snpMatrix 1.6.1
David Clayton
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/snpMatrix | | Last Changed Rev: 34836 / Revision: 38965 | | Last Changed Date: 2008-10-22 08:29:57 -0700 (Wed, 22 Oct 2008) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | [ OK ] | WARNINGS | OK |
* checking for file 'snpMatrix/DESCRIPTION' ... OK
* preparing 'snpMatrix':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'snpMatrix' ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c adler32.c -o adler32.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c bind.c -o bind.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c compress.c -o compress.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c covwin.c -o covwin.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c crc32.c -o crc32.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c deflate.c -o deflate.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c force_hom.c -o force_hom.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c glm_test.c -o glm_test.o
glm_test.c: In function 'glm_score_test':
glm_test.c:326: warning: unused variable 'test'
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:672: warning: unused variable 'err'
glm_test_R.c: In function 'pool2_glm':
glm_test_R.c:867: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:867: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:901: warning: 'RV' may be used uninitialized in this function
glm_test_R.c:901: warning: 'RU' may be used uninitialized in this function
glm_test_R.c: In function 'snp_lhs_score':
glm_test_R.c:175: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:175: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:285: warning: 'i' may be used uninitialized in this function
glm_test_R.c:205: warning: 'V' may be used uninitialized in this function
glm_test_R.c:205: warning: 'U' may be used uninitialized in this function
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:468: warning: 'Rule_names' may be used uninitialized in this function
glm_test_R.c:592: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:592: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:592: warning: 'TestNames' may be used uninitialized in this function
glm_test_R.c:674: warning: 'len' may be used uninitialized in this function
glm_test_R.c:651: warning: 'Snames' may be used uninitialized in this function
glm_test_R.c:651: warning: 'V' may be used uninitialized in this function
glm_test_R.c:651: warning: 'U' may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c gzio.c -o gzio.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c hash_index.c -o hash_index.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c ibs.c -o ibs.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c imputation.c -o imputation.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c in.c -o in.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c infback.c -o infback.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c inffast.c -o inffast.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c inflate.c -o inflate.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c inftrees.c -o inftrees.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c input.c -o input.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c inputNew.c -o inputNew.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c input_unsorted.c -o input_unsorted.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c invert.c -o invert.o
invert.c: In function 'syminv':
invert.c:63: warning: unused variable 'nn'
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c ld_with.c -o ld_with.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c mla.c -o mla.o
mla.c: In function 'wsum':
mla.c:154: warning: unused variable 'i'
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c outdata.c -o outdata.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c pairwise_linkage.c -o pairwise_linkage.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c read_chiamo.c -o read_chiamo.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c read_hapmap.c -o read_hapmap.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c read_pedfile.c -o read_pedfile.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c read_signals.c -o read_signals.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c readbed.c -o readbed.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c readped.c -o readped.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c sdfpw.c -o sdfpw.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c single_snp_tests.c -o single_snp_tests.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c snp_summary.c -o snp_summary.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c snpmpy.c -o snpmpy.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c solve_cubic.c -o solve_cubic.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c solve_quadratic.c -o solve_quadratic.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c structure.c -o structure.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c switch.c -o switch.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c tdt.c -o tdt.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c trees.c -o trees.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c uncompr.c -o uncompr.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c zutil.c -o zutil.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o snpMatrix.so adler32.o bind.o compress.o covwin.o crc32.o deflate.o force_hom.o glm_test.o glm_test_R.o gzio.o hash_index.o ibs.o imputation.o in.o infback.o inffast.o inflate.o inftrees.o input.o inputNew.o input_unsorted.o invert.o ld_graphic_eps.o ld_with.o mla.o outdata.o pairwise_linkage.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o readbed.o readped.o sdfpw.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o solve_quadratic.o structure.o switch.o tdt.o trees.o uncompr.o zutil.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c adler32.c -o adler32.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c bind.c -o bind.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c compress.c -o compress.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c covwin.c -o covwin.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c crc32.c -o crc32.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c deflate.c -o deflate.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c force_hom.c -o force_hom.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c glm_test.c -o glm_test.o
