oligo 1.40.2
Benilton Carvalho
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/oligo | | Branch: RELEASE_3_5 | | Last Commit: 625b01c | | Last Changed Date: 2017-07-21 14:08:19 -0400 (Fri, 21 Jul 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/oligo_1.40.2.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=oligo.buildbin-libdir --merge-multiarch oligo_1.40.2.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL oligo_1.40.2.zip && rm oligo_1.40.2.tar.gz oligo_1.40.2.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 14.9M 0 14354 0 0 13824 0 0:18:50 0:00:01 0:18:49 13841
28 14.9M 28 4327k 0 0 2023k 0 0:00:07 0:00:02 0:00:05 2024k
72 14.9M 72 10.7M 0 0 3516k 0 0:00:04 0:00:03 0:00:01 3517k
95 14.9M 95 14.2M 0 0 3761k 0 0:00:04 0:00:03 0:00:01 3761k
100 14.9M 100 14.9M 0 0 3926k 0 0:00:03 0:00:03 --:--:-- 3926k
install for i386
* installing *source* package 'oligo' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c DABG.c -o DABG.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ParserGzXYS.c -o ParserGzXYS.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ParserXYS.c -o ParserXYS.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c baseProfile.c -o baseProfile.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c basecontent.c -o basecontent.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c mas5calls.c -o mas5calls.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rma2.c -o rma2.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/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-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/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˜1.5-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRblas -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/oligo.buildbin-libdir/oligo/libs/i386
** R
** inst
** preparing package for lazy loading
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
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
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
install for x64
* installing *source* package 'oligo' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c DABG.c -o DABG.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ParserGzXYS.c -o ParserGzXYS.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ParserXYS.c -o ParserXYS.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c baseProfile.c -o baseProfile.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c basecontent.c -o basecontent.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c mas5calls.c -o mas5calls.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rma2.c -o rma2.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/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-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I"C:/local323/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˜1.5-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRblas -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/oligo.buildbin-libdir/oligo/libs/x64
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
* MD5 sums
packaged installation of 'oligo' as oligo_1.40.2.zip
* DONE (oligo)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'oligo' successfully unpacked and MD5 sums checked