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BioC 3.4: BUILD BIN report for QUBIC on morelia

This page was generated on 2016-09-21 03:55:50 -0700 (Wed, 21 Sep 2016).

Package 959/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QUBIC 1.1.3
Yu Zhang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/QUBIC
Last Changed Rev: 120845 / Revision: 121152
Last Changed Date: 2016-09-11 22:57:34 -0700 (Sun, 11 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: QUBIC
Version: 1.1.3
Command: rm -rf QUBIC.buildbin-libdir && mkdir QUBIC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh QUBIC_1.1.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R QUBIC.buildbin-libdir
StartedAt: 2016-09-20 15:24:26 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 15:24:42 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 15.8 seconds
RetCode: 0
Status:  OK 
PackageFile: QUBIC_1.1.3.tgz
PackageFileSize: 514.2 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf QUBIC.buildbin-libdir && mkdir QUBIC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh QUBIC_1.1.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R QUBIC.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=QUBIC.buildbin-libdir QUBIC_1.1.3.tar.gz'
>>>>>>> 

* installing *source* package ‘QUBIC’ ...
** libs
clang++ -std=c++11 -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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=c++11 -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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c charset.cc -o charset.o
clang++ -std=c++11 -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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c cluster.cc -o cluster.o
cluster.cc:131:24: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
  return e->score - b3 >= 0;
         ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^  ˜
1 warning generated.
clang++ -std=c++11 -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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c discretize.cc -o discretize.o
clang++ -std=c++11 -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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c edge_list.cc -o edge_list.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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c fib.c -o fib.o
clang++ -std=c++11 -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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c fopen_matrix.cc -o fopen_matrix.o
clang++ -std=c++11 -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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c qubic.cc -o qubic.o
clang++ -std=c++11 -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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c rcpp_qubic.cpp -o rcpp_qubic.o
clang++ -std=c++11 -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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c struct.cc -o struct.o
clang++ -std=c++11 -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 QUBIC.so RcppExports.o charset.o cluster.o discretize.o edge_list.o fib.o fopen_matrix.o qubic.o rcpp_qubic.o struct.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/QUBIC.buildbin-libdir/QUBIC/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 (QUBIC)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgcc_s.1.dylib" "QUBIC.buildbin-libdir/QUBIC/libs//QUBIC.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "QUBIC.buildbin-libdir/QUBIC/libs//QUBIC.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.5.2.dylib" "QUBIC.buildbin-libdir/QUBIC/libs//QUBIC.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "QUBIC.buildbin-libdir/QUBIC/libs//QUBIC.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "QUBIC.buildbin-libdir/QUBIC/libs//QUBIC.so"