gmapR

Package: gmapR
Maintainer: Michael Lawrence <lawrence.michael@gene.com>
License: Artistic-2.0
Title: An R interface to the GMAP/GSNAP/GSTRUCT suite
Type: Package
Author: Cory Barr, Thomas Wu, Michael Lawrence
Description: GSNAP and GMAP are a pair of tools to align short-read
data written by Tom Wu. This package provides convenience
methods to work with GMAP and GSNAP from within R. In addition,
it provides methods to tally alignment results on a
per-nucleotide basis using the bam_tally tool.
Version: 1.14.0
Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges
(>= 1.17.12), Rsamtools (>= 1.17.8)
Imports: S4Vectors (>= 0.9.25), IRanges, rtracklayer (>= 1.31.2),
GenomicFeatures (>= 1.17.13), Biostrings, VariantAnnotation (>=
1.11.4), tools, Biobase, BSgenome, GenomicAlignments (>=
1.1.9), BiocParallel
Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
LungCancerLines
Collate: GmapBamReader-class.R GmapGenomeDirectory-class.R
GmapGenome-class.R GmapSnpDirectory-class.R GmapSnps-class.R
GmapParam-class.R GsnapParam-class.R GsnapOutput-class.R
GmapOutput-class.R atoiindex-command.R BamTallyParam-class.R
bam_tally-command.R cmetindex-command.R get-genome-command.R
gmap-command.R gmap_build-command.R gsnap-command.R
iit-format.R iit_store-command.R info.R snpindex-command.R
system.R test_gmapR_package.R makeGmapGenomePackage.R
TP53Genome.R utils.R asSystemCall.R
biocViews: Alignment
NeedsCompilation: yes
Packaged: 2016-05-04 04:43:44 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'gmapR' ...
** libs
** arch - 
rm -rf samtools; mkdir samtools
ln -sf /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libbam.a samtools/libbam.a
for header in /home/ddbj/local/lib64/R/library/Rsamtools/include/samtools/*.h; do 
  ln -sf $header samtools/; 
done
cd gstruct/; 
        CFLAGS="-g -O3" 
./configure --enable-static --disable-shared 
            --prefix=/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr --includedir=/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/include/gstruct 
            --libdir=/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64 
            --with-samtools-lib=/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/samtools 
                    --disable-binaries  
                    --disable-maintainer-mode
checking package version... 2015-03-01
checking whether to enable maintainer-specific portions of Makefiles... no
loading default site script ./config.site
checking CFLAGS... -g -O3
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
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 whether gcc understands -c and -o together... yes
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... /bin/mkdir -p
checking for gawk... gawk
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... /tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/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 understands -c and -o together... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
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... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
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... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
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/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
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 X... libraries , headers 
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... 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 sam_sort... false
checking for uniqscan... false
checking for rint in -lm... yes
checking for pthreads feature... not specified so enabled by default
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... gcc
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 size of off_t... 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 MADV_SEQUENTIAL 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... no
checking for pagesize via sysconf... yes
checking for pagesize via sysctl... no
checking whether fopen accepts "b" mode... yes
checking whether fopen accepts "t" mode... yes
checking for builtin popcount/clz/ctz features... not specified so enabled by default
./configure: line 16421: ACX_BUILTIN_POPCOUNT: command not found
checking for bsr instruction in assembly... yes
checking whether sse2 is enabled... not specified so enabled by default
checking compiler is defective and requires an immediate in sse2 shift commands... no
checking whether ssse3 is enabled... not specified so enabled by default
checking whether sse4.1 is enabled... not specified so enabled by default
checking whether sse4.2 is enabled... not specified so enabled by default
checking whether avx is enabled... not specified so enabled by default
checking whether avx2 is enabled... not specified so enabled by default
checking whether simd is enabled... not specified so enabled by default
checking for x86 cpuid 0x00000001 output... 306d4:3100800:7ffafbbf:bfebfbff
checking whether mmx is enabled and supported by CPU... yes
checking whether sse is enabled and supported by CPU... yes
checking whether sse2 is enabled and supported by CPU... yes
checking whether sse3 is enabled and supported by CPU... yes
checking whether ssse3 is enabled and supported by CPU... yes
checking whether sse4.1 is enabled and supported by CPU... yes
checking whether sse4.2 is enabled and supported by CPU... yes
checking whether avx is enabled and supported by CPU... yes
checking for x86-AVX xgetbv 0x00000000 output... 7:0
checking whether avx is supported by operating system... yes
