Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-09 17:39 -0400 (Tue, 09 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4709 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 1360/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSstats 4.12.0 (landing page) Meena Choi
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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: 4.12.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MSstats_4.12.0.tar.gz |
StartedAt: 2024-07-08 01:31:00 -0400 (Mon, 08 Jul 2024) |
EndedAt: 2024-07-08 01:32:57 -0400 (Mon, 08 Jul 2024) |
EllapsedTime: 117.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MSstats.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MSstats.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MSstats_4.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MSstats.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘MSstats/DESCRIPTION’ ... OK * this is package ‘MSstats’ version ‘4.12.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘MSstats’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 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 loading without being on the library search path ... 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 ... NOTE checkRd: (-1) MSstatsSummarizationOutput.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) MSstatsSummarizationOutput.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) MSstatsSummarizationOutput.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly * 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 5.693 0.064 5.652 dot-makeQCPlot 5.229 0.080 5.243 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 6 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/MSstats.Rcheck/00check.log’ for details.
MSstats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MSstats ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘MSstats’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c common.cpp -o common.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c comparison_contrasts.cpp -o comparison_contrasts.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c linear_summary.cpp -o linear_summary.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c median_polish.cpp -o median_polish.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o MSstats.so RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -fopenmp -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/site-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 version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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;36m51ms[0m INFO [2024-07-08 01:32:38] ** Features with one or two measurements across runs are removed. INFO [2024-07-08 01:32:38] ** Fractionation handled. INFO [2024-07-08 01:32:38] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-07-08 01:32:38] ** Log2 intensities under cutoff = 3.776 were considered as censored missing values. INFO [2024-07-08 01:32:38] ** Log2 intensities = NA were considered as censored missing values. INFO [2024-07-08 01:32:38] ** Use all features that the dataset originally has. INFO [2024-07-08 01:32:38] # proteins: 2 # peptides per protein: 2-2 # features per peptide: 3-3 INFO [2024-07-08 01:32:38] 1 2 3 4 5 6 7 8 9 10 # runs 3 3 3 3 3 3 3 3 3 3 # bioreplicates 3 3 3 3 3 3 3 3 3 3 # tech. replicates 1 1 1 1 1 1 1 1 1 1 INFO [2024-07-08 01:32:38] == Start the summarization per subplot... | | | 0% | |=================================== | 