GeneticsPed 1.9.0
The R Genetics Project
| Bioconductor Changelog | | Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneticsPed | | Last Changed Rev: 42686 / Revision: 43434 | | Last Changed Date: 2009-10-27 16:45:24 -0700 (Tue, 27 Oct 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | [ OK ] | OK | OK |
* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* preparing 'GeneticsPed':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* installing *source* package ‘GeneticsPed’ ...
** libs
** arch - i386
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c ainverse.cc -o ainverse.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c eibd.cc -o eibd.o
gfortran-4.2 -arch i386 -fPIC -g -O2 -Wall -c ggmatmult.f -o ggmatmult.o
gfortran-4.2 -arch i386 -fPIC -g -O2 -Wall -c gpi.f -o gpi.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c inbreed.cc -o inbreed.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c inverseAdditive.cc -o inverseAdditive.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c meuwissen.cc -o meuwissen.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c pedSort.cc -o pedSort.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c pedtemplate.cc -o pedtemplate.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c register.cc -o register.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c sargolzaei.c -o sargolzaei.o
sargolzaei.c: In function ‘sargolzaei’:
sargolzaei.c:96: warning: comparison between pointer and integer
sargolzaei.c:19: warning: ‘S’ may be used uninitialized in this function
sargolzaei.c:19: warning: ‘MIP’ may be used uninitialized in this function
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c sortped.cc -o sortped.o
g++-4.2 -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
ld: warning __gfortrani_options has different visibility (1) in /usr/lib/gcc/i686-apple-darwin9/4.2.1/libgfortran.a(environ.o) and (2) in GeneticsPed.so
ld: warning __gfortrani_compile_options has different visibility (1) in /usr/lib/gcc/i686-apple-darwin9/4.2.1/libgfortran.a(compile_options.o) and (2) in GeneticsPed.so
** arch - ppc
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c ainverse.cc -o ainverse.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c eibd.cc -o eibd.o
gfortran-4.2 -arch ppc -fPIC -g -O2 -Wall -c ggmatmult.f -o ggmatmult.o
gfortran-4.2 -arch ppc -fPIC -g -O2 -Wall -c gpi.f -o gpi.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c inbreed.cc -o inbreed.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c inverseAdditive.cc -o inverseAdditive.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c meuwissen.cc -o meuwissen.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c pedSort.cc -o pedSort.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c pedtemplate.cc -o pedtemplate.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c register.cc -o register.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c sargolzaei.c -o sargolzaei.o
sargolzaei.c: In function ‘sargolzaei’:
sargolzaei.c:96: warning: comparison between pointer and integer
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c sortped.cc -o sortped.o
g++-4.2 -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
ld: warning __gfortrani_options has different visibility (1) in /usr/lib/gcc/powerpc-apple-darwin9/4.2.1/libgfortran.a(environ.o) and (2) in GeneticsPed.so
ld: warning __gfortrani_compile_options has different visibility (1) in /usr/lib/gcc/powerpc-apple-darwin9/4.2.1/libgfortran.a(compile_options.o) and (2) in GeneticsPed.so
** arch - x86_64
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c ainverse.cc -o ainverse.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c eibd.cc -o eibd.o
gfortran-4.2 -arch x86_64 -fPIC -g -O2 -Wall -c ggmatmult.f -o ggmatmult.o
gfortran-4.2 -arch x86_64 -fPIC -g -O2 -Wall -c gpi.f -o gpi.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c inbreed.cc -o inbreed.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c inverseAdditive.cc -o inverseAdditive.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c meuwissen.cc -o meuwissen.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c pedSort.cc -o pedSort.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c pedtemplate.cc -o pedtemplate.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c register.cc -o register.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c sargolzaei.c -o sargolzaei.o
sargolzaei.c: In function ‘sargolzaei’:
sargolzaei.c:96: warning: comparison between pointer and integer
sargolzaei.c:19: warning: ‘S’ may be used uninitialized in this function
sargolzaei.c:19: warning: ‘MIP’ may be used uninitialized in this function
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c sortped.cc -o sortped.o
g++-4.2 -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
ld: warning __gfortrani_options has different visibility (1) in /usr/lib/gcc/i686-apple-darwin9/4.2.1/x86_64/libgfortran.a(environ.o) and (2) in GeneticsPed.so
ld: warning __gfortrani_compile_options has different visibility (1) in /usr/lib/gcc/i686-apple-darwin9/4.2.1/x86_64/libgfortran.a(compile_options.o) and (2) in GeneticsPed.so
** R
** data
** inst
** preparing package for lazy loading
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 ...
* DONE (GeneticsPed)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'GeneticsPed_1.9.0.tar.gz'