Package: gmapR

Version: 1.1.11

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings gmapR_1.1.11.tar.gz

StartedAt: 2013-03-25 02:02:29 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:15:40 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 792.0 seconds

RetCode: 0

Status:  OK

CheckDir: gmapR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gmapR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gmapR’ version ‘1.1.11’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gmapR’ can be installed ... [219s/241s] OK
* checking installed package size ... NOTE
  installed size is 38.7Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    usr      31.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/gmapR/libs/gmapR.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [20s/22s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘gmapR_unit_tests.R’ [171s/212s]
 [172s/212s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00check.log’
for details.

* installing *source* package ‘gmapR’ ...
** libs
** arch - 
rm -rf samtools; mkdir samtools
ln -sf /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbam.a samtools/libbam.a
for header in /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include/samtools/*.h; do \
	  ln -sf $header samtools/; \
	done
cd gstruct/; \
	./configure --enable-static --disable-shared \
	            --prefix=/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr --includedir=/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct \
	            --libdir=/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib \
	            --with-samtools=/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools \
		    --disable-binaries #\
## does not appear to be a true dependency yet
checking package version... 2012-08-20
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 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 dependency style of gcc... gcc3
checking bindir... /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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 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... 3458764513820540925
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
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 ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
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 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... 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 gmapdb... /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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
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
make[1]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gstruct'
Making install in src
make[2]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gstruct/src'
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gstruct'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gstruct'
/bin/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
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.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
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.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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_allocated’:
access.c:125:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
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.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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 ‘IIT_debug’:
iit-read.c:3000:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_tree’:
iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1716:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1717:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1718:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1719:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_intervals’:
iit-read.c:1800:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1801:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1803:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1807:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words_debug’:
iit-read.c:2014:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2019:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_annotations’:
iit-read.c:2241:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2247:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2252:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2263:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2269:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2274:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2285:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read’:
iit-read.c:2600:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words’:
iit-read.c:1891:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1897:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read_divint’:
iit-read.c:2337:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
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.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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
genome.c: In function ‘Genome_ntcounts’:
genome.c:1710:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘genomecomp_read_current’:
genome.c:329:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘fill_buffer’:
genome.c:1218:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_get_char’:
genome.c:1554:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:1451:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:1374:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
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.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.      -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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/bash ../libtool --tag=CC   --mode=link gcc   -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3    -version-info 1:0:0  -o libgstruct-1.0.la -rpath /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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" )
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gstruct/src'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gstruct'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gstruct'
test -z "/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib" || /bin/mkdir -p "/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib"
 /bin/bash ../libtool   --mode=install /usr/bin/install -c  'libgstruct-1.0.la' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/libgstruct-1.0.la'
libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.lai /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/libgstruct-1.0.la
libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.a /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
libtool: install: chmod 644 /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
libtool: install: ranlib /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
libtool: finish: PATH="/opt/moab/bin:/app/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/variant_effect_predictor:/usr/local/root/bin:/sbin" ldconfig -n /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib

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.
----------------------------------------------------------------------
test -z "/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin" || /bin/mkdir -p "/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin"
test -z "/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct" || /bin/mkdir -p "/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct"
 /usr/bin/install -c -m 644 'config.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/config.h'
 /usr/bin/install -c -m 644 'fopen.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/fopen.h'
 /usr/bin/install -c -m 644 'bool.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/bool.h'
 /usr/bin/install -c -m 644 'types.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/types.h'
 /usr/bin/install -c -m 644 'except.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/except.h'
 /usr/bin/install -c -m 644 'assert.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/assert.h'
 /usr/bin/install -c -m 644 'mem.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/mem.h'
 /usr/bin/install -c -m 644 'intlistdef.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/intlistdef.h'
 /usr/bin/install -c -m 644 'intlist.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/intlist.h'
 /usr/bin/install -c -m 644 'listdef.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/listdef.h'
 /usr/bin/install -c -m 644 'list.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/list.h'
 /usr/bin/install -c -m 644 'littleendian.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/littleendian.h'
 /usr/bin/install -c -m 644 'bigendian.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/bigendian.h'
 /usr/bin/install -c -m 644 'interval.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/interval.h'
 /usr/bin/install -c -m 644 'uintlist.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/uintlist.h'
 /usr/bin/install -c -m 644 'stopwatch.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/stopwatch.h'
 /usr/bin/install -c -m 644 'access.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/access.h'
 /usr/bin/install -c -m 644 'iitdef.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/iitdef.h'
 /usr/bin/install -c -m 644 'iit-read.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/iit-read.h'
 /usr/bin/install -c -m 644 'chrom.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/chrom.h'
 /usr/bin/install -c -m 644 'genomicpos.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/genomicpos.h'
 /usr/bin/install -c -m 644 'md5.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/md5.h'
 /usr/bin/install -c -m 644 'complement.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/complement.h'
 /usr/bin/install -c -m 644 'sequence.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/sequence.h'
 /usr/bin/install -c -m 644 'genome.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/genome.h'
 /usr/bin/install -c -m 644 'uinttable.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/uinttable.h'
 /usr/bin/install -c -m 644 'table.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/table.h'
 /usr/bin/install -c -m 644 'chrnum.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/chrnum.h'
 /usr/bin/install -c -m 644 'bamread.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/bamread.h'
 /usr/bin/install -c -m 644 'samread.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/samread.h'
 /usr/bin/install -c -m 644 'parserange.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/parserange.h'
 /usr/bin/install -c -m 644 'tableuint.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/tableuint.h'
 /usr/bin/install -c -m 644 'iit-write.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/iit-write.h'
 /usr/bin/install -c -m 644 'ucharlist.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/ucharlist.h'
 /usr/bin/install -c -m 644 'bamtally.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/bamtally.h'
 /usr/bin/install -c -m 644 'datadir.h' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/datadir.h'
test -z "/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/pkgconfig" || /bin/mkdir -p "/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/pkgconfig"
 /usr/bin/install -c -m 644 '../lib/gstruct-1.0.pc' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/pkgconfig/gstruct-1.0.pc'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gstruct/src'
make[2]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gstruct/src'
make[2]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gstruct'
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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 `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gstruct'
make[2]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gstruct'
make[1]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gstruct'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include -I/usr/local/include   -g -fpic  -g -O2  -Wall -c bamreader.c -o bamreader.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include -I/usr/local/include   -g -fpic  -g -O2  -Wall -c bamtally.c -o bamtally.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include -I/usr/local/include   -g -fpic  -g -O2  -Wall -c iit.c -o iit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include -I/usr/local/include   -g -fpic  -g -O2  -Wall -c variantsummary.c -o variantsummary.o
In file included from variantsummary.c:5:0:
bytestream.h: In function ‘read_string’:
bytestream.h:20:24: warning: pointer targets in initialization differ in signedness [-Wpointer-sign]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include -I/usr/local/include   -g -fpic  -g -O2  -Wall -c R_init_gmapR.c -o R_init_gmapR.o
