Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1468/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
oposSOM 2.24.0 (landing page) Henry Loeffler-Wirth
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the oposSOM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oposSOM.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: oposSOM |
Version: 2.24.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:oposSOM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings oposSOM_2.24.0.tar.gz |
StartedAt: 2024-12-20 04:18:52 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:23:21 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 269.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: oposSOM.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:oposSOM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings oposSOM_2.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/oposSOM.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'oposSOM/DESCRIPTION' ... OK * this is package 'oposSOM' version '2.24.0' * 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 'oposSOM' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 18.7Mb sub-directories of 1Mb or more: data 17.2Mb * 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 ... NOTE Unexported object imported by a ':::' call: 'tools:::makeLazyLoadDB' 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 psf.overview.heatmaps: warning in heatmap(x = log1p(log1p(mean.psf.matrix)), cex.main = 2, col = color.palette(1000), scale = "r", mar = c(10, 20), ColSideColors = group.colors, cexDend = 0.6): partial argument match of 'mar' to 'margins' psf.overview.heatmaps: warning in heatmap(x = log1p(log1p(mean.psf.matrix)), cex.main = 2, col = color.palette(1000), scale = "r", mar = c(10, 20), ColSideColors = group.colors, Colv = NA, cexDend = 0.6): partial argument match of 'mar' to 'margins' Smooth.Matrix: no visible binding for global variable 'v' modules.relations: no visible global function definition for 'graph.empty' modules.relations: no visible global function definition for 'add_edges' pipeline.PSFcalculation: no visible binding for global variable 'kegg.collection' pipeline.checkInputParameters: no visible binding for global variable 'preferences' pipeline.diffExpressionStatistics : <anonymous>: no visible global function definition for 't.test' pipeline.differenceAnalyses : <anonymous>: no visible global function definition for 't.test' pipeline.groupAnalysis : <anonymous>: no visible global function definition for 't.test' pipeline.htmlPsfAnalysis: no visible binding for global variable 'kegg.collection' pipeline.prepareAnnotation: no visible binding for global variable 'opossom.genesets' pipeline.sampleSimilarityAnalysisCor: no visible global function definition for 'get.edgelist' pipeline.topologyProfiles: no visible binding for global variable 'group.labels' plot.psf.pathway.keggrest: no visible global function definition for 'rasterImage' psf.report.sheets: no visible binding for global variable 'kegg.data' spot.borders: no visible binding for global variable 'env' Undefined global functions or variables: add_edges env get.edgelist graph.empty group.labels kegg.collection kegg.data opossom.genesets preferences rasterImage t.test v Consider adding importFrom("graphics", "rasterImage") importFrom("stats", "t.test") 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: 'GeneSet.Fisher' 'GeneSet.maxmean' 'Get.Running.Average' 'Quantile.Normalization' 'Sample.GSZ' 'Smooth.Matrix' '_oposSOM_calculateDelta' '_oposSOM_calculateEuclideanDistances' '_oposSOM_calculateNeighborhoodMatrix' '_oposSOM_matrixToCodebookMatrix' 'biomart.available' 'calculateDelta' 'calculateEuclideanDistances' 'calculateNeighborhoodMatrix' 'circle' 'col.pix' 'color.palette.discrete' 'color.palette.heatmaps' 'color.palette.interlace' 'color.palette.portraits' 'color.palette.portraits.cbs' 'get.beta.statistic' 'get.neighbors' 'heatmap' 'heatmap.A4' 'matrixToCodebookMatrix' 'modules.CSV.sheets' 'modules.chromosomes' 'modules.profiles' 'modules.relations' 'modules.report.sheets' 'newProgressBar' 'pathway.expression.mapping' 'pipeline.PSFcalculation' 'pipeline.PSFoutput' 'pipeline.affymetrixQualityCheck' 'pipeline.cancerHallmarks' 'pipeline.checkInputParameters' 'pipeline.chromosomeExpressionReports' 'pipeline.detectCorrelationModules' 'pipeline.detectDMapModules' 'pipeline.detectEnsemblDataset' 'pipeline.detectGroupOverexpressionModules' 