glm_test.c: In function 'glm_score_test':
glm_test.c:326: warning: unused variable 'test'
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:672: warning: unused variable 'err'
glm_test_R.c: In function 'pool2_glm':
glm_test_R.c:867: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:867: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:901: warning: 'RV' may be used uninitialized in this function
glm_test_R.c:901: warning: 'RU' may be used uninitialized in this function
glm_test_R.c: In function 'snp_lhs_score':
glm_test_R.c:175: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:175: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:285: warning: 'i' may be used uninitialized in this function
glm_test_R.c:205: warning: 'V' may be used uninitialized in this function
glm_test_R.c:205: warning: 'U' may be used uninitialized in this function
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:468: warning: 'Rule_names' may be used uninitialized in this function
glm_test_R.c:592: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:592: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:592: warning: 'TestNames' may be used uninitialized in this function
glm_test_R.c:674: warning: 'len' may be used uninitialized in this function
glm_test_R.c:651: warning: 'Snames' may be used uninitialized in this function
glm_test_R.c:651: warning: 'V' may be used uninitialized in this function
glm_test_R.c:651: warning: 'U' may be used uninitialized in this function
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c gzio.c -o gzio.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c hash_index.c -o hash_index.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c ibs.c -o ibs.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c imputation.c -o imputation.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c in.c -o in.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c infback.c -o infback.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c inffast.c -o inffast.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c inflate.c -o inflate.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c inftrees.c -o inftrees.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c input.c -o input.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c inputNew.c -o inputNew.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c input_unsorted.c -o input_unsorted.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c invert.c -o invert.o
invert.c: In function 'syminv':
invert.c:63: warning: unused variable 'nn'
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c ld_with.c -o ld_with.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c mla.c -o mla.o
mla.c: In function 'wsum':
mla.c:154: warning: unused variable 'i'
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c outdata.c -o outdata.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c pairwise_linkage.c -o pairwise_linkage.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c read_chiamo.c -o read_chiamo.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c read_hapmap.c -o read_hapmap.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c read_pedfile.c -o read_pedfile.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c read_signals.c -o read_signals.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c readbed.c -o readbed.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c readped.c -o readped.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c sdfpw.c -o sdfpw.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c single_snp_tests.c -o single_snp_tests.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c snp_summary.c -o snp_summary.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c snpmpy.c -o snpmpy.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c solve_cubic.c -o solve_cubic.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c solve_quadratic.c -o solve_quadratic.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c structure.c -o structure.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c switch.c -o switch.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c tdt.c -o tdt.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c trees.c -o trees.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c uncompr.c -o uncompr.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c zutil.c -o zutil.o
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o snpMatrix.so adler32.o bind.o compress.o covwin.o crc32.o deflate.o force_hom.o glm_test.o glm_test_R.o gzio.o hash_index.o ibs.o imputation.o in.o infback.o inffast.o inflate.o inftrees.o input.o inputNew.o input_unsorted.o invert.o ld_graphic_eps.o ld_with.o mla.o outdata.o pairwise_linkage.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o readbed.o readped.o sdfpw.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o solve_quadratic.o structure.o switch.o tdt.o trees.o uncompr.o zutil.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c adler32.c -o adler32.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c bind.c -o bind.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c compress.c -o compress.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c covwin.c -o covwin.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c crc32.c -o crc32.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c deflate.c -o deflate.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c force_hom.c -o force_hom.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c glm_test.c -o glm_test.o
glm_test.c: In function 'glm_score_test':
glm_test.c:326: warning: unused variable 'test'
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:672: warning: unused variable 'err'
glm_test_R.c: In function 'pool2_glm':
glm_test_R.c:867: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:867: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:901: warning: 'RV' may be used uninitialized in this function
glm_test_R.c:901: warning: 'RU' may be used uninitialized in this function
glm_test_R.c: In function 'snp_lhs_score':
glm_test_R.c:175: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:175: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:205: warning: 'V' may be used uninitialized in this function
