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BioC 3.5: BUILD BIN report for affyPLM on veracruz2

This page was generated on 2017-10-18 14:27:23 -0400 (Wed, 18 Oct 2017).

Package 27/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyPLM 1.52.1
Ben Bolstad
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/affyPLM
Branch: RELEASE_3_5
Last Commit: e8613a6
Last Changed Date: 2017-05-05 15:32:27 -0400 (Fri, 05 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: affyPLM
Version: 1.52.1
Command: rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyPLM_1.52.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R affyPLM.buildbin-libdir
StartedAt: 2017-10-18 10:32:48 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 10:33:03 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 15.3 seconds
RetCode: 0
Status:  OK 
PackageFile: affyPLM_1.52.1.tgz
PackageFileSize: 3.637 MiB

Command output

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##############################################################################
###
### Running command:
###
###   rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyPLM_1.52.1.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_1.52.1.tar.gz'
>>>>>>> 

* installing *source* package ‘affyPLM’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c LESN.c -o LESN.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c PLM_avg_log.c -o PLM_avg_log.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c PLM_biweight.c -o PLM_biweight.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c PLM_log_avg.c -o PLM_log_avg.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c PLM_medianPM.c -o PLM_medianPM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c PLM_median_logPM.c -o PLM_median_logPM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c PLM_medianpolish.c -o PLM_medianpolish.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c PLM_modelmatrix.c -o PLM_modelmatrix.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SCAB.c -o SCAB.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c chipbackground.c -o chipbackground.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c common_types.c -o common_types.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c do_PLMrlm.c -o do_PLMrlm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c do_PLMrma.c -o do_PLMrma.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c do_PLMthreestep.c -o do_PLMthreestep.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c idealmismatch.c -o idealmismatch.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c lm_threestep.c -o lm_threestep.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix_functions.c -o matrix_functions.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c nthLargestPM.c -o nthLargestPM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c preprocess.c -o preprocess.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c psi_fns.c -o psi_fns.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c qnorm_probeset.c -o qnorm_probeset.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c read_rmaexpress.c -o read_rmaexpress.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c rlm_PLM.c -o rlm_PLM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c rlm_threestep.c -o rlm_threestep.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c rma_PLM.c -o rma_PLM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c scaling.c -o scaling.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c threestep.c -o threestep.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c threestep_PLM.c -o threestep_PLM.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c threestep_common.c -o threestep_common.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c threestep_summary.c -o threestep_summary.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c threestep_summary_methods.c -o threestep_summary_methods.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -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/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -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-3.5-bioc/meat/affyPLM.buildbin-libdir/affyPLM/libs
** R
** inst
** preparing package for lazy loading
** 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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/Resources/lib/libquadmath.0.dylib" "affyPLM.buildbin-libdir/affyPLM/libs//affyPLM.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "affyPLM.buildbin-libdir/affyPLM/libs//affyPLM.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "affyPLM.buildbin-libdir/affyPLM/libs//affyPLM.so"