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BioC 2.14: BUILD BIN report for GRENITS on morelia

This page was generated on 2014-10-08 09:04:59 -0700 (Wed, 08 Oct 2014).

Package 369/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRENITS 1.16.1
Edward Morrissey
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/GRENITS
Last Changed Rev: 92320 / Revision: 95116
Last Changed Date: 2014-07-09 09:07:31 -0700 (Wed, 09 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]

Summary

Package: GRENITS
Version: 1.16.1
Command: rm -rf GRENITS.buildbin-libdir && mkdir GRENITS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GRENITS_1.16.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GRENITS.buildbin-libdir
StartedAt: 2014-10-08 02:57:45 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:58:53 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 68.4 seconds
RetCode: 0
Status:  OK 
PackageFile: GRENITS_1.16.1.tgz
PackageFileSize: 437.6 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GRENITS.buildbin-libdir && mkdir GRENITS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GRENITS_1.16.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GRENITS.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GRENITS.buildbin-libdir GRENITS_1.16.1.tar.gz'
>>>>>>> 

* installing *source* package ‘GRENITS’ ...
** 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/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o
AR1_Gauss_biocond.cc:49:30: warning: unused variable 'numDiag' [-Wunused-variable]
  int           num_fixedON, numDiag, p_sqr, free_gammas;
                             ^
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/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c AR1_Student_biocond.cc -o AR1_Student_biocond.o
AR1_Student_biocond.cc:49:30: warning: unused variable 'numDiag' [-Wunused-variable]
  int           num_fixedON, numDiag, p_sqr, free_gammas;
                             ^
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/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c AR1_biocond.cc -o AR1_biocond.o
AR1_biocond.cc:48:30: warning: unused variable 'numDiag' [-Wunused-variable]
  int           num_fixedON, numDiag, p_sqr, free_gammas;
                             ^
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/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c PSplines_biocond.cc -o PSplines_biocond.o
PSplines_biocond.cc:45:63: warning: unused variable 'numDiag' [-Wunused-variable]
  int                 num_fixedON, nodesSpline, degreeSpline, numDiag, free_gammas;
                                                              ^
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/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_C_interface.cpp -o R_C_interface.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/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ReadMCMCFiles.cpp -o ReadMCMCFiles.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/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c commonFunctions.cc -o commonFunctions.o
commonFunctions.cc:440:59: warning: unused variable 'num_on' [-Wunused-variable]
  unsigned int                                            num_on;
                                                          ^
commonFunctions.cc:482:59: warning: unused variable 'num_on' [-Wunused-variable]
  unsigned int                                            num_on;
                                                          ^
2 warnings 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/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c functionsErrorModel.cc -o functionsErrorModel.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/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.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/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c updateFunctions_AR1.cc -o updateFunctions_AR1.o
updateFunctions_AR1.cc:264:59: warning: unused variable 'num_on' [-Wunused-variable]
  unsigned int                                            num_on;  
                                                          ^
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/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c updateFunctions_Splines.cc -o updateFunctions_Splines.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GRENITS.so AR1_Gauss_biocond.o AR1_Student_biocond.o AR1_biocond.o PSplines_biocond.o R_C_interface.o ReadMCMCFiles.o commonFunctions.o functionsErrorModel.o matrixManipulationFunctions.o updateFunctions_AR1.o updateFunctions_Splines.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/GRENITS.buildbin-libdir/GRENITS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GRENITS)


>>>>>>> 
>>>>>>> FIXING LINKS FOR GRENITS.buildbin-libdir/GRENITS/libs//GRENITS.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" "GRENITS.buildbin-libdir/GRENITS/libs//GRENITS.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.3.dylib" "GRENITS.buildbin-libdir/GRENITS/libs//GRENITS.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" "GRENITS.buildbin-libdir/GRENITS/libs//GRENITS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "GRENITS.buildbin-libdir/GRENITS/libs//GRENITS.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libquadmath.0.dylib" "GRENITS.buildbin-libdir/GRENITS/libs//GRENITS.so"