gmapR 1.2.0
Michael Lawrence
| Snapshot Date: 2013-06-06 17:01:04 -0700 (Thu, 06 Jun 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/gmapR | | Last Changed Rev: 75263 / Revision: 77251 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | [ ERROR ] | skipped | skipped |
* checking for file 'gmapR/DESCRIPTION' ... OK
* preparing 'gmapR':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
-----------------------------------
* installing *source* package 'gmapR' ...
** libs
** arch -
rm -rf samtools; mkdir samtools
ln -sf /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbam.a samtools/libbam.a
for header in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/*.h; do \
ln -sf $header samtools/; \
done
cd gstruct/; \
./configure --enable-static --disable-shared \
--prefix=/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr --includedir=/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/include/gstruct \
--libdir=/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/lib \
--with-samtools=/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools \
--disable-binaries #\
## does not appear to be a true dependency yet
checking package version... 2013-02-14
checking CONFIG_SITE... ./config.site
loading script ./config.site
checking CFLAGS... not set by user so using default -O3
checking build system type... x86_64-apple-darwin10.8.0
checking host system type... x86_64-apple-darwin10.8.0
checking target system type... x86_64-apple-darwin10.8.0
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking whether make supports nested variables... yes
checking dependency style of gcc... gcc3
checking bindir... /private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/bin
checking whether to link statically... not specified so disabled by default
checking for a working version of perl... /usr/bin/perl
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc and cc understand -c and -o together... yes
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld
checking if the linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-apple-darwin10.8.0 file names to x86_64-apple-darwin10.8.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin10.8.0 file names to toolchain format... func_convert_file_noop
checking for /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from gcc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.8.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for qsub... no
checking gmap program directory...
checking for get-genome... false
checking for iit_store... false
checking for iit_get... false
checking for gmap_build... false
checking for gmap... false
checking for gsnap... false
checking for uniqscan... false
checking for rint in -lm... yes
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for working volatile... yes
checking for size_t... yes
checking for off_t... yes
checking for caddr_t... yes
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for working mmap with MAP_FIXED... yes
checking for working mmap with MAP_VARIABLE... no
checking for MAP_FILE in mmap... yes
checking for MAP_VARIABLE in mmap... no
checking for MAP_SHARED in mmap... yes
checking for MAP_PRIVATE in mmap... yes
checking for MAP_FAILED in mmap... yes
checking for MADV_DONTNEED in madvise... yes
checking for MADV_WILLNEED in madvise... yes
checking for MADV_RANDOM in madvise... yes
checking for ceil... yes
checking for floor... yes
checking for index... yes
checking for log... yes
checking for madvise... yes
checking for memcpy... yes
checking for memmove... yes
checking for memset... yes
checking for munmap... yes
checking for pow... yes
checking for rint... yes
checking for stat64... yes
checking for strtoul... yes
checking for sysconf... yes
checking for sysctl... yes
checking for sigaction... yes
checking for struct stat64... yes
checking for pagesize via sysconf... yes
checking for pagesize via sysctl... yes
checking whether fopen accepts "b" mode... yes
checking whether fopen accepts "t" mode... yes
checking gmapdb... /private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share
checking whether to make binaries... disabled
checking for zlib support... enabled
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzopen in -lz... yes
checking for gzeof in -lz... yes
checking for gzgetc in -lz... yes
checking for gzgets in -lz... yes
checking for gzclose in -lz... yes
checking if zlib package is complete... working
checking for gzbuffer in -lz... no
checking for samtools library... enabled
checking for samtools... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating lib/gstruct-1.0.pc
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
cd gstruct; \
make install
Making install in src
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c -o libgstruct_1.0_la-except.lo `test -f 'except.c' || echo './'`except.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c except.c -o libgstruct_1.0_la-except.o
mv -f .deps/libgstruct_1.0_la-except.Tpo .deps/libgstruct_1.0_la-except.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c -o libgstruct_1.0_la-assert.lo `test -f 'assert.c' || echo './'`assert.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c assert.c -o libgstruct_1.0_la-assert.o
mv -f .deps/libgstruct_1.0_la-assert.Tpo .deps/libgstruct_1.0_la-assert.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c -o libgstruct_1.0_la-mem.lo `test -f 'mem.c' || echo './'`mem.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c mem.c -o libgstruct_1.0_la-mem.o
