Kieran O'Neill
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/contiBAIT |
| Branch: RELEASE_3_11 |
| Last Commit: 43200c3 |
| Last Changed Date: 2020-05-15 13:49:58 -0400 (Fri, 15 May 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:22 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE contiBAIT PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 366/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| contiBAIT 1.16.0 Kieran O'Neill
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: contiBAIT |
| Version: 1.16.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/contiBAIT_1.16.0.tar.gz && rm -rf contiBAIT.buildbin-libdir && mkdir contiBAIT.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=contiBAIT.buildbin-libdir contiBAIT_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL contiBAIT_1.16.0.zip && rm contiBAIT_1.16.0.tar.gz contiBAIT_1.16.0.zip |
| StartedAt: 2020-10-16 19:13:27 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 19:16:04 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 156.8 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/contiBAIT_1.16.0.tar.gz && rm -rf contiBAIT.buildbin-libdir && mkdir contiBAIT.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=contiBAIT.buildbin-libdir contiBAIT_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL contiBAIT_1.16.0.zip && rm contiBAIT_1.16.0.tar.gz contiBAIT_1.16.0.zip
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install for i386
* installing *source* package 'contiBAIT' ...
** 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/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c buildLinkageGroups.cpp -o buildLinkageGroups.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/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c computeSim.cpp -o computeSim.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/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c orderContigsGreedy.cpp -o orderContigsGreedy.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o contiBAIT.dll tmp.def buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -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/contiBAIT.buildbin-libdir/00LOCK-contiBAIT/00new/contiBAIT/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** help
*** installing help indices
converting help for package 'contiBAIT'
finding HTML links ... done
BAIT html
ChrTable html
ContigOrdering html
LibraryGroupList html
LinkageGroupList html
StrandFreqMatrix html
StrandReadMatrix html
StrandStateList html
StrandStateMatrix html
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method
html
clusterContigs-StrandStateMatrix-method
html
contiBAIT html
exampleChrTable html
exampleContigOrder html
exampleCrickFreq html
exampleDividedChr html
exampleLGList html
exampleLibList html
exampleReadCounts html
exampleStrandFreq html
exampleWCMatrix html
exampleWatsonFreq html
findSexGroups-LinkageGroupList-StrandStateMatrix-method
html
findSimilarLibraries html
fixLinkageGroups html
flipOrderedLinkageGroups html
highlightAssemblyErrors html
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method
html
locateMisorients html
makeBoxPlot html
makeChrTable html
mapGapFromOverlap html
mergeFlankedLGs html
orderAllLinkageGroups html
orderContigsGreedy html
orderContigsTSP html
plotContigOrder html
plotLGDistances-LinkageGroupList-StrandStateMatrix-method
html
plotWCdistribution-StrandFreqMatrix-method
html
preprocessStrandTable-StrandFreqMatrix-method
html
reorientAndMergeLGs html
show-ContigOrdering-method html
show-LibraryGroupList-method html
show-LinkageGroupList-method html
show-OrientationFrame-method html
show-StrandFreqMatrix-method html
show-StrandReadMatrix-method html
show-StrandStateList-method html
show-StrandStateMatrix-method html
strandSeqFreqTable html
thoroughBed html
writeBed html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'contiBAIT' ...
** 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/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c buildLinkageGroups.cpp -o buildLinkageGroups.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/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c computeSim.cpp -o computeSim.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/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c orderContigsGreedy.cpp -o orderContigsGreedy.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o contiBAIT.dll tmp.def buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -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/contiBAIT.buildbin-libdir/contiBAIT/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
* MD5 sums
packaged installation of 'contiBAIT' as contiBAIT_1.16.0.zip
* DONE (contiBAIT)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'contiBAIT' successfully unpacked and MD5 sums checked