oligo 1.17.1
Benilton Carvalho
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo | | Last Changed Rev: 55189 / Revision: 55359 | | Last Changed Date: 2011-04-30 16:17:17 -0700 (Sat, 30 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | [ OK ] |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* installing *source* package 'oligo' ...
** libs
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c DABG.c -o DABG.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c LESN.c -o LESN.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_avg_log.c -o PLM_avg_log.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_biweight.c -o PLM_biweight.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_log_avg.c -o PLM_log_avg.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_medianPM.c -o PLM_medianPM.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c: In function 'gzread_one_xys':
ParserGzXYS.c:74:54: warning: unused variable 'token'
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c ParserXYS.c -o ParserXYS.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c SCAB.c -o SCAB.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c baseProfile.c -o baseProfile.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c basecontent.c -o basecontent.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c common_types.c -o common_types.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c do_PLMrlm.c -o do_PLMrlm.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c do_PLMrma.c -o do_PLMrma.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c idealmismatch.c -o idealmismatch.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c lm_threestep.c -o lm_threestep.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c mas5calls.c -o mas5calls.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c matrix_functions.c -o matrix_functions.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c nthLargestPM.c -o nthLargestPM.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c preprocess.c -o preprocess.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c psi_fns.c -o psi_fns.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c qnorm_probeset.c -o qnorm_probeset.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c read_rmaexpress.c -o read_rmaexpress.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rlm_PLM.c -o rlm_PLM.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rlm_threestep.c -o rlm_threestep.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rma2.c -o rma2.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rma_PLM.c -o rma_PLM.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60:7: warning: unused variable 'i'
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c scaling.c -o scaling.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep.c -o threestep.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep_PLM.c -o threestep_PLM.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep_common.c -o threestep_common.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep_summary.c -o threestep_summary.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c transfns.c -o transfns.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c trimmed.c -o trimmed.o
gcc -shared -s -static-libgcc -o oligo.dll tmp.def DABG.o LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o ParserGzXYS.o ParserXYS.o SCAB.o baseProfile.o basecontent.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o mas5calls.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rma2.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o trimmed.o -lgfortran -LE:/biocbld/bbs-2.9-bioc/R/bin/i386 -lRlapack -LE:/biocbld/bbs-2.9-bioc/R/bin/i386 -lRblas -lRzlib -LE:/biocbld/bbs-2.9-bioc/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/oligo.buildbin-libdir/oligo/libs/i386
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
================================================================================
Welcome to oligoClasses version 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
- Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'ff'
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
Loading package bit1.1-7
package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit
Loading package ff2.2-2
- getOption("fftempdir")=="E:/biocbld/bbs-2.9-bioc/tmpdir/RtmpumnfcF"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16095641.6 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==804782080 -- consider a different value for tuning your system
Creating a new generic function for "boxplot" in "oligo"
Creating a new generic function for "summary" in "oligo"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'V1Overview.Rnw'
'V2NExpression.Rnw'
'V3AffySnpGenotype.Rnw'
'V4Experimental.Rnw'
'V5ExonGene.Rnw'
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
- Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
- Load 'ff'
- Load 'snow'
- Use options(cluster=makeCluster(...))
================================================================================
================================================================================
Welcome to oligo version 1.17.1
================================================================================
* MD5 sums
packaged installation of 'oligo' as oligo_1.17.1.zip
* DONE (oligo)