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BioC 3.0: BUILD BIN report for affyPLM on oaxaca

This page was generated on 2015-04-10 10:01:05 -0700 (Fri, 10 Apr 2015).

Package 25/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyPLM 1.42.0
Ben Bolstad
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/affyPLM
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK [ OK ]

Summary

Package: affyPLM
Version: 1.42.0
Command: rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyPLM_1.42.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R affyPLM.buildbin-libdir
StartedAt: 2015-04-10 04:23:48 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:24:09 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 20.1 seconds
RetCode: 0
Status:  OK 
PackageFile: affyPLM_1.42.0.tgz
PackageFileSize: 3.605 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyPLM_1.42.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R affyPLM.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=affyPLM.buildbin-libdir affyPLM_1.42.0.tar.gz'
>>>>>>> 

* installing *source* package ‘affyPLM’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c LESN.c -o LESN.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c PLM_avg_log.c -o PLM_avg_log.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c PLM_biweight.c -o PLM_biweight.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c PLM_log_avg.c -o PLM_log_avg.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c PLM_medianPM.c -o PLM_medianPM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c PLM_median_logPM.c -o PLM_median_logPM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c PLM_medianpolish.c -o PLM_medianpolish.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c PLM_modelmatrix.c -o PLM_modelmatrix.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c SCAB.c -o SCAB.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chipbackground.c -o chipbackground.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c common_types.c -o common_types.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c do_PLMrlm.c -o do_PLMrlm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c do_PLMrma.c -o do_PLMrma.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c do_PLMthreestep.c -o do_PLMthreestep.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c idealmismatch.c -o idealmismatch.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c lm_threestep.c -o lm_threestep.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c matrix_functions.c -o matrix_functions.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c nthLargestPM.c -o nthLargestPM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c preprocess.c -o preprocess.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c psi_fns.c -o psi_fns.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c qnorm_probeset.c -o qnorm_probeset.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c read_rmaexpress.c -o read_rmaexpress.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c rlm_PLM.c -o rlm_PLM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c rlm_threestep.c -o rlm_threestep.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c rma_PLM.c -o rma_PLM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c rma_common.c -o rma_common.o
rma_common.c:60:7: warning: unused variable 'i' [-Wunused-variable]
  int i;
      ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c scaling.c -o scaling.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c threestep.c -o threestep.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c threestep_PLM.c -o threestep_PLM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c threestep_common.c -o threestep_common.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c threestep_summary.c -o threestep_summary.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c threestep_summary_methods.c -o threestep_summary_methods.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/preprocessCore/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c transfns.c -o transfns.o
clang -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 -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/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -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 /Users/biocbuild/bbs-3.0-bioc/meat/affyPLM.buildbin-libdir/affyPLM/libs
** R
** inst
** preparing package for lazy loading
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
* DONE (affyPLM)


>>>>>>> 
>>>>>>> FIXING LINKS FOR affyPLM.buildbin-libdir/affyPLM/libs//affyPLM.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgcc_s.1.dylib" "affyPLM.buildbin-libdir/affyPLM/libs//affyPLM.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.3.dylib" "affyPLM.buildbin-libdir/affyPLM/libs//affyPLM.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.5.2.dylib" "affyPLM.buildbin-libdir/affyPLM/libs//affyPLM.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "affyPLM.buildbin-libdir/affyPLM/libs//affyPLM.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libquadmath.0.dylib" "affyPLM.buildbin-libdir/affyPLM/libs//affyPLM.so"