GeneticsPed 1.12.0
David Henderson
| Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/GeneticsPed | | Last Changed Rev: 50293 / Revision: 54281 | | Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=GeneticsPed.buildbin-libdir GeneticsPed_1.12.0.tar.gz'
>>>>>>>
* installing *source* package ‘GeneticsPed’ ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c ainverse.cc -o ainverse.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c eibd.cc -o eibd.o
gfortran -arch i386 -fPIC -g -O2 -Wall -pedantic -c ggmatmult.f -o ggmatmult.o
gfortran -arch i386 -fPIC -g -O2 -Wall -pedantic -c gpi.f -o gpi.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c inbreed.cc -o inbreed.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c inverseAdditive.cc -o inverseAdditive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c meuwissen.cc -o meuwissen.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c pedSort.cc -o pedSort.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c pedtemplate.cc -o pedtemplate.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c register.cc -o register.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c sargolzaei.c -o sargolzaei.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c sortped.cc -o sortped.o
g++ -arch i386 -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 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.7-bioc/meat/GeneticsPed.buildbin-libdir/GeneticsPed/libs/i386
*** arch - ppc
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c ainverse.cc -o ainverse.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c eibd.cc -o eibd.o
gfortran -arch ppc -fPIC -g -O2 -Wall -pedantic -c ggmatmult.f -o ggmatmult.o
gfortran -arch ppc -fPIC -g -O2 -Wall -pedantic -c gpi.f -o gpi.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c inbreed.cc -o inbreed.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c inverseAdditive.cc -o inverseAdditive.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c meuwissen.cc -o meuwissen.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c pedSort.cc -o pedSort.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c pedtemplate.cc -o pedtemplate.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c register.cc -o register.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c sargolzaei.c -o sargolzaei.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c sortped.cc -o sortped.o
g++ -arch ppc -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 -lgfortran -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.7-bioc/meat/GeneticsPed.buildbin-libdir/GeneticsPed/libs/ppc
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c ainverse.cc -o ainverse.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c eibd.cc -o eibd.o
gfortran -arch x86_64 -fPIC -g -O2 -Wall -pedantic -c ggmatmult.f -o ggmatmult.o
gfortran -arch x86_64 -fPIC -g -O2 -Wall -pedantic -c gpi.f -o gpi.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c inbreed.cc -o inbreed.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c inverseAdditive.cc -o inverseAdditive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c meuwissen.cc -o meuwissen.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c pedSort.cc -o pedSort.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c pedtemplate.cc -o pedtemplate.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c register.cc -o register.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c sargolzaei.c -o sargolzaei.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c sortped.cc -o sortped.o
g++ -arch x86_64 -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 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.7-bioc/meat/GeneticsPed.buildbin-libdir/GeneticsPed/libs/x86_64
** R
** data
** inst
** preparing package for lazy loading
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.
gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.
Attaching package: 'gdata'
The following object(s) are masked from 'package:utils':
object.size
Loading required package: combinat
Attaching package: 'combinat'
The following object(s) are masked from 'package:utils':
combn
Loading required package: gtools
Loading required package: MASS
Loading required package: mvtnorm
NOTE: THIS PACKAGE IS NOW OBSOLETE.
The R-Genetics project has developed an set of enhanced genetics
packages to replace 'genetics'. Please visit the project homepage
at http://rgenetics.org for informtion.
Attaching package: 'genetics'
The following object(s) are masked from 'package:base':
%in%, as.factor, order
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (GeneticsPed)
>>>>>>>
>>>>>>> FIXING LINKS FOR GeneticsPed.buildbin-libdir/GeneticsPed/libs/i386/GeneticsPed.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgcc_s.1.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs/i386/GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgfortran.2.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs/i386/GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.5.2.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs/i386/GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs/i386/GeneticsPed.so"
>>>>>>>
>>>>>>> FIXING LINKS FOR GeneticsPed.buildbin-libdir/GeneticsPed/libs/ppc/GeneticsPed.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgcc_s.1.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs/ppc/GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgfortran.2.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs/ppc/GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.5.2.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs/ppc/GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs/ppc/GeneticsPed.so"
>>>>>>>
>>>>>>> FIXING LINKS FOR GeneticsPed.buildbin-libdir/GeneticsPed/libs/x86_64/GeneticsPed.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgcc_s.1.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs/x86_64/GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgfortran.2.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs/x86_64/GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.5.2.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs/x86_64/GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs/x86_64/GeneticsPed.so"