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 working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/affyPLM.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49420)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.20.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affyPLM' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
Running ‘C_code_tests.R’
Running ‘PLM_tests.R’
Running ‘preprocess_tests.R’
Running ‘threestepPLM_tests.R’
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* Installing *source* package ‘affyPLM’ ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/lib/i386 -lRlapack -L/Library/Frameworks/R.framework/Versions/2.9/Resources/lib/i386 -lRblas -lz -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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/lib/ppc -lRlapack -L/Library/Frameworks/R.framework/Versions/2.9/Resources/lib/ppc -lRblas -lz -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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/lib/ppc64 -lRlapack -L/Library/Frameworks/R.framework/Versions/2.9/Resources/lib/ppc64 -lRblas -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/lib/x86_64 -lRlapack -L/Library/Frameworks/R.framework/Versions/2.9/Resources/lib/x86_64 -lRblas -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** 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)