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Package 16/294HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: affyPLM
Version: 1.18.1
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes affyPLM_1.18.1.tar.gz
StartedAt: 2009-04-18 16:03:30 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 16:13:44 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 614.3 seconds
RetCode: 0
Status: OK
CheckDir: affyPLM.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/affyPLM.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ASCII
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.18.1'
* 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 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 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
* creating affyPLM-Ex.R ... 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' ... OK
* creating affyPLM-manual.tex ... OK
* checking affyPLM-manual.tex using pdflatex ... OK

affyPLM.Rcheck/00install.out:

* Installing *source* package 'affyPLM' ...
** libs
** arch - i386
gcc -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 -c LESN.c -o LESN.o
gcc -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 -c PLM_avg_log.c -o PLM_avg_log.o
gcc -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 -c PLM_biweight.c -o PLM_biweight.o
gcc -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 -c PLM_log_avg.c -o PLM_log_avg.o
gcc -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 -c PLM_medianPM.c -o PLM_medianPM.o
gcc -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 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -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 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -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 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -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 -c SCAB.c -o SCAB.o
gcc -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 -c chipbackground.c -o chipbackground.o
gcc -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 -c common_types.c -o common_types.o
gcc -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 -c do_PLMrlm.c -o do_PLMrlm.o
gcc -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 -c do_PLMrma.c -o do_PLMrma.o
gcc -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 -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -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 -c idealmismatch.c -o idealmismatch.o
gcc -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 -c lm_threestep.c -o lm_threestep.o
gcc -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 -c matrix_functions.c -o matrix_functions.o
gcc -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 -c nthLargestPM.c -o nthLargestPM.o
gcc -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 -c preprocess.c -o preprocess.o
gcc -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 -c psi_fns.c -o psi_fns.o
gcc -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 -c qnorm_probeset.c -o qnorm_probeset.o
gcc -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 -c read_rmaexpress.c -o read_rmaexpress.o
gcc -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 -c rlm_PLM.c -o rlm_PLM.o
gcc -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 -c rlm_threestep.c -o rlm_threestep.o
gcc -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 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -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 -c rma_PLM.c -o rma_PLM.o
gcc -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 -c rma_common.c -o rma_common.o
gcc -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 -c scaling.c -o scaling.o
gcc -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 -c threestep.c -o threestep.o
gcc -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 -c threestep_PLM.c -o threestep_PLM.o
gcc -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 -c threestep_common.c -o threestep_common.o
gcc -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 -c threestep_summary.c -o threestep_summary.o
gcc -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 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -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 -c transfns.c -o transfns.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -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 -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 -c LESN.c -o LESN.o
gcc -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 -c PLM_avg_log.c -o PLM_avg_log.o
gcc -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 -c PLM_biweight.c -o PLM_biweight.o
gcc -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 -c PLM_log_avg.c -o PLM_log_avg.o
gcc -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 -c PLM_medianPM.c -o PLM_medianPM.o
gcc -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 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -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 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -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 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -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 -c SCAB.c -o SCAB.o
gcc -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 -c chipbackground.c -o chipbackground.o
gcc -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 -c common_types.c -o common_types.o
gcc -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 -c do_PLMrlm.c -o do_PLMrlm.o
gcc -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 -c do_PLMrma.c -o do_PLMrma.o
gcc -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 -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -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 -c idealmismatch.c -o idealmismatch.o
gcc -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 -c lm_threestep.c -o lm_threestep.o
gcc -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 -c matrix_functions.c -o matrix_functions.o
gcc -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 -c nthLargestPM.c -o nthLargestPM.o
gcc -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 -c preprocess.c -o preprocess.o
gcc -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 -c psi_fns.c -o psi_fns.o
gcc -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 -c qnorm_probeset.c -o qnorm_probeset.o
gcc -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 -c read_rmaexpress.c -o read_rmaexpress.o
gcc -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 -c rlm_PLM.c -o rlm_PLM.o
gcc -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 -c rlm_threestep.c -o rlm_threestep.o
gcc -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 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -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 -c rma_PLM.c -o rma_PLM.o
gcc -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 -c rma_common.c -o rma_common.o
gcc -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 -c scaling.c -o scaling.o
gcc -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 -c threestep.c -o threestep.o
gcc -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 -c threestep_PLM.c -o threestep_PLM.o
gcc -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 -c threestep_common.c -o threestep_common.o
gcc -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 -c threestep_summary.c -o threestep_summary.o
gcc -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 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -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 -c transfns.c -o transfns.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -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
** 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)