J. Toedling
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/girafe |
| Branch: RELEASE_3_7 |
| Last Commit: ec99f07 |
| Last Changed Date: 2018-04-30 10:35:13 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:34:40 -0400 (Wed, 17 Oct 2018).
| Package 617/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| girafe 1.32.0 J. Toedling
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: girafe |
| Version: 1.32.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/girafe_1.32.0.tar.gz && rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=girafe.buildbin-libdir girafe_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL girafe_1.32.0.zip && rm girafe_1.32.0.tar.gz girafe_1.32.0.zip |
| StartedAt: 2018-10-16 19:40:00 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 19:41:22 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 81.4 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/3.7/bioc/src/contrib/girafe_1.32.0.tar.gz && rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=girafe.buildbin-libdir girafe_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL girafe_1.32.0.zip && rm girafe_1.32.0.tar.gz girafe_1.32.0.zip
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install for i386
* installing *source* package 'girafe' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c coverage.cpp -o coverage.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c girafe_init.c -o girafe_init.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o girafe.dll tmp.def coverage.o girafe_init.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/girafe.buildbin-libdir/girafe/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for request: 'sort' when loading 'girafe'
Creating a generic function for 'sample' from package 'base' in package 'girafe'
** help
*** installing help indices
converting help for package 'girafe'
finding HTML links ... done
AlignedGenomeIntervals-class html
agiFromBam html
countReadsAnnotated html
fracOverlap html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaoqZoG/R.INSTALL1b2c2bc1505b/girafe/man/fracOverlap.Rd:38: file link 'interval_overlap' in package 'genomeIntervals' does not exist and so has been treated as a topic
getFeatureCounts html
girafe-internal html
intPhred html
medianByPosition html
negbinomsig html
perWindow html
plotAligned html
plotReads html
plotnegbinomfit html
reduce-extras html
trimAdapter html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaoqZoG/R.INSTALL1b2c2bc1505b/girafe/man/trimAdapter.Rd:39: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaoqZoG/R.INSTALL1b2c2bc1505b/girafe/man/trimAdapter.Rd:41: file link 'writeFastq' in package 'ShortRead' does not exist and so has been treated as a topic
weightedConsensusMatrix html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaoqZoG/R.INSTALL1b2c2bc1505b/girafe/man/weightedConsensusMatrix.Rd:23: file link 'consensusMatrix' in package 'Biostrings' does not exist and so has been treated as a topic
whichNearestMethods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaoqZoG/R.INSTALL1b2c2bc1505b/girafe/man/whichNearestMethods.Rd:44: file link 'which_nearest' in package 'intervals' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'sort' when loading 'girafe'
In R CMD INSTALL
install for x64
* installing *source* package 'girafe' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c coverage.cpp -o coverage.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c girafe_init.c -o girafe_init.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o girafe.dll tmp.def coverage.o girafe_init.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/girafe.buildbin-libdir/girafe/libs/x64
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'sort' when loading 'girafe'
* MD5 sums
packaged installation of 'girafe' as girafe_1.32.0.zip
* DONE (girafe)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'girafe' successfully unpacked and MD5 sums checked
In R CMD INSTALL