gcc -std=gnu99 -shared -L/usr/local/lib -o gmapR.so bamreader.o bamtally.o iit.o variantsummary.o R_init_gmapR.o /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/libgstruct-1.0.a samtools/libbam.a -lz  -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
cd gmap/; \
	./configure --with-gmapdb= --prefix=/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr \
	            --libdir=/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib
checking package version... 2011-12-28
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 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 dependency style of gcc... gcc3
loading script ./config.site
checking bindir... /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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 and cc understand -c and -o together... yes
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... 3458764513820540925
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
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 ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
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 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 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... 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... yes
checking for __builtin_clz... yes
checking for __builtin_ctz... yes
checking for bsr instruction in assembly... yes
checking for popcnt feature... not specified so enabled by default
checking whether -mpopcnt compiler flag works... no
checking gmapdb... /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share
checking MAX_READLENGTH... 200
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... disabled
checking for goby library... disabled
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating util/Makefile
config.status: creating util/gmap_compress.pl
config.status: creating util/gmap_uncompress.pl
config.status: creating util/gmap_process.pl
config.status: creating util/gmap_setup.pl
config.status: creating util/gmap_build.pl
config.status: creating util/gmap_reassemble.pl
config.status: creating util/md_coords.pl
config.status: creating util/fa_coords.pl
config.status: creating util/psl_splicesites.pl
config.status: creating util/psl_introns.pl
config.status: creating util/psl_genes.pl
config.status: creating util/gtf_splicesites.pl
config.status: creating util/gtf_introns.pl
config.status: creating util/gtf_genes.pl
config.status: creating util/gff3_splicesites.pl
config.status: creating util/gff3_introns.pl
config.status: creating util/gff3_genes.pl
config.status: creating util/dbsnp_iit.pl
config.status: creating tests/Makefile
config.status: creating tests/align.test
config.status: creating tests/coords1.test
config.status: creating tests/setup1.test
config.status: creating tests/iit.test
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
cd gmap; \
	make install
make[1]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
Making install in src
make[2]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/src'
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-except.o -MD -MP -MF .deps/gmap-except.Tpo -c -o gmap-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gmap-except.Tpo .deps/gmap-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-assert.o -MD -MP -MF .deps/gmap-assert.Tpo -c -o gmap-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gmap-assert.Tpo .deps/gmap-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-mem.o -MD -MP -MF .deps/gmap-mem.Tpo -c -o gmap-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gmap-mem.Tpo .deps/gmap-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intlist.o -MD -MP -MF .deps/gmap-intlist.Tpo -c -o gmap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gmap-intlist.Tpo .deps/gmap-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-list.o -MD -MP -MF .deps/gmap-list.Tpo -c -o gmap-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gmap-list.Tpo .deps/gmap-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-littleendian.o -MD -MP -MF .deps/gmap-littleendian.Tpo -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gmap-littleendian.Tpo .deps/gmap-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bigendian.o -MD -MP -MF .deps/gmap-bigendian.Tpo -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gmap-bigendian.Tpo .deps/gmap-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-interval.o -MD -MP -MF .deps/gmap-interval.Tpo -c -o gmap-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gmap-interval.Tpo .deps/gmap-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uintlist.o -MD -MP -MF .deps/gmap-uintlist.Tpo -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gmap-uintlist.Tpo .deps/gmap-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stopwatch.o -MD -MP -MF .deps/gmap-stopwatch.Tpo -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gmap-stopwatch.Tpo .deps/gmap-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-access.o -MD -MP -MF .deps/gmap-access.Tpo -c -o gmap-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_allocated’:
access.c:167:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:178:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:183:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gmap-access.Tpo .deps/gmap-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-iit-read.o -MD -MP -MF .deps/gmap-iit-read.Tpo -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
iit-read.c: In function ‘IIT_debug’:
iit-read.c:2954:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_tree’:
iit-read.c:1673:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1674:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1675:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1676:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1677:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_intervals’:
iit-read.c:1758:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1759:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1761:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1765:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words_debug’:
iit-read.c:1973:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1978:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_annotations’:
iit-read.c:2201:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2207:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2212:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2223:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2229:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2234:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2245:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read’:
iit-read.c:2557:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words’:
iit-read.c:1849:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1855:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read_divint’:
iit-read.c:2296:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gmap-iit-read.Tpo .deps/gmap-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-md5.o -MD -MP -MF .deps/gmap-md5.Tpo -c -o gmap-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gmap-md5.Tpo .deps/gmap-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-sequence.o -MD -MP -MF .deps/gmap-sequence.Tpo -c -o gmap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gmap-sequence.Tpo .deps/gmap-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-reader.o -MD -MP -MF .deps/gmap-reader.Tpo -c -o gmap-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/gmap-reader.Tpo .deps/gmap-reader.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genomicpos.o -MD -MP -MF .deps/gmap-genomicpos.Tpo -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gmap-genomicpos.Tpo .deps/gmap-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-compress.o -MD -MP -MF .deps/gmap-compress.Tpo -c -o gmap-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gmap-compress.Tpo .deps/gmap-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gbuffer.o -MD -MP -MF .deps/gmap-gbuffer.Tpo -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
mv -f .deps/gmap-gbuffer.Tpo .deps/gmap-gbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome.o -MD -MP -MF .deps/gmap-genome.Tpo -c -o gmap-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_ntcounts’:
genome.c:1727:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘genomecomp_read_current’:
genome.c:335:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘fill_buffer’:
genome.c:1224:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_get_char’:
genome.c:1571:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:1468:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:1380:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gmap-genome.Tpo .deps/gmap-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome_hr.o -MD -MP -MF .deps/gmap-genome_hr.Tpo -c -o gmap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/gmap-genome_hr.Tpo .deps/gmap-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb.o -MD -MP -MF .deps/gmap-indexdb.Tpo -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1124:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gmap-indexdb.Tpo .deps/gmap-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb_hr.o -MD -MP -MF .deps/gmap-indexdb_hr.Tpo -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
indexdb_hr.c: In function ‘positions_read_multiple’:
indexdb_hr.c:592:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gmap-indexdb_hr.Tpo .deps/gmap-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligo.o -MD -MP -MF .deps/gmap-oligo.Tpo -c -o gmap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/gmap-oligo.Tpo .deps/gmap-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-block.o -MD -MP -MF .deps/gmap-block.Tpo -c -o gmap-block.o `test -f 'block.c' || echo './'`block.c
mv -f .deps/gmap-block.Tpo .deps/gmap-block.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrom.o -MD -MP -MF .deps/gmap-chrom.Tpo -c -o gmap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gmap-chrom.Tpo .deps/gmap-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-segmentpos.o -MD -MP -MF .deps/gmap-segmentpos.Tpo -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
mv -f .deps/gmap-segmentpos.Tpo .deps/gmap-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrnum.o -MD -MP -MF .deps/gmap-chrnum.Tpo -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/gmap-chrnum.Tpo .deps/gmap-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrsubset.o -MD -MP -MF .deps/gmap-chrsubset.Tpo -c -o gmap-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c
mv -f .deps/gmap-chrsubset.Tpo .deps/gmap-chrsubset.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uinttable.o -MD -MP -MF .deps/gmap-uinttable.Tpo -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c
mv -f .deps/gmap-uinttable.Tpo .deps/gmap-uinttable.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gregion.o -MD -MP -MF .deps/gmap-gregion.Tpo -c -o gmap-gregion.o `test -f 'gregion.c' || echo './'`gregion.c
mv -f .deps/gmap-gregion.Tpo .deps/gmap-gregion.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-match.o -MD -MP -MF .deps/gmap-match.Tpo -c -o gmap-match.o `test -f 'match.c' || echo './'`match.c
mv -f .deps/gmap-match.Tpo .deps/gmap-match.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-matchpool.o -MD -MP -MF .deps/gmap-matchpool.Tpo -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c
mv -f .deps/gmap-matchpool.Tpo .deps/gmap-matchpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagnostic.o -MD -MP -MF .deps/gmap-diagnostic.Tpo -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c
mv -f .deps/gmap-diagnostic.Tpo .deps/gmap-diagnostic.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage1.o -MD -MP -MF .deps/gmap-stage1.Tpo -c -o gmap-stage1.o `test -f 'stage1.c' || echo './'`stage1.c
mv -f .deps/gmap-stage1.Tpo .deps/gmap-stage1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diag.o -MD -MP -MF .deps/gmap-diag.Tpo -c -o gmap-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/gmap-diag.Tpo .deps/gmap-diag.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagpool.o -MD -MP -MF .deps/gmap-diagpool.Tpo -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/gmap-diagpool.Tpo .deps/gmap-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-orderstat.o -MD -MP -MF .deps/gmap-orderstat.Tpo -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/gmap-orderstat.Tpo .deps/gmap-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligoindex.o -MD -MP -MF .deps/gmap-oligoindex.Tpo -c -o gmap-oligoindex.o `test -f 'oligoindex.c' || echo './'`oligoindex.c
mv -f .deps/gmap-oligoindex.Tpo .deps/gmap-oligoindex.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligoindex_hr.o -MD -MP -MF .deps/gmap-oligoindex_hr.Tpo -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/gmap-oligoindex_hr.Tpo .deps/gmap-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intron.o -MD -MP -MF .deps/gmap-intron.Tpo -c -o gmap-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/gmap-intron.Tpo .deps/gmap-intron.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent.o -MD -MP -MF .deps/gmap-maxent.Tpo -c -o gmap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/gmap-maxent.Tpo .deps/gmap-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent_hr.o -MD -MP -MF .deps/gmap-maxent_hr.Tpo -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/gmap-maxent_hr.Tpo .deps/gmap-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pair.o -MD -MP -MF .deps/gmap-pair.Tpo -c -o gmap-pair.o `test -f 'pair.c' || echo './'`pair.c
