CHECK report for bim on derby

* checking for working latex ... OK * using log directory '/Users/biocbuild/2.0d/Rpacks/bim.Rcheck' * using R version 2.5.0 Under development (unstable) (2006-10-21 r39702) * checking for file 'bim/DESCRIPTION' ... OK * this is package 'bim' version '1.7.0' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'bim' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for syntax errors ... OK * checking R files for non-ASCII characters ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking for CRLF line endings in C/C++/Fortran sources/headers ... OK * checking for portable use of $BLAS_LIBS ... OK * creating bim-Ex.R ... OK * checking examples ... OK * checking package vignettes in 'inst/doc' ... OK * creating bim-manual.tex ... OK * checking bim-manual.tex ... OK

* Installing *source* package 'bim' ... ** libs ** arch - i386 gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c INITVALS.c -o INITVALS.o In file included from INITVALS.c:13: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:28, from revjump.h:22, from INITVALS.c:13: /usr/include/architecture/i386/math.h:76:1: warning: this is the location of the previous definition /var/tmp//ccnVD9PQ.s:834:indirect jmp without `*' /var/tmp//ccnVD9PQ.s:849:indirect jmp without `*' /var/tmp//ccnVD9PQ.s:864:indirect jmp without `*' /var/tmp//ccnVD9PQ.s:879:indirect jmp without `*' /var/tmp//ccnVD9PQ.s:894:indirect jmp without `*' /var/tmp//ccnVD9PQ.s:909:indirect jmp without `*' /var/tmp//ccnVD9PQ.s:924:indirect jmp without `*' /var/tmp//ccnVD9PQ.s:939:indirect jmp without `*' /var/tmp//ccnVD9PQ.s:954:indirect jmp without `*' /var/tmp//ccnVD9PQ.s:969:indirect jmp without `*' /var/tmp//ccnVD9PQ.s:984:indirect jmp without `*' /var/tmp//ccnVD9PQ.s:999:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c QTL_MOVE.c -o QTL_MOVE.o In file included from QTL_MOVE.c:14: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:28, from revjump.h:22, from QTL_MOVE.c:14: /usr/include/architecture/i386/math.h:76:1: warning: this is the location of the previous definition /var/tmp//cczGmAss.s:918:indirect jmp without `*' /var/tmp//cczGmAss.s:933:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c R_mcmc.c -o R_mcmc.o In file included from R_mcmc.c:12: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:28, from revjump.h:22, from R_mcmc.c:12: /usr/include/architecture/i386/math.h:76:1: warning: this is the location of the previous definition /var/tmp//cczcghbn.s:2005:indirect jmp without `*' /var/tmp//cczcghbn.s:2020:indirect jmp without `*' /var/tmp//cczcghbn.s:2035:indirect jmp without `*' /var/tmp//cczcghbn.s:2050:indirect jmp without `*' /var/tmp//cczcghbn.s:2065:indirect jmp without `*' /var/tmp//cczcghbn.s:2080:indirect jmp without `*' /var/tmp//cczcghbn.s:2095:indirect jmp without `*' /var/tmp//cczcghbn.s:2110:indirect jmp without `*' /var/tmp//cczcghbn.s:2125:indirect jmp without `*' /var/tmp//cczcghbn.s:2140:indirect jmp without `*' /var/tmp//cczcghbn.s:2155:indirect jmp without `*' /var/tmp//cczcghbn.s:2170:indirect jmp without `*' /var/tmp//cczcghbn.s:2185:indirect jmp without `*' /var/tmp//cczcghbn.s:2200:indirect jmp without `*' /var/tmp//cczcghbn.s:2215:indirect jmp without `*' /var/tmp//cczcghbn.s:2230:indirect jmp without `*' /var/tmp//cczcghbn.s:2245:indirect jmp without `*' /var/tmp//cczcghbn.s:2260:indirect jmp without `*' /var/tmp//cczcghbn.s:2275:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c Utilities.c -o Utilities.o /var/tmp//cczlt9RI.s:3709:indirect jmp without `*' /var/tmp//cczlt9RI.s:3724:indirect jmp without `*' /var/tmp//cczlt9RI.s:3743:indirect jmp without `*' /var/tmp//cczlt9RI.s:3758:indirect jmp without `*' /var/tmp//cczlt9RI.s:3773:indirect jmp without `*' /var/tmp//cczlt9RI.s:3788:indirect jmp without `*' /var/tmp//cczlt9RI.s:3803:indirect jmp without `*' /var/tmp//cczlt9RI.s:3818:indirect jmp without `*' /var/tmp//cczlt9RI.s:3833:indirect jmp without `*' /var/tmp//cczlt9RI.s:3848:indirect jmp without `*' /var/tmp//cczlt9RI.s:3867:indirect jmp without `*' /var/tmp//cczlt9RI.s:3882:indirect jmp without `*' /var/tmp//cczlt9RI.s:3897:indirect jmp without `*' /var/tmp//cczlt9RI.s:3916:indirect jmp without `*' /var/tmp//cczlt9RI.s:3935:indirect jmp without `*' /var/tmp//cczlt9RI.s:3954:indirect jmp without `*' /var/tmp//cczlt9RI.s:3969:indirect jmp without `*' /var/tmp//cczlt9RI.s:3984:indirect jmp without `*' /var/tmp//cczlt9RI.s:3999:indirect jmp without `*' /var/tmp//cczlt9RI.s:4014:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c accept_birth.c -o accept_birth.o In file included from accept_birth.c:13: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:28, from revjump.h:22, from accept_birth.c:13: /usr/include/architecture/i386/math.h:76:1: warning: this is the location of the previous definition /var/tmp//ccScVdTK.s:518:indirect jmp without `*' /var/tmp//ccScVdTK.s:533:indirect jmp without `*' /var/tmp//ccScVdTK.s:548:indirect jmp without `*' /var/tmp//ccScVdTK.s:563:indirect jmp without `*' /var/tmp//ccScVdTK.s:578:indirect jmp without `*' /var/tmp//ccScVdTK.s:593:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c birth.c -o birth.o In file included from birth.c:13: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:28, from revjump.h:22, from birth.c:13: /usr/include/architecture/i386/math.h:76:1: warning: this is the location of the previous definition /var/tmp//cc7CwJ5B.s:3294:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3309:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3324:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3339:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3354:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3369:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3384:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3399:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3414:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3429:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3444:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3459:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3474:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3489:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3504:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3519:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3534:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3549:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3564:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3579:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3594:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3609:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3624:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3639:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3654:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3669:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3684:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3699:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3714:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3729:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3744:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3759:indirect jmp without `*' /var/tmp//cc7CwJ5B.s:3774:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c com.c -o com.o /var/tmp//ccGqOvAk.s:1012:indirect jmp without `*' /var/tmp//ccGqOvAk.s:1027:indirect jmp without `*' /var/tmp//ccGqOvAk.s:1046:indirect jmp without `*' /var/tmp//ccGqOvAk.s:1061:indirect jmp without `*' /var/tmp//ccGqOvAk.s:1076:indirect jmp without `*' /var/tmp//ccGqOvAk.s:1104:indirect jmp without `*' /var/tmp//ccGqOvAk.s:1129:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c death.c -o death.o In file included from death.c:13: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:28, from revjump.h:22, from death.c:13: /usr/include/architecture/i386/math.h:76:1: warning: this is the location of the previous definition /var/tmp//cchVRpH6.s:534:indirect jmp without `*' /var/tmp//cchVRpH6.s:549:indirect jmp without `*' /var/tmp//cchVRpH6.s:564:indirect jmp without `*' /var/tmp//cchVRpH6.s:579:indirect jmp without `*' /var/tmp//cchVRpH6.s:594:indirect jmp without `*' /var/tmp//cchVRpH6.s:609:indirect jmp without `*' /var/tmp//cchVRpH6.s:624:indirect jmp without `*' /var/tmp//cchVRpH6.s:639:indirect jmp without `*' /var/tmp//cchVRpH6.s:654:indirect jmp without `*' /var/tmp//cchVRpH6.s:669:indirect jmp without `*' /var/tmp//cchVRpH6.s:684:indirect jmp without `*' /var/tmp//cchVRpH6.s:699:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c mcmc.c -o mcmc.o In file included from mcmc.c:17: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:28, from revjump.h:22, from mcmc.c:17: /usr/include/architecture/i386/math.h:76:1: warning: this is the location of the previous definition /var/tmp//ccgXQGHS.s:2628:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2643:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2658:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2673:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2688:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2703:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2718:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2733:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2748:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2763:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2778:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2793:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2808:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2823:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2838:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2853:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2868:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2883:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2902:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2917:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2932:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2947:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2962:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2977:indirect jmp without `*' /var/tmp//ccgXQGHS.s:2992:indirect jmp without `*' /var/tmp//ccgXQGHS.s:3007:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c ranlib.c -o ranlib.o /var/tmp//cchSZT7i.s:6475:indirect jmp without `*' /var/tmp//cchSZT7i.s:6490:indirect jmp without `*' /var/tmp//cchSZT7i.s:6505:indirect jmp without `*' /var/tmp//cchSZT7i.s:6520:indirect jmp without `*' /var/tmp//cchSZT7i.s:6535:indirect jmp without `*' /var/tmp//cchSZT7i.s:6550:indirect jmp without `*' /var/tmp//cchSZT7i.s:6565:indirect jmp without `*' /var/tmp//cchSZT7i.s:6584:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c read_data.c -o read_data.o In file included from read_data.c:17: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:28, from revjump.h:22, from read_data.c:17: /usr/include/architecture/i386/math.h:76:1: warning: this is the location of the previous definition /var/tmp//ccYE3IlF.s:464:indirect jmp without `*' /var/tmp//ccYE3IlF.s:479:indirect jmp without `*' /var/tmp//ccYE3IlF.s:494:indirect jmp without `*' /var/tmp//ccYE3IlF.s:509:indirect jmp without `*' /var/tmp//ccYE3IlF.s:524:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c update_parms.c -o update_parms.o In file included from update_parms.c:12: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:28, from revjump.h:22, from update_parms.c:12: /usr/include/architecture/i386/math.h:76:1: warning: this is the location of the previous definition /var/tmp//ccoUrTXf.s:3753:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3768:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3783:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3798:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3813:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3828:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3843:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3858:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3873:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3888:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3903:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3918:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3933:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3948:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3963:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3978:indirect jmp without `*' /var/tmp//ccoUrTXf.s:3993:indirect jmp without `*' /var/tmp//ccoUrTXf.s:4008:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c update_qtl.c -o update_qtl.o In file included from update_qtl.c:20: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:28, from revjump.h:22, from update_qtl.c:20: /usr/include/architecture/i386/math.h:76:1: warning: this is the location of the previous definition /var/tmp//cciRAcGg.s:4829:indirect jmp without `*' /var/tmp//cciRAcGg.s:4844:indirect jmp without `*' /var/tmp//cciRAcGg.s:4859:indirect jmp without `*' /var/tmp//cciRAcGg.s:4874:indirect jmp without `*' /var/tmp//cciRAcGg.s:4889:indirect jmp without `*' /var/tmp//cciRAcGg.s:4904:indirect jmp without `*' /var/tmp//cciRAcGg.s:4919:indirect jmp without `*' /var/tmp//cciRAcGg.s:4934:indirect jmp without `*' /var/tmp//cciRAcGg.s:4949:indirect jmp without `*' /var/tmp//cciRAcGg.s:4964:indirect jmp without `*' /var/tmp//cciRAcGg.s:4979:indirect jmp without `*' /var/tmp//cciRAcGg.s:4994:indirect jmp without `*' /var/tmp//cciRAcGg.s:5009:indirect jmp without `*' /var/tmp//cciRAcGg.s:5024:indirect jmp without `*' /var/tmp//cciRAcGg.s:5039:indirect jmp without `*' /var/tmp//cciRAcGg.s:5054:indirect jmp without `*' gcc-4.0 -arch i386 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o bim.so INITVALS.o QTL_MOVE.o R_mcmc.o Utilities.o accept_birth.o birth.o com.o death.o mcmc.o ranlib.o read_data.o update_parms.o update_qtl.o -F/Library/Frameworks/R.framework/.. -framework R ** arch - ppc gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c INITVALS.c -o INITVALS.o In file included from INITVALS.c:13: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:26, from