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 |
* checking for file 'affyPLM/DESCRIPTION' ... OK
* preparing 'affyPLM':
* checking DESCRIPTION meta-information ... OK
* cleaning src
make: Nothing to be done for `clean'.
* installing the package to re-build vignettes
* Installing *source* package 'affyPLM' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c LESN.c -o LESN.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-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-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-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-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-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-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c preprocess.c -o preprocess.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-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-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c scaling.c -o scaling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep.c -o threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-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-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-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 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 -lm -L/home/biocbuild/bbs-2.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.4-bioc/R/lib -lRblas -lz -L/home/biocbuild/bbs-2.4-bioc/R/lib -lR
** 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
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
make: Nothing to be done for `clean'.
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'affyPLM_1.20.0.tar.gz'