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
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c LESN.c -o LESN.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c common_types.c -o common_types.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c preprocess.c -o preprocess.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c scaling.c -o scaling.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep.c -o threestep.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c transfns.c -o transfns.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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 -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/i386 -lRlapack -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/i386 -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c LESN.c -o LESN.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c common_types.c -o common_types.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c preprocess.c -o preprocess.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/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-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/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-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c scaling.c -o scaling.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep.c -o threestep.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c transfns.c -o transfns.o
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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 -lSystemStubs -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc -lRlapack -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c LESN.c -o LESN.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c common_types.c -o common_types.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c preprocess.c -o preprocess.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/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-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/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-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c scaling.c -o scaling.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep.c -o threestep.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c transfns.c -o transfns.o
gcc-4.2 -arch ppc64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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 -lSystemStubs -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lRlapack -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lRblas -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64/libRblas.dylib -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c LESN.c -o LESN.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c common_types.c -o common_types.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c preprocess.c -o preprocess.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c scaling.c -o scaling.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep.c -o threestep.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.8/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c transfns.c -o transfns.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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 -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/x86_64 -lRlapack -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/x86_64 -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** 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'