Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:32:36 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the oligo package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1246/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
oligo 1.54.1 (landing page) Benilton Carvalho
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: oligo |
Version: 1.54.1 |
Command: rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oligo.buildbin-libdir oligo_1.54.1.tar.gz |
StartedAt: 2021-05-06 09:40:03 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 09:41:14 -0400 (Thu, 06 May 2021) |
EllapsedTime: 71.8 seconds |
RetCode: 0 |
Status: OK |
PackageFile: oligo_1.54.1.zip |
PackageFileSize: 27.93 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oligo.buildbin-libdir oligo_1.54.1.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'oligo' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DABG.c -o DABG.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ParserGzXYS.c -o ParserGzXYS.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ParserXYS.c -o ParserXYS.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c baseProfile.c -o baseProfile.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c basecontent.c -o basecontent.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chipbackground.c -o chipbackground.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mas5calls.c -o mas5calls.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma2.c -o rma2.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c trimmed.c -o trimmed.o C:/rtools40/mingw32/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-3~1.12-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRblas -LC:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/oligo.buildbin-libdir/00LOCK-oligo/00new/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: subset = "missing", target = "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: subset = "missing", target = "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-3.12-bioc/tmpdir/RtmpAf2E93/R.INSTALL1c284c726618/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-3.12-bioc/tmpdir/RtmpAf2E93/R.INSTALL1c284c726618/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-3.12-bioc/tmpdir/RtmpAf2E93/R.INSTALL1c284c726618/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-3.12-bioc/tmpdir/RtmpAf2E93/R.INSTALL1c284c726618/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-3.12-bioc/tmpdir/RtmpAf2E93/R.INSTALL1c284c726618/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-3.12-bioc/tmpdir/RtmpAf2E93/R.INSTALL1c284c726618/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-3.12-bioc/tmpdir/RtmpAf2E93/R.INSTALL1c284c726618/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-3.12-bioc/tmpdir/RtmpAf2E93/R.INSTALL1c284c726618/oligo/man/oligoPLM-class.Rd:131: file link 'rma' in package 'oligo' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpAf2E93/R.INSTALL1c284c726618/oligo/man/oligoPLM-class.Rd:131: 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 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 'oligo' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DABG.c -o DABG.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ParserGzXYS.c -o ParserGzXYS.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ParserXYS.c -o ParserXYS.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c baseProfile.c -o baseProfile.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c basecontent.c -o basecontent.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chipbackground.c -o chipbackground.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mas5calls.c -o mas5calls.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma2.c -o rma2.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c trimmed.c -o trimmed.o C:/rtools40/mingw64/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-3~1.12-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRblas -LC:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/oligo.buildbin-libdir/oligo/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'oligo' as oligo_1.54.1.zip * DONE (oligo)