revjump.h:22, from INITVALS.c:13: /usr/include/architecture/ppc/math.h:92:1: warning: this is the location of the previous definition gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c QTL_MOVE.c -o QTL_MOVE.o In file included from QTL_MOVE.c:14: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:26, from revjump.h:22, from QTL_MOVE.c:14: /usr/include/architecture/ppc/math.h:92:1: warning: this is the location of the previous definition gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c R_mcmc.c -o R_mcmc.o In file included from R_mcmc.c:12: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:26, from revjump.h:22, from R_mcmc.c:12: /usr/include/architecture/ppc/math.h:92:1: warning: this is the location of the previous definition gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c Utilities.c -o Utilities.o gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c accept_birth.c -o accept_birth.o In file included from accept_birth.c:13: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:26, from revjump.h:22, from accept_birth.c:13: /usr/include/architecture/ppc/math.h:92:1: warning: this is the location of the previous definition gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c birth.c -o birth.o In file included from birth.c:13: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:26, from revjump.h:22, from birth.c:13: /usr/include/architecture/ppc/math.h:92:1: warning: this is the location of the previous definition gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c com.c -o com.o gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c death.c -o death.o In file included from death.c:13: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:26, from revjump.h:22, from death.c:13: /usr/include/architecture/ppc/math.h:92:1: warning: this is the location of the previous definition gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c mcmc.c -o mcmc.o In file included from mcmc.c:17: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:26, from revjump.h:22, from mcmc.c:17: /usr/include/architecture/ppc/math.h:92:1: warning: this is the location of the previous definition gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c ranlib.c -o ranlib.o gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c read_data.c -o read_data.o In file included from read_data.c:17: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:26, from revjump.h:22, from read_data.c:17: /usr/include/architecture/ppc/math.h:92:1: warning: this is the location of the previous definition gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c update_parms.c -o update_parms.o In file included from update_parms.c:12: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:26, from revjump.h:22, from update_parms.c:12: /usr/include/architecture/ppc/math.h:92:1: warning: this is the location of the previous definition gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c update_qtl.c -o update_qtl.o In file included from update_qtl.c:20: revjump.h:111:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:26, from revjump.h:22, from update_qtl.c:20: /usr/include/architecture/ppc/math.h:92:1: warning: this is the location of the previous definition gcc-4.0 -arch ppc -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o bim.so INITVALS.o QTL_MOVE.o R_mcmc.o Utilities.o accept_birth.o birth.o com.o death.o mcmc.o ranlib.o read_data.o update_parms.o update_qtl.o -F/Library/Frameworks/R.framework/.. -framework R ** R ** data ** inst ** preparing package for lazy loading Loading required package: qtl ** help >>> Building/Updating help pages for package 'bim' Formats: text html latex example Bnapus text html latex example bim-internal text html latex bim.effects text html latex example bim.fdr text html latex example bim.model text html latex example bim.qtl text html latex example bmapqtl.options text html latex example fisch text html latex example plot.bim text html latex example plot.bim.diag text html latex example plot.bim.loci text html latex example plot.bim.mcmc text html latex example plot.bim.model text html latex example read.bim text html latex example read.bmapqtl text html latex example run.bmapqtl text html latex example subset.bim text html latex example summary.bim text html latex example vern text html latex example ** building package indices ... * DONE (bim)

Package 28/208	OS	Arch	BUILD	CHECK	BUILD BIN
bim 1.7.0 Brian S. Yandell	Linux (SUSE 9.2)	x86_64	ERROR	skipped
	Linux (SUSE 10.1)	x86_64	ERROR	skipped
	Linux (SUSE 9.2)	i686	ERROR	skipped
	Solaris 2.9	sparc	ERROR	skipped
	Windows Server 2003	x86_64	ERROR	skipped	skipped
	Windows Server 2003	NA	ERROR	skipped	skipped
	Mac OS X (10.4.6)	i686	OK	[ OK ]

bim

1.7.0

Command output