glm_test_R.c:205: warning: 'U' may be used uninitialized in this function
glm_test_R.c:285: warning: 'i' may be used uninitialized in this function
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:468: warning: 'Rule_names' may be used uninitialized in this function
glm_test_R.c:592: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:592: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:592: warning: 'TestNames' may be used uninitialized in this function
glm_test_R.c:674: warning: 'len' may be used uninitialized in this function
glm_test_R.c:651: warning: 'Snames' may be used uninitialized in this function
glm_test_R.c:651: warning: 'V' may be used uninitialized in this function
glm_test_R.c:651: warning: 'U' may be used uninitialized in this function
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c gzio.c -o gzio.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c hash_index.c -o hash_index.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c ibs.c -o ibs.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c imputation.c -o imputation.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c in.c -o in.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c infback.c -o infback.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c inffast.c -o inffast.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c inflate.c -o inflate.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c inftrees.c -o inftrees.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c input.c -o input.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c inputNew.c -o inputNew.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c input_unsorted.c -o input_unsorted.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c invert.c -o invert.o
invert.c: In function 'syminv':
invert.c:63: warning: unused variable 'nn'
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c ld_with.c -o ld_with.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c mla.c -o mla.o
mla.c: In function 'wsum':
mla.c:154: warning: unused variable 'i'
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c outdata.c -o outdata.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c pairwise_linkage.c -o pairwise_linkage.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c read_chiamo.c -o read_chiamo.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c read_hapmap.c -o read_hapmap.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c read_pedfile.c -o read_pedfile.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c read_signals.c -o read_signals.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c readbed.c -o readbed.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c readped.c -o readped.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c sdfpw.c -o sdfpw.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c single_snp_tests.c -o single_snp_tests.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c snp_summary.c -o snp_summary.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c snpmpy.c -o snpmpy.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c solve_cubic.c -o solve_cubic.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c solve_quadratic.c -o solve_quadratic.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c structure.c -o structure.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c switch.c -o switch.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c tdt.c -o tdt.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c trees.c -o trees.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c uncompr.c -o uncompr.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c zutil.c -o zutil.o
gcc-4.2 -arch ppc64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o snpMatrix.so adler32.o bind.o compress.o covwin.o crc32.o deflate.o force_hom.o glm_test.o glm_test_R.o gzio.o hash_index.o ibs.o imputation.o in.o infback.o inffast.o inflate.o inftrees.o input.o inputNew.o input_unsorted.o invert.o ld_graphic_eps.o ld_with.o mla.o outdata.o pairwise_linkage.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o readbed.o readped.o sdfpw.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o solve_quadratic.o structure.o switch.o tdt.o trees.o uncompr.o zutil.o -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64/libRblas.dylib -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c adler32.c -o adler32.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c bind.c -o bind.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c compress.c -o compress.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c covwin.c -o covwin.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c crc32.c -o crc32.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c deflate.c -o deflate.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c force_hom.c -o force_hom.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c glm_test.c -o glm_test.o
glm_test.c: In function 'glm_score_test':
glm_test.c:326: warning: unused variable 'test'
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:672: warning: unused variable 'err'
glm_test_R.c: In function 'pool2_glm':
glm_test_R.c:867: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:867: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:901: warning: 'RV' may be used uninitialized in this function
glm_test_R.c:901: warning: 'RU' may be used uninitialized in this function
glm_test_R.c: In function 'snp_lhs_score':
glm_test_R.c:175: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:175: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:205: warning: 'U' may be used uninitialized in this function
glm_test_R.c:285: warning: 'i' may be used uninitialized in this function
glm_test_R.c:205: warning: 'V' may be used uninitialized in this function
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:468: warning: 'Rule_names' may be used uninitialized in this function
glm_test_R.c:592: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:592: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:592: warning: 'TestNames' may be used uninitialized in this function
glm_test_R.c:674: warning: 'len' may be used uninitialized in this function
glm_test_R.c:651: warning: 'Snames' may be used uninitialized in this function
glm_test_R.c:651: warning: 'V' may be used uninitialized in this function
glm_test_R.c:651: warning: 'U' may be used uninitialized in this function
