Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:58:02 -0400 (Tue, 09 Apr 2019).
Package 671/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
girafe 1.35.0 J. Toedling
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: girafe |
Version: 1.35.0 |
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/girafe_1.35.0.tar.gz && rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=girafe.buildbin-libdir girafe_1.35.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL girafe_1.35.0.zip && rm girafe_1.35.0.tar.gz girafe_1.35.0.zip |
StartedAt: 2019-04-08 19:52:47 -0400 (Mon, 08 Apr 2019) |
EndedAt: 2019-04-08 19:54:10 -0400 (Mon, 08 Apr 2019) |
EllapsedTime: 83.5 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/girafe_1.35.0.tar.gz && rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=girafe.buildbin-libdir girafe_1.35.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL girafe_1.35.0.zip && rm girafe_1.35.0.tar.gz girafe_1.35.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1062k 100 1062k 0 0 12.5M 0 --:--:-- --:--:-- --:--:-- 13.6M install for i386 * installing *source* package 'girafe' ... ** libs C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-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˜1.9-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˜1.9-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/girafe.buildbin-libdir/00LOCK-girafe/00new/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-3.9-bioc/tmpdir/RtmpqeReKg/R.INSTALL21144dc04b81/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-3.9-bioc/tmpdir/RtmpqeReKg/R.INSTALL21144dc04b81/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-3.9-bioc/tmpdir/RtmpqeReKg/R.INSTALL21144dc04b81/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-3.9-bioc/tmpdir/RtmpqeReKg/R.INSTALL21144dc04b81/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-3.9-bioc/tmpdir/RtmpqeReKg/R.INSTALL21144dc04b81/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 from temporary location No methods found in package 'IRanges' for request: 'sort' when loading 'girafe' ** testing if installed package can be loaded from final location No methods found in package 'IRanges' for request: 'sort' when loading 'girafe' ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'girafe' ... ** libs C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-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˜1.9-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˜1.9-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.9-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_1.35.0.zip * DONE (girafe) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'girafe' successfully unpacked and MD5 sums checked