affyPLM 1.20.0
Ben Bolstad
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/affyPLM | | Last Changed Rev: 39013 / Revision: 42512 | | Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | [ OK ] |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* Installing *source* package 'affyPLM' ...
Using auto-selected zip options ''
** libs
making DLL ...
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c LESN.c -o LESN.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_avg_log.c -o PLM_avg_log.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_biweight.c -o PLM_biweight.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_log_avg.c -o PLM_log_avg.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_medianPM.c -o PLM_medianPM.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c SCAB.c -o SCAB.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c common_types.c -o common_types.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c do_PLMrlm.c -o do_PLMrlm.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c do_PLMrma.c -o do_PLMrma.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c idealmismatch.c -o idealmismatch.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c lm_threestep.c -o lm_threestep.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c matrix_functions.c -o matrix_functions.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c nthLargestPM.c -o nthLargestPM.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c preprocess.c -o preprocess.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c psi_fns.c -o psi_fns.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c qnorm_probeset.c -o qnorm_probeset.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c read_rmaexpress.c -o read_rmaexpress.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rlm_PLM.c -o rlm_PLM.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rlm_threestep.c -o rlm_threestep.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c rma_PLM.c -o rma_PLM.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-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: warning: unused variable 'i'
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c scaling.c -o scaling.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep.c -o threestep.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep_PLM.c -o threestep_PLM.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep_common.c -o threestep_common.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep_summary.c -o threestep_summary.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include" -O3 -Wall -std=gnu99 -c transfns.c -o transfns.o
gcc -shared -s -o affyPLM.dll tmp.def 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 SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.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 -lgfortran -LE:/biocbld/bbs-2.4-bioc/R/bin -lRlapack -LE:/biocbld/bbs-2.4-bioc/R/bin -lRblas -lRzlib -LE:/biocbld/bbs-2.4-bioc/R/bin -lR
... done
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: Biostrings
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
cbind,
duplicated,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rank,
rbind,
rep.int,
sapply,
sort,
table,
unique
** help
*** installing help indices
>>> Building/Updating help pages for package 'affyPLM'
Formats: text html latex example chm
Note: removing empty section \usage in file 'MAplot.Rd'
Note: removing empty section \usage in file 'MAplot.Rd'
MAplot text html latex chm
Note: removing empty section \examples in file 'PLMset-class.Rd'
Note: removing empty section \examples in file 'PLMset-class.Rd'
PLMset-class text html latex chm
PLMset2exprSet text html latex example chm
ReadRMAExpress text html latex chm
affyPLM-internal text html latex chm
bg.correct.LESN text html latex example chm
fitPLM text html latex example chm
normalize.exprSet text html latex example chm
normalize.quantiles.probeset text html latex chm
normalize.scaling text html latex example chm
preprocess text html latex example chm
Note: removing empty section \examples in file 'pseudo.Rd'
Note: removing empty section \examples in file 'pseudo.Rd'
pseudo text html latex chm
rmaPLM text html latex example chm
threestep text html latex example chm
threestepPLM text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.4-bioc\tmpdir\Rtmp4ciw11\R.INSTALL678418be\affyPLM\chm\affyPLM.chm
Compile time: 0 minutes, 2 seconds
16 Topics
120 Local links
3 Internet links
1 Graphic
Created e:\biocbld\bbs-2.4-bioc\tmpdir\Rtmp4ciw11\R.INSTALL678418be\affyPLM\chm\affyPLM.chm, 38,932 bytes
Compression decreased file by 52,338 bytes.
** building package indices ...
** MD5 sums
packaged installation of 'affyPLM' as affyPLM_1.20.0.zip
* DONE (affyPLM)