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BioC 3.1: INSTALL report for affyPLM on petty

This page was generated on 2015-10-09 09:32:32 -0700 (Fri, 09 Oct 2015).

Package 25/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyPLM 1.44.0
Ben Bolstad
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/affyPLM
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affyPLM
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL affyPLM
StartedAt: 2015-10-08 18:08:10 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 18:08:29 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 18.6 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL affyPLM
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library’
* installing *source* package ‘affyPLM’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c LESN.c -o LESN.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PLM_avg_log.c -o PLM_avg_log.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PLM_biweight.c -o PLM_biweight.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PLM_log_avg.c -o PLM_log_avg.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PLM_medianPM.c -o PLM_medianPM.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PLM_median_logPM.c -o PLM_median_logPM.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PLM_medianpolish.c -o PLM_medianpolish.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PLM_modelmatrix.c -o PLM_modelmatrix.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c SCAB.c -o SCAB.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c chipbackground.c -o chipbackground.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c common_types.c -o common_types.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c do_PLMrlm.c -o do_PLMrlm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c do_PLMrma.c -o do_PLMrma.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c do_PLMthreestep.c -o do_PLMthreestep.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c idealmismatch.c -o idealmismatch.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c lm_threestep.c -o lm_threestep.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c matrix_functions.c -o matrix_functions.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c nthLargestPM.c -o nthLargestPM.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c preprocess.c -o preprocess.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c psi_fns.c -o psi_fns.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c qnorm_probeset.c -o qnorm_probeset.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c read_rmaexpress.c -o read_rmaexpress.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c rlm_PLM.c -o rlm_PLM.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c rlm_threestep.c -o rlm_threestep.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c rma_PLM.c -o rma_PLM.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -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’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c scaling.c -o scaling.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c threestep.c -o threestep.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c threestep_PLM.c -o threestep_PLM.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c threestep_common.c -o threestep_common.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c threestep_summary.c -o threestep_summary.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c threestep_summary_methods.c -o threestep_summary_methods.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c transfns.c -o transfns.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -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 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/affyPLM/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘summary’ from package ‘base’ in package ‘affyPLM’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (affyPLM)