormat | 0.223 | 0.017 | 0.274 | |
FragPipetoMSstatsFormat | 0.098 | 0.013 | 0.136 | |
MSstatsGroupComparison | 0.599 | 0.031 | 0.735 | |
MSstatsGroupComparisonOutput | 0.521 | 0.012 | 0.665 | |
MSstatsGroupComparisonSingleProtein | 0.406 | 0.007 | 0.496 | |
MSstatsHandleMissing | 0.106 | 0.008 | 0.130 | |
MSstatsMergeFractions | 0.114 | 0.006 | 0.135 | |
MSstatsNormalize | 0.101 | 0.006 | 0.135 | |
MSstatsPrepareForDataProcess | 0.091 | 0.005 | 0.115 | |
MSstatsPrepareForGroupComparison | 0.279 | 0.008 | 0.336 | |
MSstatsPrepareForSummarization | 0.092 | 0.005 | 0.111 | |
MSstatsSelectFeatures | 0.438 | 0.020 | 0.532 | |
MSstatsSummarizationOutput | 0.510 | 0.013 | 0.605 | |
MSstatsSummarize | 0.489 | 0.010 | 0.570 | |
MSstatsSummarizeSingleLinear | 0.146 | 0.005 | 0.170 | |
MSstatsSummarizeSingleTMP | 0.184 | 0.004 | 0.207 | |
MaxQtoMSstatsFormat | 0.286 | 0.016 | 0.353 | |
OpenMStoMSstatsFormat | 0.099 | 0.003 | 0.117 | |
OpenSWATHtoMSstatsFormat | 0.118 | 0.007 | 0.152 | |
PDtoMSstatsFormat | 0.119 | 0.007 | 0.147 | |
ProgenesistoMSstatsFormat | 0.110 | 0.004 | 0.128 | |
SDRFtoAnnotation | 0.025 | 0.007 | 0.037 | |
SRMRawData | 0.005 | 0.001 | 0.010 | |
SkylinetoMSstatsFormat | 0.187 | 0.013 | 0.245 | |
SpectronauttoMSstatsFormat | 0.094 | 0.004 | 0.115 | |
checkRepeatedDesign | 0.254 | 0.003 | 0.304 | |
dataProcess | 0.796 | 0.015 | 0.938 | |
dataProcessPlots | 13.173 | 0.128 | 15.419 | |
designSampleSize | 0.521 | 0.019 | 0.646 | |
designSampleSizePlots | 0.544 | 0.017 | 0.666 | |
dot-makeQCPlot | 12.016 | 0.113 | 14.118 | |
extractSDRF | 0.273 | 0.010 | 0.319 | |
getProcessed | 0.120 | 0.010 | 0.139 | |
getSamplesInfo | 0.579 | 0.010 | 0.652 | |
groupComparison | 0.443 | 0.011 | 0.504 | |
groupComparisonPlots | 5.957 | 0.083 | 6.913 | |
makePeptidesDictionary | 0.006 | 0.002 | 0.008 | |
modelBasedQCPlots | 1.680 | 0.025 | 3.271 | |
quantification | 0.327 | 0.013 | 0.412 | |