checking whether popcnt is enabled and supported by CPU... yes
checking for x86 cpuid 0x80000001 output... 0:0:121:2c100800
checking whether lzcnt is enabled and supported by CPU... yes
checking for x86 cpuid 0x00000007 output... 0:21c27ab:0:0
checking whether avx2 is enabled and supported by CPU... yes
checking whether bmi1 is enabled and supported by CPU... yes
checking whether bmi2 is enabled and supported by CPU... yes
checking whether C compiler accepts -mmmx... yes
checking for mmintrin.h header file... yes
checking whether C compiler accepts -msse... yes
checking for xmmintrin.h header file... yes
checking whether C compiler accepts -msse2... yes
checking for emmintrin.h header file... yes
checking whether C compiler accepts -msse3... yes
checking for pmmintrin.h header file... yes
checking whether C compiler accepts -mssse3... yes
checking for tmmintrin.h header file... yes
checking whether C compiler accepts -msse4.1... yes
checking for smmintrin.h header file... yes
checking whether C compiler accepts -msse4.2... yes
checking for nmmintrin.h header file... yes
checking whether C compiler accepts -mavx... yes
checking for immintrin.h header file... yes
checking whether C compiler accepts -mavx2... yes
checking for immintrin.h header file... yes
checking gmapdb... /tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/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... yes
checking for samtools program... checking for samtools library... provided by --with-samtools-lib
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
configure: WARNING:

WARNING: You don't seem to have gsnap specified.

checking Standard compiler and flags to be used... gcc -g -O3
checking Standard linker flags to be used... 
checking pthread compiler flags to be used... -pthread
checking popcnt compiler flags to be used... 
checking SIMD features available on computer...  mmx sse sse2 sse3 ssse3 sse4.1 sse4.2 avx avx2
checking SIMD compiler flags to be used...  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2
cd gstruct; 
make install
make[1]: Entering directory '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/gstruct'
Making install in src
make[2]: Entering directory '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/gstruct/src'
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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
littleendian.c: In function 'Littleendian_write_uint':
littleendian.c:17:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/libgstruct_1.0_la-littleendian.Tpo .deps/libgstruct_1.0_la-littleendian.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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
bigendian.c: In function 'Bigendian_write_uint':
bigendian.c:296:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function 'Bigendian_fileio_read_uint':
bigendian.c:457:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function 'Bigendian_fileio_read_uint8':
bigendian.c:758:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/libgstruct_1.0_la-bigendian.Tpo .deps/libgstruct_1.0_la-bigendian.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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:59:7: warning: implicit declaration of function 'stat64' [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:39:0:
access.c: In function 'Access_allocated':
littleendian.h:18:29: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(unsigned int),n,fp)
                             ^
access.c:125:3: note: in expansion of macro 'FREAD_UINTS'
   FREAD_UINTS(memory,(*len)/eltsize,fp);
   ^
mv -f .deps/libgstruct_1.0_la-access.Tpo .deps/libgstruct_1.0_la-access.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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
In file included from iit-read.c:12:0:
iit-read.c: In function 'IIT_read_divint':
littleendian.h:15:25: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2345:5: note: in expansion of macro 'FREAD_INT'
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function 'IIT_read':
littleendian.h:15:25: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2608:5: note: in expansion of macro 'FREAD_INT'
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function 'read_tree':
iit-read.c:1723:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1724:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1725:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1726:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1727:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function 'read_intervals':
iit-read.c:1808:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1809:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1811:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1815:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function 'read_words':
littleendian.h:20:27: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1899:5: note: in expansion of macro 'FREAD_UINT8'
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:16:26: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(unsigned int),1,fp)
                          ^
iit-read.c:1905:5: note: in expansion of macro 'FREAD_UINT'
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function 'read_annotations':
iit-read.c:2249:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2255:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2260:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(unsigned int));
     ^
iit-read.c:2271:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2277:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2282:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(unsigned int));
