affyPLM 1.18.1
Ben Bolstad
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/affyPLM | | Last Changed Rev: 36979 / Revision: 38965 | | Last Changed Date: 2009-01-27 09:35:24 -0800 (Tue, 27 Jan 2009) |
| wilson2 | 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 (10.5.6) / i386 | OK | OK | OK |
* checking for file 'affyPLM/DESCRIPTION' ... OK
* preparing 'affyPLM':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'affyPLM' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c LESN.c -o LESN.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c preprocess.c -o preprocess.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c:100: warning: ‘rlmPLM_alloc_space’ defined but not used
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_common.c -o rma_common.o
rma_common.c: In function ‘median’:
rma_common.c:60: warning: unused variable ‘i’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c scaling.c -o scaling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep.c -o threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.3-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c transfns.c -o transfns.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o affyPLM.so chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o LESN.o lm_threestep.o matrix_functions.o nthLargestPM.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_median_logPM.o PLM_medianPM.o PLM_medianpolish.o PLM_modelmatrix.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rma_common.o rma_PLM.o rmaPLM_pseudo.o SCAB.o scaling.o threestep.o threestep_common.o threestep_PLM.o threestep_summary.o threestep_summary_methods.o transfns.o -lgfortran -lm -L/home/biocbuild/bbs-2.3-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.3-bioc/R/lib -lRblas -L/home/biocbuild/bbs-2.3-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
Loading required package: affy
Loading required package: Biobase
Loading required package: tools
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: gcrma
Loading required package: matchprobes
Loading required package: splines
Loading required package: preprocessCore
Creating a new generic function for "weights" in "affyPLM"
Creating a new generic function for "summary" in "affyPLM"
Creating a new generic function for "resid" in "affyPLM"
Creating a new generic function for "residuals" in "affyPLM"
** help
>>> Building/Updating help pages for package 'affyPLM'
Formats: text html latex example
Note: removing empty section \usage in file 'MAplot.Rd'
MAplot text html latex
Note: removing empty section \examples in file 'PLMset-class.Rd'
PLMset-class text html latex
PLMset2exprSet text html latex example
ReadRMAExpress text html latex
affyPLM-internal text html latex
bg.correct.LESN text html latex example
fitPLM text html latex example
normalize.exprSet text html latex example
normalize.quantiles.probeset text html latex
normalize.scaling text html latex example
preprocess text html latex example
Note: removing empty section \examples in file 'pseudo.Rd'
pseudo text html latex
rmaPLM text html latex example
threestep text html latex example
threestepPLM text html latex example
** building package indices ...
* DONE (affyPLM)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'affyPLM_1.18.1.tar.gz'