Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:32:30 -0400 (Wed, 17 Oct 2018).
Package 1012/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
oligo 1.44.0 Benilton Carvalho
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: oligo |
Version: 1.44.0 |
Command: rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oligo.buildbin-libdir oligo_1.44.0.tar.gz |
StartedAt: 2018-10-17 06:44:47 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 06:45:50 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 62.8 seconds |
RetCode: 0 |
Status: OK |
PackageFile: oligo_1.44.0.zip |
PackageFileSize: 27.84 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oligo.buildbin-libdir oligo_1.44.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'oligo' ... ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c DABG.c -o DABG.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ParserGzXYS.c -o ParserGzXYS.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ParserXYS.c -o ParserXYS.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c baseProfile.c -o baseProfile.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c basecontent.c -o basecontent.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c chipbackground.c -o chipbackground.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c mas5calls.c -o mas5calls.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c rma2.c -o rma2.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c rma_common.c -o rma_common.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c trimmed.c -o trimmed.o C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o oligo.dll tmp.def DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRblas -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -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/oligo.buildbin-libdir/oligo/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading Note: in method for 'pm<-' with signature 'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"': expanding the signature to include omitted arguments in definition: = "missing" Note: in method for 'mm<-' with signature 'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"': expanding the signature to include omitted arguments in definition: = "missing" ** help *** installing help indices converting help for package 'oligo' finding HTML links ... done Index-methods html IntensityMatrix-methods html MAplot-methods html Sequences-methods html basecontent html basicPLM html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpmgsSVz/R.INSTALL1ff8646f4341/oligo/man/basicPLM.Rd:42: file link 'rcModelPLM' in package 'preprocessCore' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpmgsSVz/R.INSTALL1ff8646f4341/oligo/man/basicPLM.Rd:44: file link 'rcModelPLMrr' in package 'preprocessCore' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpmgsSVz/R.INSTALL1ff8646f4341/oligo/man/basicPLM.Rd:45: file link 'rcModelPLMrc' in package 'preprocessCore' does not exist and so has been treated as a topic basicRMA html boxplot html chromosome html colors html coordinates html crlmm html fitProbeLevelModel html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpmgsSVz/R.INSTALL1ff8646f4341/oligo/man/fitProbeLevelModel.Rd:9: file link 'FeatureSet' in package 'oligoClasses' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpmgsSVz/R.INSTALL1ff8646f4341/oligo/man/fitProbeLevelModel.Rd:17: file link 'FeatureSet' in package 'oligoClasses' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpmgsSVz/R.INSTALL1ff8646f4341/oligo/man/fitProbeLevelModel.Rd:50: file link 'rma' in package 'oligo' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpmgsSVz/R.INSTALL1ff8646f4341/oligo/man/fitProbeLevelModel.Rd:50: file link 'summarizationMethods' in package 'oligo' does not exist and so has been treated as a topic getAffinitySplineCoefficients html getBaseProfile html getContainer html getCrlmmSummaries html getNetAffx html getNgsColorsInfo html getPlatformDesign html getProbeInfo html hist html image html justSNPRMA html list.xysfiles html oligo-package html oligoDefunct html oligoPLM-class html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpmgsSVz/R.INSTALL1ff8646f4341/oligo/man/oligoPLM-class.Rd:125: file link 'rma' in package 'oligo' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpmgsSVz/R.INSTALL1ff8646f4341/oligo/man/oligoPLM-class.Rd:125: file link 'summarize' in package 'oligo' does not exist and so has been treated as a topic paCalls html plotM-methods html pmAllele html pmFragmentLength html pmPosition html pmStrand html preprocessTools html probeNames html read.celfiles html read.xysfiles html readSummaries html rma-methods html runDate html sequenceDesignMatrix html snprma html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'oligo' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c DABG.c -o DABG.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ParserGzXYS.c -o ParserGzXYS.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ParserXYS.c -o ParserXYS.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c baseProfile.c -o baseProfile.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c basecontent.c -o basecontent.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c chipbackground.c -o chipbackground.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c mas5calls.c -o mas5calls.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c rma2.c -o rma2.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c rma_common.c -o rma_common.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c trimmed.c -o trimmed.o C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o oligo.dll tmp.def DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRblas -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -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/oligo.buildbin-libdir/oligo/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'oligo' as oligo_1.44.0.zip * DONE (oligo) In R CMD INSTALL In R CMD INSTALL