Benilton Carvalho
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/oligo |
| Branch: RELEASE_3_7 |
| Last Commit: 0f3b9d1 |
| Last Changed Date: 2018-04-30 10:35:02 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:32:30 -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: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/oligo_1.44.0.tar.gz && 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 && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL oligo_1.44.0.zip && rm oligo_1.44.0.tar.gz oligo_1.44.0.zip |
| StartedAt: 2018-10-16 19:44:42 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 19:46:57 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 135.2 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/oligo_1.44.0.tar.gz && 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 && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL oligo_1.44.0.zip && rm oligo_1.44.0.tar.gz oligo_1.44.0.zip
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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/Rtmpyq4l3x/R.INSTALLc1033b39aa/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/Rtmpyq4l3x/R.INSTALLc1033b39aa/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/Rtmpyq4l3x/R.INSTALLc1033b39aa/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/Rtmpyq4l3x/R.INSTALLc1033b39aa/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/Rtmpyq4l3x/R.INSTALLc1033b39aa/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/Rtmpyq4l3x/R.INSTALLc1033b39aa/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/Rtmpyq4l3x/R.INSTALLc1033b39aa/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/Rtmpyq4l3x/R.INSTALLc1033b39aa/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/Rtmpyq4l3x/R.INSTALLc1033b39aa/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
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'oligo' successfully unpacked and MD5 sums checked
In R CMD INSTALL