     ^
iit-read.c:2293:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function 'IIT_debug':
littleendian.h:15:25: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:3008:5: note: in expansion of macro 'FREAD_INT'
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function 'read_words_debug':
littleendian.h:20:27: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:2022:5: note: in expansion of macro 'FREAD_UINT8'
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:16:26: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(unsigned int),1,fp)
                          ^
iit-read.c:2027:5: note: in expansion of macro 'FREAD_UINT'
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/libgstruct_1.0_la-iit-read.Tpo .deps/libgstruct_1.0_la-iit-read.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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
genome.c: In function 'fill_buffer':
genome.c:1218:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function 'genomecomp_read_current':
genome.c:329:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
   read(this->fd,buffer,4);
   ^
genome.c: In function 'Genome_fill_buffer_simple':
genome.c:1374:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function 'Genome_fill_buffer_simple_alt':
genome.c:1451:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function 'Genome_get_char':
genome.c:1554:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,/*length*/1);
       ^
genome.c: In function 'Genome_ntcounts':
genome.c:1710:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer,length);
       ^
mv -f .deps/libgstruct_1.0_la-genome.Tpo .deps/libgstruct_1.0_la-genome.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c -o libgstruct_1.0_la-matchpool.lo `test -f 'matchpool.c' || echo './'`matchpool.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c matchpool.c -o libgstruct_1.0_la-matchpool.o
mv -f .deps/libgstruct_1.0_la-matchpool.Tpo .deps/libgstruct_1.0_la-matchpool.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c -o libgstruct_1.0_la-mismatchpool.lo `test -f 'mismatchpool.c' || echo './'`mismatchpool.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c mismatchpool.c -o libgstruct_1.0_la-mismatchpool.o
mv -f .deps/libgstruct_1.0_la-mismatchpool.Tpo .deps/libgstruct_1.0_la-mismatchpool.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c -o libgstruct_1.0_la-tally.lo `test -f 'tally.c' || echo './'`tally.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c tally.c -o libgstruct_1.0_la-tally.o
mv -f .deps/libgstruct_1.0_la-tally.Tpo .deps/libgstruct_1.0_la-tally.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c -o libgstruct_1.0_la-translation.lo `test -f 'translation.c' || echo './'`translation.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c translation.c -o libgstruct_1.0_la-translation.o
mv -f .deps/libgstruct_1.0_la-translation.Tpo .deps/libgstruct_1.0_la-translation.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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
bamtally.c: In function 'print_allele_counts_simple':
bamtally.c:997:16: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=]
     fprintf(fp," _%ld",this->delcounts_plus + this->delcounts_minus);
                ^
bamtally.c: In function 'print_zeroes':
bamtally.c:1252:9: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int' [-Wformat=]
  printf(">%ld %s:%u..%u\n",/*total*/0,printchr,blockstart,blockend-1U);
         ^
bamtally.c:1267:9: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int' [-Wformat=]
  printf(">%ld %s:%u..%u\n",/*total*/0,printchr,blockstart,blockend-1U);
         ^
bamtally.c: In function 'print_block':
bamtally.c:3594:14: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int' [-Wformat=]
       printf("(%ld@%d",this->matches_byshift_minus[shift],-shift);
              ^
bamtally.c:3597:14: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int' [-Wformat=]
       printf(",%ld@%d",this->matches_byshift_minus[shift],-shift);
              ^
bamtally.c:3605:14: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int' [-Wformat=]
       printf("(%ld@%d",this->matches_byshift_plus[shift],shift);
              ^
bamtally.c:3608:14: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int' [-Wformat=]
       printf(",%ld@%d",this->matches_byshift_plus[shift],shift);
              ^
bamtally.c:3637:14: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int' [-Wformat=]
       printf("(%ldNM%d",this->matches_bynm[nm],nm);
              ^
bamtally.c:3640:14: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int' [-Wformat=]
       printf(",%ldNM%d",this->matches_bynm[nm],nm);
              ^
bamtally.c:3682:14: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int' [-Wformat=]
       printf("(%ldXS",this->matches_byxs[xs]);
              ^
bamtally.c:3685:14: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'int' [-Wformat=]
       printf(",%ldXS",this->matches_byxs[xs]);
              ^
mv -f .deps/libgstruct_1.0_la-bamtally.Tpo .deps/libgstruct_1.0_la-bamtally.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -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/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET="x86_64-unknown-linux-gnu" -DGMAPDB="/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/share" -g -O3   -pthread -version-info 1:0:0  -o libgstruct-1.0.la -rpath /tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64 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-matchpool.lo libgstruct_1.0_la-mismatchpool.lo libgstruct_1.0_la-tally.lo libgstruct_1.0_la-translation.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-matchpool.o libgstruct_1.0_la-mismatchpool.o libgstruct_1.0_la-tally.o libgstruct_1.0_la-translation.o libgstruct_1.0_la-bamtally.o libgstruct_1.0_la-datadir.o