mv -f .deps/gmap-pair.Tpo .deps/gmap-pair.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pairpool.o -MD -MP -MF .deps/gmap-pairpool.Tpo -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/gmap-pairpool.Tpo .deps/gmap-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage2.o -MD -MP -MF .deps/gmap-stage2.Tpo -c -o gmap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
mv -f .deps/gmap-stage2.Tpo .deps/gmap-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-smooth.o -MD -MP -MF .deps/gmap-smooth.Tpo -c -o gmap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/gmap-smooth.Tpo .deps/gmap-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie_build.o -MD -MP -MF .deps/gmap-splicetrie_build.Tpo -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
mv -f .deps/gmap-splicetrie_build.Tpo .deps/gmap-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie.o -MD -MP -MF .deps/gmap-splicetrie.Tpo -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/gmap-splicetrie.Tpo .deps/gmap-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-boyer-moore.o -MD -MP -MF .deps/gmap-boyer-moore.Tpo -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/gmap-boyer-moore.Tpo .deps/gmap-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-dynprog.o -MD -MP -MF .deps/gmap-dynprog.Tpo -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/gmap-dynprog.Tpo .deps/gmap-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-translation.o -MD -MP -MF .deps/gmap-translation.Tpo -c -o gmap-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/gmap-translation.Tpo .deps/gmap-translation.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pbinom.o -MD -MP -MF .deps/gmap-pbinom.Tpo -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/gmap-pbinom.Tpo .deps/gmap-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-changepoint.o -MD -MP -MF .deps/gmap-changepoint.Tpo -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/gmap-changepoint.Tpo .deps/gmap-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage3.o -MD -MP -MF .deps/gmap-stage3.Tpo -c -o gmap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/gmap-stage3.Tpo .deps/gmap-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-request.o -MD -MP -MF .deps/gmap-request.Tpo -c -o gmap-request.o `test -f 'request.c' || echo './'`request.c
mv -f .deps/gmap-request.Tpo .deps/gmap-request.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-result.o -MD -MP -MF .deps/gmap-result.Tpo -c -o gmap-result.o `test -f 'result.c' || echo './'`result.c
mv -f .deps/gmap-result.Tpo .deps/gmap-result.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-inbuffer.o -MD -MP -MF .deps/gmap-inbuffer.Tpo -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
mv -f .deps/gmap-inbuffer.Tpo .deps/gmap-inbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-outbuffer.o -MD -MP -MF .deps/gmap-outbuffer.Tpo -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
mv -f .deps/gmap-outbuffer.Tpo .deps/gmap-outbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chimera.o -MD -MP -MF .deps/gmap-chimera.Tpo -c -o gmap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/gmap-chimera.Tpo .deps/gmap-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-datadir.o -MD -MP -MF .deps/gmap-datadir.Tpo -c -o gmap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/gmap-datadir.Tpo .deps/gmap-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-getopt.o -MD -MP -MF .deps/gmap-getopt.Tpo -c -o gmap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/gmap-getopt.Tpo .deps/gmap-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-getopt1.o -MD -MP -MF .deps/gmap-getopt1.Tpo -c -o gmap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/gmap-getopt1.Tpo .deps/gmap-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gmap.o -MD -MP -MF .deps/gmap-gmap.Tpo -c -o gmap-gmap.o `test -f 'gmap.c' || echo './'`gmap.c
mv -f .deps/gmap-gmap.Tpo .deps/gmap-gmap.Po
/bin/bash ../libtool --tag=CC   --mode=link gcc  -pthread  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3   -pthread  -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read.o gmap-md5.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-orderstat.o gmap-oligoindex.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-stage2.o gmap-smooth.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o  -lz -lm 
libtool: link: gcc -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -pthread -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read.o gmap-md5.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-orderstat.o gmap-oligoindex.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-stage2.o gmap-smooth.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o  -lz -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-except.o -MD -MP -MF .deps/get_genome-except.Tpo -c -o get_genome-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/get_genome-except.Tpo .deps/get_genome-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-assert.o -MD -MP -MF .deps/get_genome-assert.Tpo -c -o get_genome-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/get_genome-assert.Tpo .deps/get_genome-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-mem.o -MD -MP -MF .deps/get_genome-mem.Tpo -c -o get_genome-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/get_genome-mem.Tpo .deps/get_genome-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-intlist.o -MD -MP -MF .deps/get_genome-intlist.Tpo -c -o get_genome-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/get_genome-intlist.Tpo .deps/get_genome-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-list.o -MD -MP -MF .deps/get_genome-list.Tpo -c -o get_genome-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/get_genome-list.Tpo .deps/get_genome-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-littleendian.o -MD -MP -MF .deps/get_genome-littleendian.Tpo -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/get_genome-littleendian.Tpo .deps/get_genome-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-bigendian.o -MD -MP -MF .deps/get_genome-bigendian.Tpo -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/get_genome-bigendian.Tpo .deps/get_genome-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-interval.o -MD -MP -MF .deps/get_genome-interval.Tpo -c -o get_genome-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/get_genome-interval.Tpo .deps/get_genome-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-uintlist.o -MD -MP -MF .deps/get_genome-uintlist.Tpo -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/get_genome-uintlist.Tpo .deps/get_genome-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-stopwatch.o -MD -MP -MF .deps/get_genome-stopwatch.Tpo -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/get_genome-stopwatch.Tpo .deps/get_genome-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-access.o -MD -MP -MF .deps/get_genome-access.Tpo -c -o get_genome-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_allocated’:
access.c:167:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:178:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:183:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/get_genome-access.Tpo .deps/get_genome-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-iit-read.o -MD -MP -MF .deps/get_genome-iit-read.Tpo -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
iit-read.c: In function ‘IIT_debug’:
iit-read.c:2954:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_tree’:
iit-read.c:1673:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1674:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1675:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1676:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1677:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_intervals’:
iit-read.c:1758:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1759:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1761:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1765:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words_debug’:
iit-read.c:1973:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1978:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_annotations’:
iit-read.c:2201:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2207:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2212:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2223:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2229:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2234:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2245:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read’:
iit-read.c:2557:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words’:
iit-read.c:1849:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1855:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read_divint’:
iit-read.c:2296:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/get_genome-iit-read.Tpo .deps/get_genome-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-md5.o -MD -MP -MF .deps/get_genome-md5.Tpo -c -o get_genome-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/get_genome-md5.Tpo .deps/get_genome-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-sequence.o -MD -MP -MF .deps/get_genome-sequence.Tpo -c -o get_genome-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/get_genome-sequence.Tpo .deps/get_genome-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-genome.o -MD -MP -MF .deps/get_genome-genome.Tpo -c -o get_genome-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_ntcounts’:
genome.c:1727:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘genomecomp_read_current’:
genome.c:335:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘fill_buffer’:
genome.c:1224:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_get_char’:
genome.c:1571:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:1468:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:1380:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/get_genome-genome.Tpo .deps/get_genome-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-genomicpos.o -MD -MP -MF .deps/get_genome-genomicpos.Tpo -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/get_genome-genomicpos.Tpo .deps/get_genome-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-chrom.o -MD -MP -MF .deps/get_genome-chrom.Tpo -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/get_genome-chrom.Tpo .deps/get_genome-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-chrnum.o -MD -MP -MF .deps/get_genome-chrnum.Tpo -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/get_genome-chrnum.Tpo .deps/get_genome-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-chrsubset.o -MD -MP -MF .deps/get_genome-chrsubset.Tpo -c -o get_genome-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c
mv -f .deps/get_genome-chrsubset.Tpo .deps/get_genome-chrsubset.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-datadir.o -MD -MP -MF .deps/get_genome-datadir.Tpo -c -o get_genome-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/get_genome-datadir.Tpo .deps/get_genome-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-parserange.o -MD -MP -MF .deps/get_genome-parserange.Tpo -c -o get_genome-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
mv -f .deps/get_genome-parserange.Tpo .deps/get_genome-parserange.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-getopt.o -MD -MP -MF .deps/get_genome-getopt.Tpo -c -o get_genome-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/get_genome-getopt.Tpo .deps/get_genome-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-getopt1.o -MD -MP -MF .deps/get_genome-getopt1.Tpo -c -o get_genome-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/get_genome-getopt1.Tpo .deps/get_genome-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT get_genome-get-genome.o -MD -MP -MF .deps/get_genome-get-genome.Tpo -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo './'`get-genome.c
mv -f .deps/get_genome-get-genome.Tpo .deps/get_genome-get-genome.Po
/bin/bash ../libtool --tag=CC   --mode=link gcc  -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3   -pthread  -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read.o get_genome-md5.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o  -lz -lm 
