Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:45 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE scater PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1584/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
scater 1.16.2 Davis McCarthy
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: scater |
Version: 1.16.2 |
Command: rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scater.buildbin-libdir scater_1.16.2.tar.gz |
StartedAt: 2020-10-17 11:35:16 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 11:37:07 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 110.8 seconds |
RetCode: 0 |
Status: OK |
PackageFile: scater_1.16.2.zip |
PackageFileSize: 3.864 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scater.buildbin-libdir scater_1.16.2.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'scater' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c combined_qc.cpp -o combined_qc.o combined_qc.cpp: In function 'void check_topset(const IntegerVector&)': combined_qc.cpp:14:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare] for (size_t t=1; t<top.size(); ++t) { ~^~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sum_counts.cpp -o sum_counts.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def RcppExports.o combined_qc.o sum_counts.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/scater.buildbin-libdir/00LOCK-scater/00new/scater/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'scater' finding HTML links ... done SCESet html accessors html finding level-2 HTML links ... done addPerCellQC html annotateBMFeatures html bootstraps html calculateAverage html calculateCPM html calculateFPKM html calculateTPM html defunct html getExplanatoryPCs html getVarianceExplained html ggsce html isOutlier html librarySizeFactors html logNormCounts html makePerCellDF html makePerFeatureDF html medianSizeFactors html mockSCE html multiplot html nexprs html normalizeCounts html numDetectedAcrossCells html numDetectedAcrossFeatures html perCellQCMetrics html perFeatureQCMetrics html plotColData html plotDots html plotExplanatoryPCs html plotExplanatoryVariables html plotExpression html plotHeatmap html plotHighestExprs html plotPlatePosition html plotRLE html plotReducedDim html Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpuUTIgV/R.INSTALL18dc57e71b3/scater/man/plotReducedDim.Rd:33: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic plotRowData html plotScater html plot_reddim html quickPerCellQC html readSparseCounts html retrieveCellInfo html retrieveFeatureInfo html runColDataPCA html runDiffusionMap html Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpuUTIgV/R.INSTALL18dc57e71b3/scater/man/runDiffusionMap.Rd:42: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpuUTIgV/R.INSTALL18dc57e71b3/scater/man/runDiffusionMap.Rd:77: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpuUTIgV/R.INSTALL18dc57e71b3/scater/man/runDiffusionMap.Rd:78: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpuUTIgV/R.INSTALL18dc57e71b3/scater/man/runDiffusionMap.Rd:147: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpuUTIgV/R.INSTALL18dc57e71b3/scater/man/runDiffusionMap.Rd:149: file link 'plotDiffusionMap' in package 'scater' does not exist and so has been treated as a topic runMDS html Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpuUTIgV/R.INSTALL18dc57e71b3/scater/man/runMDS.Rd:143: file link 'plotMDS' in package 'scater' does not exist and so has been treated as a topic runMultiUMAP html runNMF html runPCA html Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpuUTIgV/R.INSTALL18dc57e71b3/scater/man/runPCA.Rd:153: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic runTSNE html Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpuUTIgV/R.INSTALL18dc57e71b3/scater/man/runTSNE.Rd:109: file link 'Rtsne_neighbors' in package 'Rtsne' does not exist and so has been treated as a topic runUMAP html scater-plot-args html scater-utils html sumCountsAcrossCells html sumCountsAcrossFeatures html toSingleCellExperiment html uniquifyFeatureNames 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 'scater' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c combined_qc.cpp -o combined_qc.o combined_qc.cpp: In function 'void check_topset(const IntegerVector&)': combined_qc.cpp:14:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] for (size_t t=1; t<top.size(); ++t) { ~^~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sum_counts.cpp -o sum_counts.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/beachmat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def RcppExports.o combined_qc.o sum_counts.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/scater.buildbin-libdir/scater/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'scater' as scater_1.16.2.zip * DONE (scater)