mv -f .deps/libgstruct_1.0_la-mem.Tpo .deps/libgstruct_1.0_la-mem.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c -o libgstruct_1.0_la-intlist.lo `test -f 'intlist.c' || echo './'`intlist.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c intlist.c -o libgstruct_1.0_la-intlist.o
mv -f .deps/libgstruct_1.0_la-intlist.Tpo .deps/libgstruct_1.0_la-intlist.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c -o libgstruct_1.0_la-list.lo `test -f 'list.c' || echo './'`list.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c list.c -o libgstruct_1.0_la-list.o
mv -f .deps/libgstruct_1.0_la-list.Tpo .deps/libgstruct_1.0_la-list.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c -o libgstruct_1.0_la-littleendian.lo `test -f 'littleendian.c' || echo './'`littleendian.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c littleendian.c -o libgstruct_1.0_la-littleendian.o
mv -f .deps/libgstruct_1.0_la-littleendian.Tpo .deps/libgstruct_1.0_la-littleendian.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c -o libgstruct_1.0_la-bigendian.lo `test -f 'bigendian.c' || echo './'`bigendian.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c bigendian.c -o libgstruct_1.0_la-bigendian.o
mv -f .deps/libgstruct_1.0_la-bigendian.Tpo .deps/libgstruct_1.0_la-bigendian.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c -o libgstruct_1.0_la-interval.lo `test -f 'interval.c' || echo './'`interval.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c interval.c -o libgstruct_1.0_la-interval.o
mv -f .deps/libgstruct_1.0_la-interval.Tpo .deps/libgstruct_1.0_la-interval.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c -o libgstruct_1.0_la-uintlist.lo `test -f 'uintlist.c' || echo './'`uintlist.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c uintlist.c -o libgstruct_1.0_la-uintlist.o
mv -f .deps/libgstruct_1.0_la-uintlist.Tpo .deps/libgstruct_1.0_la-uintlist.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c -o libgstruct_1.0_la-stopwatch.lo `test -f 'stopwatch.c' || echo './'`stopwatch.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c stopwatch.c -o libgstruct_1.0_la-stopwatch.o
mv -f .deps/libgstruct_1.0_la-stopwatch.Tpo .deps/libgstruct_1.0_la-stopwatch.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c -o libgstruct_1.0_la-access.lo `test -f 'access.c' || echo './'`access.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c access.c -o libgstruct_1.0_la-access.o
access.c: In function 'Access_file_exists_p':
access.c:59: warning: 'stat64' is deprecated (declared at /usr/include/sys/stat.h:465)
access.c: In function 'Access_filesize':
access.c:79: warning: 'stat64' is deprecated (declared at /usr/include/sys/stat.h:465)
mv -f .deps/libgstruct_1.0_la-access.Tpo .deps/libgstruct_1.0_la-access.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c -o libgstruct_1.0_la-iit-read.lo `test -f 'iit-read.c' || echo './'`iit-read.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c iit-read.c -o libgstruct_1.0_la-iit-read.o
iit-read.c: In function 'skip_trees':
iit-read.c:1595: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:1595: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c: In function 'read_tree':
iit-read.c:1622: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:1622: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:1634: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:1634: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:1656: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:1656: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:1677: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:1677: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:1726: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:1726: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c: In function 'skip_intervals':
iit-read.c:1763: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:1763: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c: In function 'read_intervals':
iit-read.c:1818: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:1818: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c: In function 'IIT_read_divint':
iit-read.c:2328: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2328: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2344: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2344: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2356: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2356: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2365: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2365: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2392: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2392: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2413: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2413: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2430: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2430: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2450: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2450: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2479: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2479: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c: In function 'IIT_read':