libtool: link: gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -pthread -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read.o get_genome-md5.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o  -lz -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-except.o -MD -MP -MF .deps/gmapindex-except.Tpo -c -o gmapindex-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gmapindex-except.Tpo .deps/gmapindex-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-assert.o -MD -MP -MF .deps/gmapindex-assert.Tpo -c -o gmapindex-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gmapindex-assert.Tpo .deps/gmapindex-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-mem.o -MD -MP -MF .deps/gmapindex-mem.Tpo -c -o gmapindex-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gmapindex-mem.Tpo .deps/gmapindex-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-intlist.o -MD -MP -MF .deps/gmapindex-intlist.Tpo -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gmapindex-intlist.Tpo .deps/gmapindex-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-list.o -MD -MP -MF .deps/gmapindex-list.Tpo -c -o gmapindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gmapindex-list.Tpo .deps/gmapindex-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-littleendian.o -MD -MP -MF .deps/gmapindex-littleendian.Tpo -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gmapindex-littleendian.Tpo .deps/gmapindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-bigendian.o -MD -MP -MF .deps/gmapindex-bigendian.Tpo -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gmapindex-bigendian.Tpo .deps/gmapindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-interval.o -MD -MP -MF .deps/gmapindex-interval.Tpo -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gmapindex-interval.Tpo .deps/gmapindex-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-uintlist.o -MD -MP -MF .deps/gmapindex-uintlist.Tpo -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gmapindex-uintlist.Tpo .deps/gmapindex-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-stopwatch.o -MD -MP -MF .deps/gmapindex-stopwatch.Tpo -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gmapindex-stopwatch.Tpo .deps/gmapindex-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-access.o -MD -MP -MF .deps/gmapindex-access.Tpo -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_allocated’:
access.c:167:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:178:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:183:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gmapindex-access.Tpo .deps/gmapindex-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-iit-read.o -MD -MP -MF .deps/gmapindex-iit-read.Tpo -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
iit-read.c: In function ‘IIT_debug’:
iit-read.c:2954:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_tree’:
iit-read.c:1673:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1674:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1675:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1676:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1677:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_intervals’:
iit-read.c:1758:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1759:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1761:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1765:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words_debug’:
iit-read.c:1973:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1978:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_annotations’:
iit-read.c:2201:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2207:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2212:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2223:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2229:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2234:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2245:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read’:
iit-read.c:2557:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words’:
iit-read.c:1849:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1855:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read_divint’:
iit-read.c:2296:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gmapindex-iit-read.Tpo .deps/gmapindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-iit-write.o -MD -MP -MF .deps/gmapindex-iit-write.Tpo -c -o gmapindex-iit-write.o `test -f 'iit-write.c' || echo './'`iit-write.c
mv -f .deps/gmapindex-iit-write.Tpo .deps/gmapindex-iit-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-genomicpos.o -MD -MP -MF .deps/gmapindex-genomicpos.Tpo -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gmapindex-genomicpos.Tpo .deps/gmapindex-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-compress.o -MD -MP -MF .deps/gmapindex-compress.Tpo -c -o gmapindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gmapindex-compress.Tpo .deps/gmapindex-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-genome-write.o -MD -MP -MF .deps/gmapindex-genome-write.Tpo -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
mv -f .deps/gmapindex-genome-write.Tpo .deps/gmapindex-genome-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-genome_hr.o -MD -MP -MF .deps/gmapindex-genome_hr.Tpo -c -o gmapindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/gmapindex-genome_hr.Tpo .deps/gmapindex-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-indexdb.o -MD -MP -MF .deps/gmapindex-indexdb.Tpo -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1124:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gmapindex-indexdb.Tpo .deps/gmapindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-table.o -MD -MP -MF .deps/gmapindex-table.Tpo -c -o gmapindex-table.o `test -f 'table.c' || echo './'`table.c
mv -f .deps/gmapindex-table.Tpo .deps/gmapindex-table.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-tableint.o -MD -MP -MF .deps/gmapindex-tableint.Tpo -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo './'`tableint.c
mv -f .deps/gmapindex-tableint.Tpo .deps/gmapindex-tableint.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-chrom.o -MD -MP -MF .deps/gmapindex-chrom.Tpo -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gmapindex-chrom.Tpo .deps/gmapindex-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-segmentpos.o -MD -MP -MF .deps/gmapindex-segmentpos.Tpo -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
mv -f .deps/gmapindex-segmentpos.Tpo .deps/gmapindex-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT gmapindex-gmapindex.o -MD -MP -MF .deps/gmapindex-gmapindex.Tpo -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo './'`gmapindex.c
mv -f .deps/gmapindex-gmapindex.Tpo .deps/gmapindex-gmapindex.Po
/bin/bash ../libtool --tag=CC   --mode=link gcc  -pthread -O3   -pthread  -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read.o gmapindex-iit-write.o gmapindex-genomicpos.o gmapindex-compress.o gmapindex-genome-write.o gmapindex-genome_hr.o gmapindex-indexdb.o gmapindex-table.o gmapindex-tableint.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-gmapindex.o  -lm 
libtool: link: gcc -pthread -O3 -pthread -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read.o gmapindex-iit-write.o gmapindex-genomicpos.o gmapindex-compress.o gmapindex-genome-write.o gmapindex-genome_hr.o gmapindex-indexdb.o gmapindex-table.o gmapindex-tableint.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-gmapindex.o  -lm -pthread
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-except.o -MD -MP -MF .deps/iit_store-except.Tpo -c -o iit_store-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/iit_store-except.Tpo .deps/iit_store-except.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-assert.o -MD -MP -MF .deps/iit_store-assert.Tpo -c -o iit_store-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/iit_store-assert.Tpo .deps/iit_store-assert.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-mem.o -MD -MP -MF .deps/iit_store-mem.Tpo -c -o iit_store-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/iit_store-mem.Tpo .deps/iit_store-mem.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-intlist.o -MD -MP -MF .deps/iit_store-intlist.Tpo -c -o iit_store-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/iit_store-intlist.Tpo .deps/iit_store-intlist.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-list.o -MD -MP -MF .deps/iit_store-list.Tpo -c -o iit_store-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/iit_store-list.Tpo .deps/iit_store-list.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-littleendian.o -MD -MP -MF .deps/iit_store-littleendian.Tpo -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/iit_store-littleendian.Tpo .deps/iit_store-littleendian.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-bigendian.o -MD -MP -MF .deps/iit_store-bigendian.Tpo -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/iit_store-bigendian.Tpo .deps/iit_store-bigendian.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-interval.o -MD -MP -MF .deps/iit_store-interval.Tpo -c -o iit_store-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/iit_store-interval.Tpo .deps/iit_store-interval.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-uintlist.o -MD -MP -MF .deps/iit_store-uintlist.Tpo -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/iit_store-uintlist.Tpo .deps/iit_store-uintlist.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-stopwatch.o -MD -MP -MF .deps/iit_store-stopwatch.Tpo -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/iit_store-stopwatch.Tpo .deps/iit_store-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-access.o -MD -MP -MF .deps/iit_store-access.Tpo -c -o iit_store-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_allocated’:
access.c:167:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:178:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:183:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/iit_store-access.Tpo .deps/iit_store-access.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-iit-write.o -MD -MP -MF .deps/iit_store-iit-write.Tpo -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo './'`iit-write.c
mv -f .deps/iit_store-iit-write.Tpo .deps/iit_store-iit-write.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-tableint.o -MD -MP -MF .deps/iit_store-tableint.Tpo -c -o iit_store-tableint.o `test -f 'tableint.c' || echo './'`tableint.c
mv -f .deps/iit_store-tableint.Tpo .deps/iit_store-tableint.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-table.o -MD -MP -MF .deps/iit_store-table.Tpo -c -o iit_store-table.o `test -f 'table.c' || echo './'`table.c
mv -f .deps/iit_store-table.Tpo .deps/iit_store-table.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-chrom.o -MD -MP -MF .deps/iit_store-chrom.Tpo -c -o iit_store-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/iit_store-chrom.Tpo .deps/iit_store-chrom.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-getopt.o -MD -MP -MF .deps/iit_store-getopt.Tpo -c -o iit_store-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/iit_store-getopt.Tpo .deps/iit_store-getopt.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-getopt1.o -MD -MP -MF .deps/iit_store-getopt1.Tpo -c -o iit_store-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/iit_store-getopt1.Tpo .deps/iit_store-getopt1.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -O3 -MT iit_store-iit_store.o -MD -MP -MF .deps/iit_store-iit_store.Tpo -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo './'`iit_store.c
iit_store.c: In function ‘parse_fieldlist’:
iit_store.c:432:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
iit_store.c: In function ‘parse_fasta’:
iit_store.c:467:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
iit_store.c:470:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/iit_store-iit_store.Tpo .deps/iit_store-iit_store.Po
/bin/bash ../libtool --tag=CC   --mode=link gcc   -pthread -O3   -pthread  -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o  -lm 
libtool: link: gcc -pthread -O3 -pthread -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o  -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-except.o -MD -MP -MF .deps/iit_get-except.Tpo -c -o iit_get-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/iit_get-except.Tpo .deps/iit_get-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-assert.o -MD -MP -MF .deps/iit_get-assert.Tpo -c -o iit_get-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/iit_get-assert.Tpo .deps/iit_get-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-mem.o -MD -MP -MF .deps/iit_get-mem.Tpo -c -o iit_get-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/iit_get-mem.Tpo .deps/iit_get-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-intlist.o -MD -MP -MF .deps/iit_get-intlist.Tpo -c -o iit_get-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/iit_get-intlist.Tpo .deps/iit_get-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-list.o -MD -MP -MF .deps/iit_get-list.Tpo -c -o iit_get-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/iit_get-list.Tpo .deps/iit_get-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-littleendian.o -MD -MP -MF .deps/iit_get-littleendian.Tpo -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/iit_get-littleendian.Tpo .deps/iit_get-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-bigendian.o -MD -MP -MF .deps/iit_get-bigendian.Tpo -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/iit_get-bigendian.Tpo .deps/iit_get-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-interval.o -MD -MP -MF .deps/iit_get-interval.Tpo -c -o iit_get-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/iit_get-interval.Tpo .deps/iit_get-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-uintlist.o -MD -MP -MF .deps/iit_get-uintlist.Tpo -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/iit_get-uintlist.Tpo .deps/iit_get-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-stopwatch.o -MD -MP -MF .deps/iit_get-stopwatch.Tpo -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/iit_get-stopwatch.Tpo .deps/iit_get-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-access.o -MD -MP -MF .deps/iit_get-access.Tpo -c -o iit_get-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_allocated’:
