Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:17:20 -0400 (Wed, 15 Apr 2020).
Package 1171/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
oligo 1.50.0 Benilton Carvalho
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: oligo |
Version: 1.50.0 |
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/oligo_1.50.0.tar.gz && rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oligo.buildbin-libdir oligo_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL oligo_1.50.0.zip && rm oligo_1.50.0.tar.gz oligo_1.50.0.zip |
StartedAt: 2020-04-14 19:38:26 -0400 (Tue, 14 Apr 2020) |
EndedAt: 2020-04-14 19:39:48 -0400 (Tue, 14 Apr 2020) |
EllapsedTime: 82.3 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/oligo_1.50.0.tar.gz && rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oligo.buildbin-libdir oligo_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL oligo_1.50.0.zip && rm oligo_1.50.0.tar.gz oligo_1.50.0.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 14.9M 100 14.9M 0 0 87.3M 0 --:--:-- --:--:-- --:--:-- 89.2M install for i386 * installing *source* package 'oligo' ... ** using staged installation ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c DABG.c -o DABG.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ParserGzXYS.c -o ParserGzXYS.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ParserXYS.c -o ParserXYS.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c baseProfile.c -o baseProfile.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c basecontent.c -o basecontent.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c mas5calls.c -o mas5calls.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rma2.c -o rma2.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -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-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -LC:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/oligo.buildbin-libdir/00LOCK-oligo/00new/oligo/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo' 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-3.10-bioc/tmpdir/RtmpsFVG7b/R.INSTALL9206aa44171/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-3.10-bioc/tmpdir/RtmpsFVG7b/R.INSTALL9206aa44171/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-3.10-bioc/tmpdir/RtmpsFVG7b/R.INSTALL9206aa44171/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-3.10-bioc/tmpdir/RtmpsFVG7b/R.INSTALL9206aa44171/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-3.10-bioc/tmpdir/RtmpsFVG7b/R.INSTALL9206aa44171/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-3.10-bioc/tmpdir/RtmpsFVG7b/R.INSTALL9206aa44171/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-3.10-bioc/tmpdir/RtmpsFVG7b/R.INSTALL9206aa44171/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-3.10-bioc/tmpdir/RtmpsFVG7b/R.INSTALL9206aa44171/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-3.10-bioc/tmpdir/RtmpsFVG7b/R.INSTALL9206aa44171/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 from temporary location No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo' ** testing if installed package can be loaded from final location No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo' ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'oligo' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c DABG.c -o DABG.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ParserGzXYS.c -o ParserGzXYS.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ParserXYS.c -o ParserXYS.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c baseProfile.c -o baseProfile.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c basecontent.c -o basecontent.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c mas5calls.c -o mas5calls.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rma2.c -o rma2.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -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-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -LC:/Users/biocbuild/bbs-3.10-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/oligo.buildbin-libdir/oligo/libs/x64 ** testing if installed package can be loaded No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'oligo' * MD5 sums packaged installation of 'oligo' as oligo_1.50.0.zip * DONE (oligo) * installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library' package 'oligo' successfully unpacked and MD5 sums checked