iit-read.c:2589: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2589: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2607: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2607: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2624: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2624: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2633: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2633: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2662: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2662: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2683: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2683: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2700: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2700: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2725: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2725: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2751: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2751: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:2804: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2804: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c: In function 'IIT_debug':
iit-read.c:2991: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:2991: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:3007: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:3007: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:3024: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:3024: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:3033: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:3033: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:3062: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:3062: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:3088: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:3088: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:3105: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:3105: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:3130: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:3130: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:3156: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:3156: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
iit-read.c:3201: warning: format '%ld' expects type 'long int', but argument 4 has type 'off_t'
iit-read.c:3201: warning: format '%ld' expects type 'long int', but argument 5 has type 'off_t'
mv -f .deps/libgstruct_1.0_la-iit-read.Tpo .deps/libgstruct_1.0_la-iit-read.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c -o libgstruct_1.0_la-chrom.lo `test -f 'chrom.c' || echo './'`chrom.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c chrom.c -o libgstruct_1.0_la-chrom.o
mv -f .deps/libgstruct_1.0_la-chrom.Tpo .deps/libgstruct_1.0_la-chrom.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c -o libgstruct_1.0_la-genomicpos.lo `test -f 'genomicpos.c' || echo './'`genomicpos.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c genomicpos.c -o libgstruct_1.0_la-genomicpos.o
mv -f .deps/libgstruct_1.0_la-genomicpos.Tpo .deps/libgstruct_1.0_la-genomicpos.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c -o libgstruct_1.0_la-md5.lo `test -f 'md5.c' || echo './'`md5.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c md5.c -o libgstruct_1.0_la-md5.o
mv -f .deps/libgstruct_1.0_la-md5.Tpo .deps/libgstruct_1.0_la-md5.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c -o libgstruct_1.0_la-sequence.lo `test -f 'sequence.c' || echo './'`sequence.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c sequence.c -o libgstruct_1.0_la-sequence.o
mv -f .deps/libgstruct_1.0_la-sequence.Tpo .deps/libgstruct_1.0_la-sequence.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c -o libgstruct_1.0_la-genome.lo `test -f 'genome.c' || echo './'`genome.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c genome.c -o libgstruct_1.0_la-genome.o
mv -f .deps/libgstruct_1.0_la-genome.Tpo .deps/libgstruct_1.0_la-genome.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c -o libgstruct_1.0_la-uinttable.lo `test -f 'uinttable.c' || echo './'`uinttable.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c uinttable.c -o libgstruct_1.0_la-uinttable.o
mv -f .deps/libgstruct_1.0_la-uinttable.Tpo .deps/libgstruct_1.0_la-uinttable.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c -o libgstruct_1.0_la-table.lo `test -f 'table.c' || echo './'`table.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c table.c -o libgstruct_1.0_la-table.o
mv -f .deps/libgstruct_1.0_la-table.Tpo .deps/libgstruct_1.0_la-table.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c -o libgstruct_1.0_la-chrnum.lo `test -f 'chrnum.c' || echo './'`chrnum.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c chrnum.c -o libgstruct_1.0_la-chrnum.o
mv -f .deps/libgstruct_1.0_la-chrnum.Tpo .deps/libgstruct_1.0_la-chrnum.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c -o libgstruct_1.0_la-bamread.lo `test -f 'bamread.c' || echo './'`bamread.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c bamread.c -o libgstruct_1.0_la-bamread.o
mv -f .deps/libgstruct_1.0_la-bamread.Tpo .deps/libgstruct_1.0_la-bamread.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c -o libgstruct_1.0_la-samread.lo `test -f 'samread.c' || echo './'`samread.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c samread.c -o libgstruct_1.0_la-samread.o