access.c:167:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:178:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:183:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/iit_get-access.Tpo .deps/iit_get-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-iit-read.o -MD -MP -MF .deps/iit_get-iit-read.Tpo -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
iit-read.c: In function ‘IIT_debug’:
iit-read.c:2954:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_tree’:
iit-read.c:1673:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1674:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1675:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1676:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1677:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_intervals’:
iit-read.c:1758:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1759:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1761:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1765:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words_debug’:
iit-read.c:1973:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1978:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_annotations’:
iit-read.c:2201:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2207:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2212:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2223:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2229:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2234:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2245:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read’:
iit-read.c:2557:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words’:
iit-read.c:1849:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1855:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read_divint’:
iit-read.c:2296:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/iit_get-iit-read.Tpo .deps/iit_get-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-parserange.o -MD -MP -MF .deps/iit_get-parserange.Tpo -c -o iit_get-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
mv -f .deps/iit_get-parserange.Tpo .deps/iit_get-parserange.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-getopt.o -MD -MP -MF .deps/iit_get-getopt.Tpo -c -o iit_get-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/iit_get-getopt.Tpo .deps/iit_get-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-getopt1.o -MD -MP -MF .deps/iit_get-getopt1.Tpo -c -o iit_get-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/iit_get-getopt1.Tpo .deps/iit_get-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_get-iit_get.o -MD -MP -MF .deps/iit_get-iit_get.Tpo -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo './'`iit_get.c
mv -f .deps/iit_get-iit_get.Tpo .deps/iit_get-iit_get.Po
/bin/bash ../libtool --tag=CC   --mode=link gcc  -pthread -O3   -pthread  -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o  -lm 
libtool: link: gcc -pthread -O3 -pthread -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o  -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-except.o -MD -MP -MF .deps/iit_dump-except.Tpo -c -o iit_dump-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/iit_dump-except.Tpo .deps/iit_dump-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-assert.o -MD -MP -MF .deps/iit_dump-assert.Tpo -c -o iit_dump-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/iit_dump-assert.Tpo .deps/iit_dump-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-mem.o -MD -MP -MF .deps/iit_dump-mem.Tpo -c -o iit_dump-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/iit_dump-mem.Tpo .deps/iit_dump-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-littleendian.o -MD -MP -MF .deps/iit_dump-littleendian.Tpo -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/iit_dump-littleendian.Tpo .deps/iit_dump-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-bigendian.o -MD -MP -MF .deps/iit_dump-bigendian.Tpo -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/iit_dump-bigendian.Tpo .deps/iit_dump-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-intlist.o -MD -MP -MF .deps/iit_dump-intlist.Tpo -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/iit_dump-intlist.Tpo .deps/iit_dump-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-list.o -MD -MP -MF .deps/iit_dump-list.Tpo -c -o iit_dump-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/iit_dump-list.Tpo .deps/iit_dump-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-interval.o -MD -MP -MF .deps/iit_dump-interval.Tpo -c -o iit_dump-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/iit_dump-interval.Tpo .deps/iit_dump-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-uintlist.o -MD -MP -MF .deps/iit_dump-uintlist.Tpo -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/iit_dump-uintlist.Tpo .deps/iit_dump-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-stopwatch.o -MD -MP -MF .deps/iit_dump-stopwatch.Tpo -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/iit_dump-stopwatch.Tpo .deps/iit_dump-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-access.o -MD -MP -MF .deps/iit_dump-access.Tpo -c -o iit_dump-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_allocated’:
access.c:167:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:178:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:183:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/iit_dump-access.Tpo .deps/iit_dump-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-iit-read.o -MD -MP -MF .deps/iit_dump-iit-read.Tpo -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
iit-read.c: In function ‘IIT_debug’:
iit-read.c:2954:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_tree’:
iit-read.c:1673:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1674:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1675:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1676:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1677:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_intervals’:
iit-read.c:1758:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1759:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1761:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1765:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words_debug’:
iit-read.c:1973:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1978:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_annotations’:
iit-read.c:2201:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2207:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2212:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2223:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2229:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2234:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2245:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read’:
iit-read.c:2557:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words’:
iit-read.c:1849:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1855:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read_divint’:
iit-read.c:2296:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/iit_dump-iit-read.Tpo .deps/iit_dump-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-getopt.o -MD -MP -MF .deps/iit_dump-getopt.Tpo -c -o iit_dump-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/iit_dump-getopt.Tpo .deps/iit_dump-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-getopt1.o -MD -MP -MF .deps/iit_dump-getopt1.Tpo -c -o iit_dump-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/iit_dump-getopt1.Tpo .deps/iit_dump-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -O3 -MT iit_dump-iit_dump.o -MD -MP -MF .deps/iit_dump-iit_dump.Tpo -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo './'`iit_dump.c
mv -f .deps/iit_dump-iit_dump.Tpo .deps/iit_dump-iit_dump.Po
/bin/bash ../libtool --tag=CC   --mode=link gcc  -pthread -O3   -pthread  -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o  -lm 
libtool: link: gcc -pthread -O3 -pthread -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o  -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-except.o -MD -MP -MF .deps/gsnap-except.Tpo -c -o gsnap-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gsnap-except.Tpo .deps/gsnap-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-assert.o -MD -MP -MF .deps/gsnap-assert.Tpo -c -o gsnap-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gsnap-assert.Tpo .deps/gsnap-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-mem.o -MD -MP -MF .deps/gsnap-mem.Tpo -c -o gsnap-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gsnap-mem.Tpo .deps/gsnap-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-intlist.o -MD -MP -MF .deps/gsnap-intlist.Tpo -c -o gsnap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gsnap-intlist.Tpo .deps/gsnap-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-list.o -MD -MP -MF .deps/gsnap-list.Tpo -c -o gsnap-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gsnap-list.Tpo .deps/gsnap-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-littleendian.o -MD -MP -MF .deps/gsnap-littleendian.Tpo -c -o gsnap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gsnap-littleendian.Tpo .deps/gsnap-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-bigendian.o -MD -MP -MF .deps/gsnap-bigendian.Tpo -c -o gsnap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gsnap-bigendian.Tpo .deps/gsnap-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-interval.o -MD -MP -MF .deps/gsnap-interval.Tpo -c -o gsnap-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gsnap-interval.Tpo .deps/gsnap-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-uintlist.o -MD -MP -MF .deps/gsnap-uintlist.Tpo -c -o gsnap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gsnap-uintlist.Tpo .deps/gsnap-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-stopwatch.o -MD -MP -MF .deps/gsnap-stopwatch.Tpo -c -o gsnap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gsnap-stopwatch.Tpo .deps/gsnap-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-access.o -MD -MP -MF .deps/gsnap-access.Tpo -c -o gsnap-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_allocated’:
access.c:167:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:178:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:183:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gsnap-access.Tpo .deps/gsnap-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-iit-read.o -MD -MP -MF .deps/gsnap-iit-read.Tpo -c -o gsnap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
iit-read.c: In function ‘IIT_debug’:
iit-read.c:2954:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_tree’:
iit-read.c:1673:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1674:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1675:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1676:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1677:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_intervals’:
iit-read.c:1758:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1759:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1761:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1765:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words_debug’:
iit-read.c:1973:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1978:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_annotations’:
iit-read.c:2201:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2207:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2212:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2223:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2229:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2234:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2245:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read’:
iit-read.c:2557:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words’:
iit-read.c:1849:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1855:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read_divint’:
iit-read.c:2296:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gsnap-iit-read.Tpo .deps/gsnap-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-md5.o -MD -MP -MF .deps/gsnap-md5.Tpo -c -o gsnap-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gsnap-md5.Tpo .deps/gsnap-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-sequence.o -MD -MP -MF .deps/gsnap-sequence.Tpo -c -o gsnap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gsnap-sequence.Tpo .deps/gsnap-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-reader.o -MD -MP -MF .deps/gsnap-reader.Tpo -c -o gsnap-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/gsnap-reader.Tpo .deps/gsnap-reader.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-genomicpos.o -MD -MP -MF .deps/gsnap-genomicpos.Tpo -c -o gsnap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gsnap-genomicpos.Tpo .deps/gsnap-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-compress.o -MD -MP -MF .deps/gsnap-compress.Tpo -c -o gsnap-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gsnap-compress.Tpo .deps/gsnap-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-genome.o -MD -MP -MF .deps/gsnap-genome.Tpo -c -o gsnap-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_ntcounts’:
genome.c:1727:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘genomecomp_read_current’:
genome.c:335:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘fill_buffer’:
genome.c:1224:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_get_char’:
genome.c:1571:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:1468:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:1380:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gsnap-genome.Tpo .deps/gsnap-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-genome_hr.o -MD -MP -MF .deps/gsnap-genome_hr.Tpo -c -o gsnap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/gsnap-genome_hr.Tpo .deps/gsnap-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-indexdb.o -MD -MP -MF .deps/gsnap-indexdb.Tpo -c -o gsnap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1124:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gsnap-indexdb.Tpo .deps/gsnap-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-indexdb_hr.o -MD -MP -MF .deps/gsnap-indexdb_hr.Tpo -c -o gsnap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
indexdb_hr.c: In function ‘positions_read_multiple’:
indexdb_hr.c:592:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gsnap-indexdb_hr.Tpo .deps/gsnap-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-oligo.o -MD -MP -MF .deps/gsnap-oligo.Tpo -c -o gsnap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/gsnap-oligo.Tpo .deps/gsnap-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-chrom.o -MD -MP -MF .deps/gsnap-chrom.Tpo -c -o gsnap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gsnap-chrom.Tpo .deps/gsnap-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-segmentpos.o -MD -MP -MF .deps/gsnap-segmentpos.Tpo -c -o gsnap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
mv -f .deps/gsnap-segmentpos.Tpo .deps/gsnap-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-chrnum.o -MD -MP -MF .deps/gsnap-chrnum.Tpo -c -o gsnap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/gsnap-chrnum.Tpo .deps/gsnap-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-maxent_hr.o -MD -MP -MF .deps/gsnap-maxent_hr.Tpo -c -o gsnap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/gsnap-maxent_hr.Tpo .deps/gsnap-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-samprint.o -MD -MP -MF .deps/gsnap-samprint.Tpo -c -o gsnap-samprint.o `test -f 'samprint.c' || echo './'`samprint.c
mv -f .deps/gsnap-samprint.Tpo .deps/gsnap-samprint.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-mapq.o -MD -MP -MF .deps/gsnap-mapq.Tpo -c -o gsnap-mapq.o `test -f 'mapq.c' || echo './'`mapq.c
mv -f .deps/gsnap-mapq.Tpo .deps/gsnap-mapq.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-shortread.o -MD -MP -MF .deps/gsnap-shortread.Tpo -c -o gsnap-shortread.o `test -f 'shortread.c' || echo './'`shortread.c
mv -f .deps/gsnap-shortread.Tpo .deps/gsnap-shortread.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-substring.o -MD -MP -MF .deps/gsnap-substring.Tpo -c -o gsnap-substring.o `test -f 'substring.c' || echo './'`substring.c
mv -f .deps/gsnap-substring.Tpo .deps/gsnap-substring.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-stage3hr.o -MD -MP -MF .deps/gsnap-stage3hr.Tpo -c -o gsnap-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c
mv -f .deps/gsnap-stage3hr.Tpo .deps/gsnap-stage3hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-goby.o -MD -MP -MF .deps/gsnap-goby.Tpo -c -o gsnap-goby.o `test -f 'goby.c' || echo './'`goby.c
mv -f .deps/gsnap-goby.Tpo .deps/gsnap-goby.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-spanningelt.o -MD -MP -MF .deps/gsnap-spanningelt.Tpo -c -o gsnap-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c
mv -f .deps/gsnap-spanningelt.Tpo .deps/gsnap-spanningelt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-cmet.o -MD -MP -MF .deps/gsnap-cmet.Tpo -c -o gsnap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/gsnap-cmet.Tpo .deps/gsnap-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-atoi.o -MD -MP -MF .deps/gsnap-atoi.Tpo -c -o gsnap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/gsnap-atoi.Tpo .deps/gsnap-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-maxent.o -MD -MP -MF .deps/gsnap-maxent.Tpo -c -o gsnap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/gsnap-maxent.Tpo .deps/gsnap-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-pair.o -MD -MP -MF .deps/gsnap-pair.Tpo -c -o gsnap-pair.o `test -f 'pair.c' || echo './'`pair.c
mv -f .deps/gsnap-pair.Tpo .deps/gsnap-pair.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-pairpool.o -MD -MP -MF .deps/gsnap-pairpool.Tpo -c -o gsnap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/gsnap-pairpool.Tpo .deps/gsnap-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-diag.o -MD -MP -MF .deps/gsnap-diag.Tpo -c -o gsnap-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/gsnap-diag.Tpo .deps/gsnap-diag.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-diagpool.o -MD -MP -MF .deps/gsnap-diagpool.Tpo -c -o gsnap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/gsnap-diagpool.Tpo .deps/gsnap-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-orderstat.o -MD -MP -MF .deps/gsnap-orderstat.Tpo -c -o gsnap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/gsnap-orderstat.Tpo .deps/gsnap-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-oligoindex.o -MD -MP -MF .deps/gsnap-oligoindex.Tpo -c -o gsnap-oligoindex.o `test -f 'oligoindex.c' || echo './'`oligoindex.c
mv -f .deps/gsnap-oligoindex.Tpo .deps/gsnap-oligoindex.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-oligoindex_hr.o -MD -MP -MF .deps/gsnap-oligoindex_hr.Tpo -c -o gsnap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/gsnap-oligoindex_hr.Tpo .deps/gsnap-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-stage2.o -MD -MP -MF .deps/gsnap-stage2.Tpo -c -o gsnap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
mv -f .deps/gsnap-stage2.Tpo .deps/gsnap-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-intron.o -MD -MP -MF .deps/gsnap-intron.Tpo -c -o gsnap-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/gsnap-intron.Tpo .deps/gsnap-intron.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-boyer-moore.o -MD -MP -MF .deps/gsnap-boyer-moore.Tpo -c -o gsnap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/gsnap-boyer-moore.Tpo .deps/gsnap-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-changepoint.o -MD -MP -MF .deps/gsnap-changepoint.Tpo -c -o gsnap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/gsnap-changepoint.Tpo .deps/gsnap-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-pbinom.o -MD -MP -MF .deps/gsnap-pbinom.Tpo -c -o gsnap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/gsnap-pbinom.Tpo .deps/gsnap-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-dynprog.o -MD -MP -MF .deps/gsnap-dynprog.Tpo -c -o gsnap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/gsnap-dynprog.Tpo .deps/gsnap-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-gbuffer.o -MD -MP -MF .deps/gsnap-gbuffer.Tpo -c -o gsnap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
mv -f .deps/gsnap-gbuffer.Tpo .deps/gsnap-gbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-translation.o -MD -MP -MF .deps/gsnap-translation.Tpo -c -o gsnap-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/gsnap-translation.Tpo .deps/gsnap-translation.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-smooth.o -MD -MP -MF .deps/gsnap-smooth.Tpo -c -o gsnap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/gsnap-smooth.Tpo .deps/gsnap-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-chimera.o -MD -MP -MF .deps/gsnap-chimera.Tpo -c -o gsnap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/gsnap-chimera.Tpo .deps/gsnap-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-stage3.o -MD -MP -MF .deps/gsnap-stage3.Tpo -c -o gsnap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/gsnap-stage3.Tpo .deps/gsnap-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-splicetrie_build.o -MD -MP -MF .deps/gsnap-splicetrie_build.Tpo -c -o gsnap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
mv -f .deps/gsnap-splicetrie_build.Tpo .deps/gsnap-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-splicetrie.o -MD -MP -MF .deps/gsnap-splicetrie.Tpo -c -o gsnap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/gsnap-splicetrie.Tpo .deps/gsnap-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-stage1hr.o -MD -MP -MF .deps/gsnap-stage1hr.Tpo -c -o gsnap-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c
mv -f .deps/gsnap-stage1hr.Tpo .deps/gsnap-stage1hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-request.o -MD -MP -MF .deps/gsnap-request.Tpo -c -o gsnap-request.o `test -f 'request.c' || echo './'`request.c
mv -f .deps/gsnap-request.Tpo .deps/gsnap-request.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-resulthr.o -MD -MP -MF .deps/gsnap-resulthr.Tpo -c -o gsnap-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c
mv -f .deps/gsnap-resulthr.Tpo .deps/gsnap-resulthr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-inbuffer.o -MD -MP -MF .deps/gsnap-inbuffer.Tpo -c -o gsnap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
mv -f .deps/gsnap-inbuffer.Tpo .deps/gsnap-inbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-outbuffer.o -MD -MP -MF .deps/gsnap-outbuffer.Tpo -c -o gsnap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
mv -f .deps/gsnap-outbuffer.Tpo .deps/gsnap-outbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-datadir.o -MD -MP -MF .deps/gsnap-datadir.Tpo -c -o gsnap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/gsnap-datadir.Tpo .deps/gsnap-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-getopt.o -MD -MP -MF .deps/gsnap-getopt.Tpo -c -o gsnap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/gsnap-getopt.Tpo .deps/gsnap-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-getopt1.o -MD -MP -MF .deps/gsnap-getopt1.Tpo -c -o gsnap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/gsnap-getopt1.Tpo .deps/gsnap-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-gsnap.o -MD -MP -MF .deps/gsnap-gsnap.Tpo -c -o gsnap-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c
mv -f .deps/gsnap-gsnap.Tpo .deps/gsnap-gsnap.Po
/bin/bash ../libtool --tag=CC   --mode=link gcc  -pthread   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3   -pthread   -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read.o gsnap-md5.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex.o gsnap-oligoindex_hr.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o  -lz  -lm 
libtool: link: gcc -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -pthread -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read.o gsnap-md5.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex.o gsnap-oligoindex_hr.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o  -lz -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-except.o -MD -MP -MF .deps/snpindex-except.Tpo -c -o snpindex-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/snpindex-except.Tpo .deps/snpindex-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-assert.o -MD -MP -MF .deps/snpindex-assert.Tpo -c -o snpindex-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/snpindex-assert.Tpo .deps/snpindex-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-mem.o -MD -MP -MF .deps/snpindex-mem.Tpo -c -o snpindex-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/snpindex-mem.Tpo .deps/snpindex-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-intlist.o -MD -MP -MF .deps/snpindex-intlist.Tpo -c -o snpindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/snpindex-intlist.Tpo .deps/snpindex-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-list.o -MD -MP -MF .deps/snpindex-list.Tpo -c -o snpindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/snpindex-list.Tpo .deps/snpindex-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-littleendian.o -MD -MP -MF .deps/snpindex-littleendian.Tpo -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/snpindex-littleendian.Tpo .deps/snpindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-bigendian.o -MD -MP -MF .deps/snpindex-bigendian.Tpo -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/snpindex-bigendian.Tpo .deps/snpindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-interval.o -MD -MP -MF .deps/snpindex-interval.Tpo -c -o snpindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/snpindex-interval.Tpo .deps/snpindex-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-uintlist.o -MD -MP -MF .deps/snpindex-uintlist.Tpo -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/snpindex-uintlist.Tpo .deps/snpindex-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-stopwatch.o -MD -MP -MF .deps/snpindex-stopwatch.Tpo -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/snpindex-stopwatch.Tpo .deps/snpindex-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-access.o -MD -MP -MF .deps/snpindex-access.Tpo -c -o snpindex-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_allocated’:
access.c:167:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:178:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:183:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/snpindex-access.Tpo .deps/snpindex-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-iit-read.o -MD -MP -MF .deps/snpindex-iit-read.Tpo -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
iit-read.c: In function ‘IIT_debug’:
iit-read.c:2954:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_tree’:
iit-read.c:1673:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1674:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1675:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1676:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1677:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_intervals’:
iit-read.c:1758:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1759:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1761:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1765:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words_debug’:
iit-read.c:1973:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1978:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_annotations’:
iit-read.c:2201:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2207:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2212:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2223:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2229:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2234:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2245:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read’:
iit-read.c:2557:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words’:
iit-read.c:1849:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1855:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read_divint’:
iit-read.c:2296:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/snpindex-iit-read.Tpo .deps/snpindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-genomicpos.o -MD -MP -MF .deps/snpindex-genomicpos.Tpo -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/snpindex-genomicpos.Tpo .deps/snpindex-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-compress.o -MD -MP -MF .deps/snpindex-compress.Tpo -c -o snpindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/snpindex-compress.Tpo .deps/snpindex-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-genome_hr.o -MD -MP -MF .deps/snpindex-genome_hr.Tpo -c -o snpindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/snpindex-genome_hr.Tpo .deps/snpindex-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-indexdb.o -MD -MP -MF .deps/snpindex-indexdb.Tpo -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1124:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/snpindex-indexdb.Tpo .deps/snpindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-chrom.o -MD -MP -MF .deps/snpindex-chrom.Tpo -c -o snpindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/snpindex-chrom.Tpo .deps/snpindex-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-md5.o -MD -MP -MF .deps/snpindex-md5.Tpo -c -o snpindex-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/snpindex-md5.Tpo .deps/snpindex-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-sequence.o -MD -MP -MF .deps/snpindex-sequence.Tpo -c -o snpindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/snpindex-sequence.Tpo .deps/snpindex-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-genome.o -MD -MP -MF .deps/snpindex-genome.Tpo -c -o snpindex-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_ntcounts’:
genome.c:1727:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘genomecomp_read_current’:
genome.c:335:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘fill_buffer’:
genome.c:1224:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_get_char’:
genome.c:1571:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:1468:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:1380:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/snpindex-genome.Tpo .deps/snpindex-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-datadir.o -MD -MP -MF .deps/snpindex-datadir.Tpo -c -o snpindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/snpindex-datadir.Tpo .deps/snpindex-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-getopt.o -MD -MP -MF .deps/snpindex-getopt.Tpo -c -o snpindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/snpindex-getopt.Tpo .deps/snpindex-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-getopt1.o -MD -MP -MF .deps/snpindex-getopt1.Tpo -c -o snpindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/snpindex-getopt1.Tpo .deps/snpindex-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-snpindex.o -MD -MP -MF .deps/snpindex-snpindex.Tpo -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo './'`snpindex.c
mv -f .deps/snpindex-snpindex.Tpo .deps/snpindex-snpindex.Po
/bin/bash ../libtool --tag=CC   --mode=link gcc  -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3   -pthread  -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-genome_hr.o snpindex-indexdb.o snpindex-chrom.o snpindex-md5.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o  -lz -lm 
libtool: link: gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -pthread -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-genome_hr.o snpindex-indexdb.o snpindex-chrom.o snpindex-md5.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o  -lz -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-except.o -MD -MP -MF .deps/cmetindex-except.Tpo -c -o cmetindex-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/cmetindex-except.Tpo .deps/cmetindex-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-assert.o -MD -MP -MF .deps/cmetindex-assert.Tpo -c -o cmetindex-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/cmetindex-assert.Tpo .deps/cmetindex-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-mem.o -MD -MP -MF .deps/cmetindex-mem.Tpo -c -o cmetindex-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/cmetindex-mem.Tpo .deps/cmetindex-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-littleendian.o -MD -MP -MF .deps/cmetindex-littleendian.Tpo -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/cmetindex-littleendian.Tpo .deps/cmetindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-bigendian.o -MD -MP -MF .deps/cmetindex-bigendian.Tpo -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/cmetindex-bigendian.Tpo .deps/cmetindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-genomicpos.o -MD -MP -MF .deps/cmetindex-genomicpos.Tpo -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/cmetindex-genomicpos.Tpo .deps/cmetindex-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-stopwatch.o -MD -MP -MF .deps/cmetindex-stopwatch.Tpo -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/cmetindex-stopwatch.Tpo .deps/cmetindex-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-access.o -MD -MP -MF .deps/cmetindex-access.Tpo -c -o cmetindex-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_allocated’:
access.c:167:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:178:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:183:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/cmetindex-access.Tpo .deps/cmetindex-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-interval.o -MD -MP -MF .deps/cmetindex-interval.Tpo -c -o cmetindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/cmetindex-interval.Tpo .deps/cmetindex-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-iit-read.o -MD -MP -MF .deps/cmetindex-iit-read.Tpo -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
iit-read.c: In function ‘IIT_debug’:
iit-read.c:2954:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_tree’:
iit-read.c:1673:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1674:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1675:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1676:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1677:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_intervals’:
iit-read.c:1758:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1759:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1761:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1765:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words_debug’:
iit-read.c:1973:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1978:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_annotations’:
iit-read.c:2201:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2207:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2212:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2223:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2229:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2234:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2245:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read’:
iit-read.c:2557:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words’:
iit-read.c:1849:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1855:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read_divint’:
iit-read.c:2296:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/cmetindex-iit-read.Tpo .deps/cmetindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-compress.o -MD -MP -MF .deps/cmetindex-compress.Tpo -c -o cmetindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/cmetindex-compress.Tpo .deps/cmetindex-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-genome_hr.o -MD -MP -MF .deps/cmetindex-genome_hr.Tpo -c -o cmetindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/cmetindex-genome_hr.Tpo .deps/cmetindex-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-indexdb.o -MD -MP -MF .deps/cmetindex-indexdb.Tpo -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1124:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/cmetindex-indexdb.Tpo .deps/cmetindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-cmet.o -MD -MP -MF .deps/cmetindex-cmet.Tpo -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/cmetindex-cmet.Tpo .deps/cmetindex-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-list.o -MD -MP -MF .deps/cmetindex-list.Tpo -c -o cmetindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/cmetindex-list.Tpo .deps/cmetindex-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-datadir.o -MD -MP -MF .deps/cmetindex-datadir.Tpo -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/cmetindex-datadir.Tpo .deps/cmetindex-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-getopt.o -MD -MP -MF .deps/cmetindex-getopt.Tpo -c -o cmetindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/cmetindex-getopt.Tpo .deps/cmetindex-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-getopt1.o -MD -MP -MF .deps/cmetindex-getopt1.Tpo -c -o cmetindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/cmetindex-getopt1.Tpo .deps/cmetindex-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-cmetindex.o -MD -MP -MF .deps/cmetindex-cmetindex.Tpo -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo './'`cmetindex.c
mv -f .deps/cmetindex-cmetindex.Tpo .deps/cmetindex-cmetindex.Po
/bin/bash ../libtool --tag=CC   --mode=link gcc  -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3   -pthread  -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-interval.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-genome_hr.o cmetindex-indexdb.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o  -lm 