50% | |======================================================================| 100% INFO [2024-07-08 01:32:38] == Summarization is done. test_dataProcess.R............ 0 tests INFO [2024-07-08 01:32:38] ** Features with one or two measurements across runs are removed. INFO [2024-07-08 01:32:38] ** Fractionation handled. INFO [2024-07-08 01:32:39] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-07-08 01:32:39] ** Use all features that the dataset originally has. INFO [2024-07-08 01:32:39] # proteins: 6 # peptides per protein: 11-32 # features per peptide: 1-1 INFO [2024-07-08 01:32:39] C1 C2 C3 C4 C5 C6 # runs 3 3 3 3 3 3 # bioreplicates 1 1 1 1 1 1 # tech. replicates 3 3 3 3 3 3 INFO [2024-07-08 01:32:39] Some features are completely missing in at least one condition: D.GPLTGTYR_23_23_NA_NA, F.HFHWGSSDDQGSEHTVDR_402_402_NA_NA, G.PLTGTYR_8_8_NA_NA, H.SFNVEYDDSQDK_465_465_NA_NA, K.AVVQDPALKPL_156_156_NA_NA ... INFO [2024-07-08 01:32:39] == Start the summarization per subplot... | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% INFO [2024-07-08 01:32:39] == Summarization is done. test_dataProcess.R............ 0 tests INFO [2024-07-08 01:32:39] ** Features with one or two measurements across runs are removed. INFO [2024-07-08 01:32:39] ** Fractionation handled. INFO [2024-07-08 01:32:39] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-07-08 01:32:39] ** Log2 intensities under cutoff = 3.776 were considered as censored missing values. INFO [2024-07-08 01:32:39] ** Log2 intensities = NA were considered as censored missing values. INFO [2024-07-08 01:32:39] ** Use all features that the dataset originally has. INFO [2024-07-08 01:32:39] # proteins: 2 # peptides per protein: 2-2 # features per peptide: 3-3 INFO [2024-07-08 01:32:39] 1 2 3 4 5 6 7 8 9 10 # runs 3 3 3 3 3 3 3 3 3 3 # bioreplicates 3 3 3 3 3 3 3 3 3 3 # tech. replicates 1 1 1 1 1 1 1 1 1 1 INFO [2024-07-08 01:32:39] == Start the summarization per subplot... INFO [2024-07-08 01:32:42] == Summarization is done. test_dataProcess.R............ 0 tests INFO [2024-07-08 01:32:42] ** Features with one or two measurements across runs are removed. INFO [2024-07-08 01:32:42] ** Fractionation handled. INFO [2024-07-08 01:32:42] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-07-08 01:32:42] ** Use all features that the dataset originally has. INFO [2024-07-08 01:32:42] # proteins: 6 # peptides per protein: 11-32 # features per peptide: 1-1 INFO [2024-07-08 01:32:43] C1 C2 C3 C4 C5 C6 # runs 3 3 3 3 3 3 # bioreplicates 1 1 1 1 1 1 # tech. replicates 3 3 3 3 3 3 INFO [2024-07-08 01:32:43] Some features are completely missing in at least one condition: D.GPLTGTYR_23_23_NA_NA, F.HFHWGSSDDQGSEHTVDR_402_402_NA_NA, G.PLTGTYR_8_8_NA_NA, H.SFNVEYDDSQDK_465_465_NA_NA, K.AVVQDPALKPL_156_156_NA_NA ... INFO [2024-07-08 01:32:43] == Start the summarization per subplot... INFO [2024-07-08 01:32:46] == Summarization is done. test_dataProcess.R............ 0 tests test_dataProcess.R............ 1 tests [0;32mOK[0m test_dataProcess.R............ 2 tests [0;32mOK[0m [0;34m8.3s[0m INFO [2024-07-08 01:32:47] ** Features with one or two measurements across runs are removed. INFO [2024-07-08 01:32:47] ** Fractionation handled. INFO [2024-07-08 01:32:47] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-07-08 01:32:47] ** Log2 intensities under cutoff = 3.776 were considered as censored missing values. INFO [2024-07-08 01:32:47] ** Log2 intensities = NA were considered as censored missing values. INFO [2024-07-08 01:32:47] ** Use all features that the dataset