Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.14: BUILD BIN report for GeneticsPed on morelia

This page was generated on 2014-10-08 09:03:10 -0700 (Wed, 08 Oct 2014).

Package 330/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneticsPed 1.26.0
David Henderson
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/GeneticsPed
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 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  ERROR [ OK ]

Summary

Package: GeneticsPed
Version: 1.26.0
Command: rm -rf GeneticsPed.buildbin-libdir && mkdir GeneticsPed.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GeneticsPed_1.26.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GeneticsPed.buildbin-libdir
StartedAt: 2014-10-08 02:56:08 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:56:19 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 11.0 seconds
RetCode: 0
Status:  OK 
PackageFile: GeneticsPed_1.26.0.tgz
PackageFileSize: 598.1 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GeneticsPed.buildbin-libdir && mkdir GeneticsPed.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GeneticsPed_1.26.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GeneticsPed.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GeneticsPed.buildbin-libdir GeneticsPed_1.26.0.tar.gz'
>>>>>>> 

* installing *source* package ‘GeneticsPed’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c ainverse.cc -o ainverse.o
In file included from ainverse.cc:9:
./../include/ainverse.h:14:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
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    -fPIC  -Wall -mtune=core2 -g -O2  -c eibd.cc -o eibd.o
In file included from eibd.cc:15:
./../include/eibd.h:19:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
1 warning generated.
gfortran-4.8   -fPIC  -g -O2 -Wall  -c ggmatmult.f -o ggmatmult.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c gpi.f -o gpi.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c inbreed.cc -o inbreed.o
In file included from inbreed.cc:10:
./../include/inbreed.h:14:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
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    -fPIC  -Wall -mtune=core2 -g -O2  -c inverseAdditive.cc -o inverseAdditive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c meuwissen.cc -o meuwissen.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c pedSort.cc -o pedSort.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c pedtemplate.cc -o pedtemplate.o
In file included from pedtemplate.cc:15:
./../include/pedtemplate.h:18:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
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    -fPIC  -Wall -mtune=core2 -g -O2  -c register.cc -o register.o
In file included from register.cc:8:
./../include/meuwissen.h:4:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
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    -fPIC  -Wall -mtune=core2 -g -O2  -c sargolzaei.c -o sargolzaei.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c sortped.cc -o sortped.o
In file included from sortped.cc:1:
./../include/sortped.h:7:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
In file included from sortped.cc:1:
In file included from ./../include/sortped.h:9:
./../include/../include/pedtemplate.h:18:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
2 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneticsPed.so ainverse.o eibd.o ggmatmult.o gpi.o inbreed.o inverseAdditive.o meuwissen.o pedSort.o pedtemplate.o register.o sargolzaei.o sortped.o -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/GeneticsPed.buildbin-libdir/GeneticsPed/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 (GeneticsPed)


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