* install options are ' --no-html'

* installing *source* package 'bim' ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c INITVALS.c -o INITVALS.o
In file included from INITVALS.c:13:
revjump.h:110:1: 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
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c QTL_MOVE.c -o QTL_MOVE.o
In file included from QTL_MOVE.c:14:
revjump.h:110:1: 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
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c R_mcmc.c -o R_mcmc.o
In file included from R_mcmc.c:12:
revjump.h:110:1: 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
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c Utilities.c -o Utilities.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c accept_birth.c -o accept_birth.o
In file included from accept_birth.c:13:
revjump.h:110:1: 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
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c birth.c -o birth.o
In file included from birth.c:13:
revjump.h:110:1: 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
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c com.c -o com.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c death.c -o death.o
In file included from death.c:13:
revjump.h:110:1: 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
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c mcmc.c -o mcmc.o
In file included from mcmc.c:17:
revjump.h:110:1: 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
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c ranlib.c -o ranlib.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c read_data.c -o read_data.o
In file included from read_data.c:17:
revjump.h:110:1: 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
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c update_parms.c -o update_parms.o
In file included from update_parms.c:12:
revjump.h:110:1: 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
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c update_qtl.c -o update_qtl.o
In file included from update_qtl.c:20:
revjump.h:110:1: 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
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 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 -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -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:110:1: 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-4.2 -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:110:1: 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-4.2 -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:110:1: 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-4.2 -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-4.2 -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:110:1: 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-4.2 -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:110:1: 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-4.2 -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-4.2 -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:110:1: 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-4.2 -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:110:1: 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-4.2 -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-4.2 -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:110:1: 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-4.2 -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:110:1: 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-4.2 -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:110:1: 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-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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 -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c INITVALS.c -o INITVALS.o
In file included from INITVALS.c:13:
revjump.h:110:1: 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
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c QTL_MOVE.c -o QTL_MOVE.o
In file included from QTL_MOVE.c:14:
revjump.h:110:1: 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
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c R_mcmc.c -o R_mcmc.o
In file included from R_mcmc.c:12:
revjump.h:110:1: 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
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c Utilities.c -o Utilities.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c accept_birth.c -o accept_birth.o
In file included from accept_birth.c:13:
revjump.h:110:1: 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
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c birth.c -o birth.o
In file included from birth.c:13:
revjump.h:110:1: 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
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c com.c -o com.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c death.c -o death.o
In file included from death.c:13:
revjump.h:110:1: 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
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c mcmc.c -o mcmc.o
In file included from mcmc.c:17:
revjump.h:110:1: 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
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c ranlib.c -o ranlib.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c read_data.c -o read_data.o
In file included from read_data.c:17:
revjump.h:110:1: 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
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c update_parms.c -o update_parms.o
In file included from update_parms.c:12:
revjump.h:110:1: 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
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -c update_qtl.c -o update_qtl.o
In file included from update_qtl.c:20:
revjump.h:110:1: 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
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 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 -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** preparing package for lazy loading
** help
Warning: ./man/Bnapus.Rd:35: unknown macro '\item'
Warning: ./man/Bnapus.Rd:36: unknown macro '\item'
Warning: ./man/Bnapus.Rd:37: unknown macro '\item'
Warning: ./man/Bnapus.Rd:38: unknown macro '\item'
Warning: ./man/Bnapus.Rd:43: unknown macro '\item'
Warning: ./man/Bnapus.Rd:47: unknown macro '\item'
Warning: ./man/Bnapus.Rd:48: unknown macro '\item'
Warning: ./man/Bnapus.Rd:52: unknown macro '\item'
Warning: ./man/Bnapus.Rd:58: unknown macro '\item'
Warning: bad markup (extra space?) at bim.qtl.Rd:38:13
Warning: ./man/read.bim.Rd:41: unexpected '}'
Warning: ./man/run.bmapqtl.Rd:52: unknown macro '\item'
Warning: ./man/run.bmapqtl.Rd:53: unknown macro '\item'
Warning: ./man/run.bmapqtl.Rd:59: unknown macro '\item'
Warning: ./man/run.bmapqtl.Rd:68: unknown macro '\item'
Warning: ./man/vern.Rd:28: unknown macro '\item'
Warning: ./man/vern.Rd:29: unknown macro '\item'
Warning: ./man/vern.Rd:33: unknown macro '\item'
Warning: ./man/vern.Rd:38: unknown macro '\item'
*** installing help indices
** building package indices ...
* DONE (bim)