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c gzio.c -o gzio.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c hash_index.c -o hash_index.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c ibs.c -o ibs.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c imputation.c -o imputation.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c in.c -o in.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c infback.c -o infback.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c inffast.c -o inffast.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c inflate.c -o inflate.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c inftrees.c -o inftrees.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c input.c -o input.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c inputNew.c -o inputNew.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c input_unsorted.c -o input_unsorted.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c invert.c -o invert.o
invert.c: In function 'syminv':
invert.c:63: warning: unused variable 'nn'
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c ld_with.c -o ld_with.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c mla.c -o mla.o
mla.c: In function 'wsum':
mla.c:154: warning: unused variable 'i'
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c outdata.c -o outdata.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c pairwise_linkage.c -o pairwise_linkage.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c read_chiamo.c -o read_chiamo.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c read_hapmap.c -o read_hapmap.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c read_pedfile.c -o read_pedfile.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c read_signals.c -o read_signals.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c readbed.c -o readbed.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c readped.c -o readped.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c sdfpw.c -o sdfpw.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c single_snp_tests.c -o single_snp_tests.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c snp_summary.c -o snp_summary.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c snpmpy.c -o snpmpy.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c solve_cubic.c -o solve_cubic.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c solve_quadratic.c -o solve_quadratic.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c structure.c -o structure.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c switch.c -o switch.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c tdt.c -o tdt.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c trees.c -o trees.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c uncompr.c -o uncompr.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c zutil.c -o zutil.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o snpMatrix.so adler32.o bind.o compress.o covwin.o crc32.o deflate.o force_hom.o glm_test.o glm_test_R.o gzio.o hash_index.o ibs.o imputation.o in.o infback.o inffast.o inflate.o inftrees.o input.o inputNew.o input_unsorted.o invert.o ld_graphic_eps.o ld_with.o mla.o outdata.o pairwise_linkage.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o readbed.o readped.o sdfpw.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o solve_quadratic.o structure.o switch.o tdt.o trees.o uncompr.o zutil.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** preparing package for lazy loading
Loading required package: survival
Loading required package: splines
Creating a new generic function for "plot" in "snpMatrix"
** help
>>> Building/Updating help pages for package 'snpMatrix'
Formats: text html latex example
X.snp-class text html latex example
X.snp.matrix-class text html latex example
chi.squared text html latex example
epsout.ld.snp text html latex example
families text html latex example
filter.rules text html latex example
for.exercise text html latex example
glm.test.control text html latex
Note: removing empty section \references in file 'ibs.stats.Rd'
Note: removing empty section \seealso in file 'ibs.stats.Rd'
ibs.stats text html latex example
ibsCount text html latex example
ibsDist text html latex example
imputation.maf text html latex example
impute.snps text html latex example
ld.snp text html latex example
ld.with text html latex example
misinherits text html latex example
pair.result.ld.snp text html latex example
plot.snp.dprime text html latex example
pool text html latex example
pool2 text html latex
qq.chisq text html latex example
read.HapMap.data text html latex example
Note: removing empty section \examples in file 'read.pedfile.info.Rd'
read.pedfile.info text html latex
Note: removing empty section \examples in file 'read.pedfile.map.Rd'
read.pedfile.map text html latex
read.plink text html latex
Note: removing empty section \note in file 'read.snps.chiamo.Rd'
read.snps.chiamo text html latex example
read.snps.long text html latex
read.snps.long.old text html latex
read.snps.pedfile text html latex
Note: removing empty section \seealso in file 'read.wtccc.signals.Rd'
read.wtccc.signals text html latex example
row.summary text html latex example
WARNING: \code inside code block in file 'single.snp.tests.Rd'
single.snp.tests text html latex example
snp-class text html latex example
snp.cbind text html latex example
snp.cor text html latex example
snp.dprime-class text html latex example
snp.imputation text html latex example
snp.lhs.tests text html latex example
snp.matrix-class text html latex example
snp.pre text html latex example
snp.reg.imputation-class text html latex example
snp.rhs.tests text html latex example
snp.tests.glm-class text html latex example
snp.tests.single-class text html latex example
snpMatrix-internal text html latex
snpMatrix-package text html latex
switch.alleles text html latex example
tdt.snp text html latex example
test.allele.switch text html latex example
testdata text html latex example
write.snp.matrix text html latex
Note: removing empty section \note in file 'wtccc.sample.list.Rd'
Note: removing empty section \examples in file 'wtccc.sample.list.Rd'
wtccc.sample.list text html latex
xxt text html latex example
** building package indices ...
* DONE (snpMatrix)
* 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 'snpMatrix_1.6.1.tar.gz'