originally has. INFO [2024-07-08 01:32:47] # proteins: 2 # peptides per protein: 2-2 # features per peptide: 3-3 INFO [2024-07-08 01:32:47] 1 2 3 4 5 6 7 8 9 10 # runs 3 3 3 3 3 3 3 3 3 3 # bioreplicates 3 3 3 3 3 3 3 3 3 3 # tech. replicates 1 1 1 1 1 1 1 1 1 1 INFO [2024-07-08 01:32:47] == Start the summarization per subplot... | | | 0% | |=================================== | 50% | |======================================================================| 100% INFO [2024-07-08 01:32:47] == Summarization is done. test_groupComparison.R........ 0 tests test_groupComparison.R........ 0 tests test_groupComparison.R........ 0 tests test_groupComparison.R........ 0 tests test_groupComparison.R........ 0 tests INFO [2024-07-08 01:32:47] == Start to test and get inference in whole plot ... | | | 0% | |=================================== | 50% | |======================================================================| 100% INFO [2024-07-08 01:32:47] == Comparisons for all proteins are done. test_groupComparison.R........ 0 tests INFO [2024-07-08 01:32:47] == Start to test and get inference in whole plot ... INFO [2024-07-08 01:32:51] == Comparisons for all proteins are done. test_groupComparison.R........ 0 tests test_groupComparison.R........ 1 tests [0;32mOK[0m [0;34m4.1s[0m [0;36m2ms[0m All ok, 4 results (12.4s) > > proc.time() user system elapsed 4.189 0.479 15.524
MSstats.Rcheck/MSstats-Ex.timings
name | user | system | elapsed | |
DDARawData | 0.006 | 0.001 | 0.006 | |
DDARawData.Skyline | 0.005 | 0.000 | 0.005 | |
DIANNtoMSstatsFormat | 0 | 0 | 0 | |
DIARawData | 0.002 | 0.000 | 0.002 | |
DIAUmpiretoMSstatsFormat | 0.132 | 0.000 | 0.118 | |
FragPipetoMSstatsFormat | 0.040 | 0.014 | 0.045 | |
MSstatsGroupComparison | 0.301 | 0.017 | 0.301 | |
MSstatsGroupComparisonOutput | 0.248 | 0.000 | 0.223 | |
MSstatsGroupComparisonSingleProtein | 0.242 | 0.000 | 0.199 | |
MSstatsHandleMissing | 0.092 | 0.003 | 0.051 | |
MSstatsMergeFractions | 0.098 | 0.000 | 0.053 | |
MSstatsNormalize | 0.083 | 0.000 | 0.044 | |
MSstatsPrepareForDataProcess | 0.072 | 0.008 | 0.044 | |
MSstatsPrepareForGroupComparison | 0.135 | 0.004 | 0.121 | |
MSstatsPrepareForSummarization | 0.077 | 0.004 | 0.044 | |
MSstatsSelectFeatures | 0.376 | 0.024 | 0.283 | |
MSstatsSummarizationOutput | 0.331 | 0.008 | 0.261 | |
MSstatsSummarize | 0.30 | 0.00 | 0.24 | |
MSstatsSummarizeSingleLinear | 0.119 | 0.004 | 0.071 | |
MSstatsSummarizeSingleTMP | 0.161 | 0.000 | 0.099 | |
MaxQtoMSstatsFormat | 0.157 | 0.000 | 0.094 | |
OpenMStoMSstatsFormat | 0.071 | 0.000 | 0.060 | |
OpenSWATHtoMSstatsFormat | 0.073 | 0.000 | 0.062 | |
PDtoMSstatsFormat | 0.077 | 0.012 | 0.076 | |
ProgenesistoMSstatsFormat | 0.075 | 0.003 | 0.065 | |
SDRFtoAnnotation | 0.012 | 0.004 | 0.016 | |
SRMRawData | 0.003 | 0.000 | 0.003 | |
SkylinetoMSstatsFormat | 0.129 | 0.020 | 0.119 | |
SpectronauttoMSstatsFormat | 0.073 | 0.000 | 0.056 | |
checkRepeatedDesign | 0.171 | 0.012 | 0.146 | |
dataProcess | 0.449 | 0.012 | 0.373 | |
dataProcessPlots | 5.693 | 0.064 | 5.652 | |
designSampleSize | 0.300 | 0.020 | 0.277 | |
designSampleSizePlots | 0.292 | 0.012 | 0.260 | |
dot-makeQCPlot | 5.229 | 0.080 | 5.243 | |
extractSDRF | 0.175 | 0.008 | 0.124 | |
getProcessed | 0.142 | 0.000 | 0.073 | |
getSamplesInfo | 0.337 | 0.004 | 0.257 | |
groupComparison | 0.207 | 0.000 | 0.185 | |
groupComparisonPlots | 2.547 | 0.029 | 2.550 | |
makePeptidesDictionary | 0.004 | 0.000 | 0.004 | |
modelBasedQCPlots | 0.827 | 0.008 | 0.788 | |
quantification | 0.232 | 0.000 | 0.188 | |