ar: `u' modifier ignored since `D' is the default (see `U')
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" )
make[3]: Entering directory '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/gstruct/src'
 /bin/mkdir -p '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libgstruct-1.0.la '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64'
libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.lai /tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64/libgstruct-1.0.la
libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.a /tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64/libgstruct-1.0.a
libtool: install: chmod 644 /tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64/libgstruct-1.0.a
libtool: install: ranlib /tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64/libgstruct-1.0.a
libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/sbin" ldconfig -n /tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64
----------------------------------------------------------------------
Libraries have been installed in:
   /tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /bin/mkdir -p '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/include/gstruct'
 /usr/bin/install -c -m 644 config.h fopen.h bool.h types.h except.h assert.h mem.h intlistdef.h intlist.h listdef.h list.h littleendian.h bigendian.h interval.h uintlist.h stopwatch.h access.h iitdef.h iit-read.h chrom.h genomicpos.h md5.h complement.h sequence.h genome.h uinttable.h table.h chrnum.h bamread.h samread.h parserange.h dynprog.h dynprog_nogap.h dynprog_simd.h dynprog_cigar.h dynprog_single.h tableuint.h iit-write.h ucharlist.h matchdef.h '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/include/gstruct'
 /usr/bin/install -c -m 644 matchpool.h mismatchdef.h mismatchpool.h tally.h translation.h bamtally.h datadir.h '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/include/gstruct'
 /bin/mkdir -p '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64/pkgconfig'
 /usr/bin/install -c -m 644 ../lib/gstruct-1.0.pc '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64/pkgconfig'
make[3]: Leaving directory '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/gstruct/src'
make[2]: Leaving directory '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/gstruct/src'
make[2]: Entering directory '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/gstruct'
make[3]: Entering directory '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/gstruct'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/gstruct'
make[2]: Leaving directory '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/gstruct'
make[1]: Leaving directory '/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/gstruct'
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/include -I/usr/local/include   -g -O3 -fpic  -g -O2  -c bamreader.c -o bamreader.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/include -I/usr/local/include   -g -O3 -fpic  -g -O2  -c bamtally.c -o bamtally.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/include -I/usr/local/include   -g -O3 -fpic  -g -O2  -c iit.c -o iit.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/include -I/usr/local/include   -g -O3 -fpic  -g -O2  -c variantsummary.c -o variantsummary.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/include -I/usr/local/include   -g -O3 -fpic  -g -O2  -c genome.c -o genome.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/include -I/usr/local/include   -g -O3 -fpic  -g -O2  -c R_init_gmapR.c -o R_init_gmapR.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o gmapR.so bamreader.o bamtally.o iit.o variantsummary.o genome.o R_init_gmapR.o /tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64/libgstruct-1.0.a samtools/libbam.a -lz  -L/home/ddbj/local/lib64/R/lib -lR
cd gmap/; 
 ./configure --with-gmapdb= --prefix=/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr 
            --libdir=/tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/lib64 --disable-maintainer-mode
checking package version... 2013-11-01
checking whether to enable maintainer-specific portions of Makefiles... no
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-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
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 whether gcc understands -c and -o together... yes
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... /bin/mkdir -p
checking for gawk... gawk
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... /tmp/RtmpENK2L7/R.INSTALL5d7b31371efc/gmapR/src/../inst/usr/bin
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 understands -c and -o together... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
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... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
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... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
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/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
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... yes
checking whether to build static libraries... yes
checking for rint in -lm... yes
checking for pthreads feature... not specifi