'pipeline.detectKMeansModules' 'pipeline.detectOverexpressionModules' 'pipeline.detectSpotsModules' 'pipeline.detectUnderexpressionModules' 'pipeline.diffExpressionStatistics' 'pipeline.differenceAnalyses' 'pipeline.entropyProfiles' 'pipeline.geneLists' 'pipeline.generateSOM' 'pipeline.genesetOverviews' 'pipeline.genesetProfilesAndMaps' 'pipeline.genesetStatisticModules' 'pipeline.genesetStatisticSamples' 'pipeline.groupAnalysis' 'pipeline.groupAssignment' 'pipeline.groupSpecificGenesets' 'pipeline.htmlDifferencesSummary' 'pipeline.htmlGenesetAnalysis' 'pipeline.htmlGroupSummary' 'pipeline.htmlModuleSummary' 'pipeline.htmlPsfAnalysis' 'pipeline.htmlSampleSummary' 'pipeline.htmlSummary' 'pipeline.moduleCorrelationMap' 'pipeline.patAssignment' 'pipeline.prepareAnnotation' 'pipeline.prepareIndata' 'pipeline.qualityCheck' 'pipeline.sampleExpressionPortraits' 'pipeline.sampleSimilarityAnalysisCor' 'pipeline.sampleSimilarityAnalysisED' 'pipeline.sampleSimilarityAnalysisICA' 'pipeline.sampleSimilarityAnalysisSOM' 'pipeline.summarySheetsGroups' 'pipeline.summarySheetsModules' 'pipeline.summarySheetsPATs' 'pipeline.summarySheetsSamples' 'pipeline.supportingMaps' 'pipeline.topologyProfiles' 'plot.psf.pathway.keggrest' 'plot.psf.titlepage' 'psf.flow' 'psf.overview.heatmaps' 'psf.report.sheets' 'radarchart' 'som.linear.init' 'som.linear.init.subdata' 'som.training' 'som.training.phase' 'sort.label' 'spot.borders' 'util.call' 'util.cat' 'util.fatal' 'util.info' 'util.load' 'util.log' 'util.progress' 'util.progress.terminate' 'util.save' 'util.warn' 'workspace.check' Undocumented data sets: 'hsa03320.RData' 'hsa04010.RData' 'hsa04012.RData' 'hsa04014.RData' 'hsa04015.RData' 'hsa04020.RData' 'hsa04022.RData' 'hsa04024.RData' 'hsa04062.RData' 'hsa04064.RData' 'hsa04066.RData' 'hsa04068.RData' 'hsa04070.RData' 'hsa04071.RData' 'hsa04072.RData' 'hsa04115.RData' 'hsa04150.RData' 'hsa04151.RData' 'hsa04152.RData' 'hsa04261.RData' 'hsa04310.RData' 'hsa04330.RData' 'hsa04340.RData' 'hsa04350.RData' 'hsa04370.RData' 'hsa04371.RData' 'hsa04390.RData' 'hsa04392.RData' 'hsa04550.RData' 'hsa04620.RData' 'hsa04621.RData' 'hsa04622.RData' 'hsa04625.RData' 'hsa04630.RData' 'hsa04657.RData' 'hsa04660.RData' 'hsa04662.RData' 'hsa04664.RData' 'hsa04668.RData' 'hsa04722.RData' 'hsa04723.RData' 'hsa04910.RData' 'hsa04912.RData' 'hsa04915.RData' 'hsa04917.RData' 'hsa04919.RData' 'hsa04920.RData' 'hsa04921.RData' 'hsa04922.RData' 'hsa04926.RData' 'hsa04933.RData' 'hsa05120.RData' 'kegg.collection.RData' 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 ... 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 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 ... WARNING Found the following file(s) containing GNU extensions: src/Makevars Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), $(wildcard), ifeq ... endif, .NOTPARALLEL See section 'Writing portable packages' in the 'Writing R Extensions' manual. * 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 x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/oposSOM/libs/x64/oposSOM.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... WARNING Found the following significant warnings: Warning: working directory was changed to 'F:/biocbuild/bbs-3.20-bioc/meat/oposSOM.Rcheck/Example - Results', resetting Warning: working directory was changed to 'F:/biocbuild/bbs-3.20-bioc/meat/oposSOM.Rcheck/Example+ - Results', resetting * 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: 3 WARNINGs, 5 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/oposSOM.Rcheck/00check.log' for details.
oposSOM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL oposSOM ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'oposSOM' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DeltaMatrix.cpp -o DeltaMatrix.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DistanceCalculator.cpp -o DistanceCalculator.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NeighborhoodMatrix.cpp -o NeighborhoodMatrix.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -shared -s -static-libgcc -o oposSOM.dll tmp.def DeltaMatrix.o DistanceCalculator.o NeighborhoodMatrix.o RcppExports.o -LF:/biocbuild/bbs-3.20-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-oposSOM/00new/oposSOM/libs/x64 ** R ** data ** 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 (oposSOM)
oposSOM.Rcheck/oposSOM-Ex.timings
name | user | system | elapsed | |
opossom.new | 0.14 | 0.01 | 0.16 | |