Davis McCarthy
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/scater |
| Branch: RELEASE_3_11 |
| Last Commit: e01dfed |
| Last Changed Date: 2020-06-26 14:17:15 -0400 (Fri, 26 Jun 2020) |
| 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: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/scater_1.16.2.tar.gz && 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 && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL scater_1.16.2.zip && rm scater_1.16.2.tar.gz scater_1.16.2.zip |
| StartedAt: 2020-10-16 18:32:06 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 18:35:04 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 177.8 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/scater_1.16.2.tar.gz && 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 && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL scater_1.16.2.zip && rm scater_1.16.2.tar.gz scater_1.16.2.zip
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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/RtmpqSuaEc/R.INSTALL23e833725752/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/RtmpqSuaEc/R.INSTALL23e833725752/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/RtmpqSuaEc/R.INSTALL23e833725752/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/RtmpqSuaEc/R.INSTALL23e833725752/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/RtmpqSuaEc/R.INSTALL23e833725752/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/RtmpqSuaEc/R.INSTALL23e833725752/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/RtmpqSuaEc/R.INSTALL23e833725752/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/RtmpqSuaEc/R.INSTALL23e833725752/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/RtmpqSuaEc/R.INSTALL23e833725752/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)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'scater' successfully unpacked and MD5 sums checked