mv -f .deps/libgstruct_1.0_la-samread.Tpo .deps/libgstruct_1.0_la-samread.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c -o libgstruct_1.0_la-parserange.lo `test -f 'parserange.c' || echo './'`parserange.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c parserange.c -o libgstruct_1.0_la-parserange.o
mv -f .deps/libgstruct_1.0_la-parserange.Tpo .deps/libgstruct_1.0_la-parserange.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c -o libgstruct_1.0_la-tableuint.lo `test -f 'tableuint.c' || echo './'`tableuint.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c tableuint.c -o libgstruct_1.0_la-tableuint.o
mv -f .deps/libgstruct_1.0_la-tableuint.Tpo .deps/libgstruct_1.0_la-tableuint.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c -o libgstruct_1.0_la-iit-write.lo `test -f 'iit-write.c' || echo './'`iit-write.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c iit-write.c -o libgstruct_1.0_la-iit-write.o
mv -f .deps/libgstruct_1.0_la-iit-write.Tpo .deps/libgstruct_1.0_la-iit-write.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-ucharlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-ucharlist.Tpo -c -o libgstruct_1.0_la-ucharlist.lo `test -f 'ucharlist.c' || echo './'`ucharlist.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-ucharlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-ucharlist.Tpo -c ucharlist.c -o libgstruct_1.0_la-ucharlist.o
mv -f .deps/libgstruct_1.0_la-ucharlist.Tpo .deps/libgstruct_1.0_la-ucharlist.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c -o libgstruct_1.0_la-bamtally.lo `test -f 'bamtally.c' || echo './'`bamtally.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c bamtally.c -o libgstruct_1.0_la-bamtally.o
mv -f .deps/libgstruct_1.0_la-bamtally.Tpo .deps/libgstruct_1.0_la-bamtally.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c -o libgstruct_1.0_la-datadir.lo `test -f 'datadir.c' || echo './'`datadir.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c datadir.c -o libgstruct_1.0_la-datadir.o
mv -f .deps/libgstruct_1.0_la-datadir.Tpo .deps/libgstruct_1.0_la-datadir.Plo
/bin/sh ../libtool --tag=CC --mode=link gcc -I/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-apple-darwin10.8.0\" -DGMAPDB=\"/private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/share\" -O3 -version-info 1:0:0 -o libgstruct-1.0.la -rpath /private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/../inst/usr/lib libgstruct_1.0_la-except.lo libgstruct_1.0_la-assert.lo libgstruct_1.0_la-mem.lo libgstruct_1.0_la-intlist.lo libgstruct_1.0_la-list.lo libgstruct_1.0_la-littleendian.lo libgstruct_1.0_la-bigendian.lo libgstruct_1.0_la-interval.lo libgstruct_1.0_la-uintlist.lo libgstruct_1.0_la-stopwatch.lo libgstruct_1.0_la-access.lo libgstruct_1.0_la-iit-read.lo libgstruct_1.0_la-chrom.lo libgstruct_1.0_la-genomicpos.lo libgstruct_1.0_la-md5.lo libgstruct_1.0_la-sequence.lo libgstruct_1.0_la-genome.lo libgstruct_1.0_la-uinttable.lo libgstruct_1.0_la-table.lo libgstruct_1.0_la-chrnum.lo libgstruct_1.0_la-bamread.lo libgstruct_1.0_la-samread.lo libgstruct_1.0_la-parserange.lo libgstruct_1.0_la-tableuint.lo libgstruct_1.0_la-iit-write.lo libgstruct_1.0_la-ucharlist.lo libgstruct_1.0_la-bamtally.lo libgstruct_1.0_la-datadir.lo -lz -lm
libtool: link: ar cru .libs/libgstruct-1.0.a libgstruct_1.0_la-except.o libgstruct_1.0_la-assert.o libgstruct_1.0_la-mem.o libgstruct_1.0_la-intlist.o libgstruct_1.0_la-list.o libgstruct_1.0_la-littleendian.o libgstruct_1.0_la-bigendian.o libgstruct_1.0_la-interval.o libgstruct_1.0_la-uintlist.o libgstruct_1.0_la-stopwatch.o libgstruct_1.0_la-access.o libgstruct_1.0_la-iit-read.o libgstruct_1.0_la-chrom.o libgstruct_1.0_la-genomicpos.o libgstruct_1.0_la-md5.o libgstruct_1.0_la-sequence.o libgstruct_1.0_la-genome.o libgstruct_1.0_la-uinttable.o libgstruct_1.0_la-table.o libgstruct_1.0_la-chrnum.o libgstruct_1.0_la-bamread.o libgstruct_1.0_la-samread.o libgstruct_1.0_la-parserange.o libgstruct_1.0_la-tableuint.o libgstruct_1.0_la-iit-write.o libgstruct_1.0_la-ucharlist.o libgstruct_1.0_la-bamtally.o libgstruct_1.0_la-datadir.o
libtool: link: ranlib .libs/libgstruct-1.0.a
libtool: link: ( cd ".libs" && rm -f "libgstruct-1.0.la" && ln -s "../libgstruct-1.0.la" "libgstruct-1.0.la" )
(CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/sh /private/tmp/RtmpJqt0er/Rbuild8d024a0b8982/gmapR/src/gstruct/config/missing autoheader)
aclocal.m4:21: warning: this file was generated for autoconf 2.69.
You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.
configure.ac:66: error: Autoconf version 2.65 or higher is required
aclocal.m4:529: AM_INIT_AUTOMAKE is expanded from...
configure.ac:66: the top level
autom4te: /usr/bin/gm4 failed with exit status: 63
autoheader: '/usr/bin/autom4te' failed with exit status: 63
WARNING: 'autoheader' is probably too old.
You should only need it if you modified 'acconfig.h' or
'configure.ac' or m4 files included by 'configure.ac'.
The 'autoheader' program is part of the GNU Autoconf package:
<http://www.gnu.org/software/autoconf/>
It also requires GNU m4 and Perl in order to run:
<http://www.gnu.org/software/m4/>
<http://www.perl.org/>
make[2]: *** [config.h.in] Error 63
make[1]: *** [install-recursive] Error 1
make: *** [gstruct] Error 2
ERROR: compilation failed for package 'gmapR'
* removing '/private/tmp/RtmpJqt0er/Rinst8d023b70dbc8/gmapR'
-----------------------------------
ERROR: package installation failed