libtool: link: gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -pthread -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-interval.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-genome_hr.o cmetindex-indexdb.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o  -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-except.o -MD -MP -MF .deps/atoiindex-except.Tpo -c -o atoiindex-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/atoiindex-except.Tpo .deps/atoiindex-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-assert.o -MD -MP -MF .deps/atoiindex-assert.Tpo -c -o atoiindex-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/atoiindex-assert.Tpo .deps/atoiindex-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-mem.o -MD -MP -MF .deps/atoiindex-mem.Tpo -c -o atoiindex-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/atoiindex-mem.Tpo .deps/atoiindex-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-littleendian.o -MD -MP -MF .deps/atoiindex-littleendian.Tpo -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/atoiindex-littleendian.Tpo .deps/atoiindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-bigendian.o -MD -MP -MF .deps/atoiindex-bigendian.Tpo -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/atoiindex-bigendian.Tpo .deps/atoiindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-genomicpos.o -MD -MP -MF .deps/atoiindex-genomicpos.Tpo -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/atoiindex-genomicpos.Tpo .deps/atoiindex-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-stopwatch.o -MD -MP -MF .deps/atoiindex-stopwatch.Tpo -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/atoiindex-stopwatch.Tpo .deps/atoiindex-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-access.o -MD -MP -MF .deps/atoiindex-access.Tpo -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_allocated’:
access.c:167:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:178:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:183:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/atoiindex-access.Tpo .deps/atoiindex-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-interval.o -MD -MP -MF .deps/atoiindex-interval.Tpo -c -o atoiindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/atoiindex-interval.Tpo .deps/atoiindex-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-iit-read.o -MD -MP -MF .deps/atoiindex-iit-read.Tpo -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
iit-read.c: In function ‘IIT_debug’:
iit-read.c:2954:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_tree’:
iit-read.c:1673:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1674:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1675:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1676:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1677:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_intervals’:
iit-read.c:1758:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1759:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1761:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1765:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words_debug’:
iit-read.c:1973:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1978:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_annotations’:
iit-read.c:2201:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2207:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2212:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2223:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2229:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2234:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2245:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read’:
iit-read.c:2557:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words’:
iit-read.c:1849:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1855:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read_divint’:
iit-read.c:2296:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/atoiindex-iit-read.Tpo .deps/atoiindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-compress.o -MD -MP -MF .deps/atoiindex-compress.Tpo -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/atoiindex-compress.Tpo .deps/atoiindex-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-genome_hr.o -MD -MP -MF .deps/atoiindex-genome_hr.Tpo -c -o atoiindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/atoiindex-genome_hr.Tpo .deps/atoiindex-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-indexdb.o -MD -MP -MF .deps/atoiindex-indexdb.Tpo -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1124:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/atoiindex-indexdb.Tpo .deps/atoiindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-atoi.o -MD -MP -MF .deps/atoiindex-atoi.Tpo -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/atoiindex-atoi.Tpo .deps/atoiindex-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-list.o -MD -MP -MF .deps/atoiindex-list.Tpo -c -o atoiindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/atoiindex-list.Tpo .deps/atoiindex-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-datadir.o -MD -MP -MF .deps/atoiindex-datadir.Tpo -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/atoiindex-datadir.Tpo .deps/atoiindex-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-getopt.o -MD -MP -MF .deps/atoiindex-getopt.Tpo -c -o atoiindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/atoiindex-getopt.Tpo .deps/atoiindex-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-getopt1.o -MD -MP -MF .deps/atoiindex-getopt1.Tpo -c -o atoiindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/atoiindex-getopt1.Tpo .deps/atoiindex-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-atoiindex.o -MD -MP -MF .deps/atoiindex-atoiindex.Tpo -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo './'`atoiindex.c
mv -f .deps/atoiindex-atoiindex.Tpo .deps/atoiindex-atoiindex.Po
/bin/bash ../libtool --tag=CC   --mode=link gcc  -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3   -pthread  -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-interval.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-genome_hr.o atoiindex-indexdb.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o  -lm 
libtool: link: gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -pthread -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-interval.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-genome_hr.o atoiindex-indexdb.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o  -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-except.o -MD -MP -MF .deps/gsnap_tally-except.Tpo -c -o gsnap_tally-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gsnap_tally-except.Tpo .deps/gsnap_tally-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-assert.o -MD -MP -MF .deps/gsnap_tally-assert.Tpo -c -o gsnap_tally-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gsnap_tally-assert.Tpo .deps/gsnap_tally-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-mem.o -MD -MP -MF .deps/gsnap_tally-mem.Tpo -c -o gsnap_tally-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gsnap_tally-mem.Tpo .deps/gsnap_tally-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-intlist.o -MD -MP -MF .deps/gsnap_tally-intlist.Tpo -c -o gsnap_tally-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gsnap_tally-intlist.Tpo .deps/gsnap_tally-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-list.o -MD -MP -MF .deps/gsnap_tally-list.Tpo -c -o gsnap_tally-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gsnap_tally-list.Tpo .deps/gsnap_tally-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-littleendian.o -MD -MP -MF .deps/gsnap_tally-littleendian.Tpo -c -o gsnap_tally-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gsnap_tally-littleendian.Tpo .deps/gsnap_tally-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-bigendian.o -MD -MP -MF .deps/gsnap_tally-bigendian.Tpo -c -o gsnap_tally-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gsnap_tally-bigendian.Tpo .deps/gsnap_tally-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-interval.o -MD -MP -MF .deps/gsnap_tally-interval.Tpo -c -o gsnap_tally-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gsnap_tally-interval.Tpo .deps/gsnap_tally-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-uintlist.o -MD -MP -MF .deps/gsnap_tally-uintlist.Tpo -c -o gsnap_tally-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gsnap_tally-uintlist.Tpo .deps/gsnap_tally-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-stopwatch.o -MD -MP -MF .deps/gsnap_tally-stopwatch.Tpo -c -o gsnap_tally-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gsnap_tally-stopwatch.Tpo .deps/gsnap_tally-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-access.o -MD -MP -MF .deps/gsnap_tally-access.Tpo -c -o gsnap_tally-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_allocated’:
access.c:167:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:178:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
access.c:183:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gsnap_tally-access.Tpo .deps/gsnap_tally-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-iit-read.o -MD -MP -MF .deps/gsnap_tally-iit-read.Tpo -c -o gsnap_tally-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
iit-read.c: In function ‘IIT_debug’:
iit-read.c:2954:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_tree’:
iit-read.c:1673:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1674:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1675:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1676:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1677:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_intervals’:
iit-read.c:1758:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1759:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1761:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1765:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words_debug’:
iit-read.c:1973:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1978:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_annotations’:
iit-read.c:2201:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2207:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2212:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2223:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2229:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2234:9: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:2245:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read’:
iit-read.c:2557:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘read_words’:
iit-read.c:1849:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c:1855:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
iit-read.c: In function ‘IIT_read_divint’:
iit-read.c:2296:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gsnap_tally-iit-read.Tpo .deps/gsnap_tally-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-chrom.o -MD -MP -MF .deps/gsnap_tally-chrom.Tpo -c -o gsnap_tally-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gsnap_tally-chrom.Tpo .deps/gsnap_tally-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-genomicpos.o -MD -MP -MF .deps/gsnap_tally-genomicpos.Tpo -c -o gsnap_tally-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gsnap_tally-genomicpos.Tpo .deps/gsnap_tally-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-md5.o -MD -MP -MF .deps/gsnap_tally-md5.Tpo -c -o gsnap_tally-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gsnap_tally-md5.Tpo .deps/gsnap_tally-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-sequence.o -MD -MP -MF .deps/gsnap_tally-sequence.Tpo -c -o gsnap_tally-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gsnap_tally-sequence.Tpo .deps/gsnap_tally-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-genome.o -MD -MP -MF .deps/gsnap_tally-genome.Tpo -c -o gsnap_tally-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_ntcounts’:
genome.c:1727:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘genomecomp_read_current’:
genome.c:335:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘fill_buffer’:
genome.c:1224:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_get_char’:
genome.c:1571:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:1468:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:1380:11: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/gsnap_tally-genome.Tpo .deps/gsnap_tally-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-gsnapread.o -MD -MP -MF .deps/gsnap_tally-gsnapread.Tpo -c -o gsnap_tally-gsnapread.o `test -f 'gsnapread.c' || echo './'`gsnapread.c
mv -f .deps/gsnap_tally-gsnapread.Tpo .deps/gsnap_tally-gsnapread.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-datadir.o -MD -MP -MF .deps/gsnap_tally-datadir.Tpo -c -o gsnap_tally-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/gsnap_tally-datadir.Tpo .deps/gsnap_tally-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-getopt.o -MD -MP -MF .deps/gsnap_tally-getopt.Tpo -c -o gsnap_tally-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/gsnap_tally-getopt.Tpo .deps/gsnap_tally-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-getopt1.o -MD -MP -MF .deps/gsnap_tally-getopt1.Tpo -c -o gsnap_tally-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/gsnap_tally-getopt1.Tpo .deps/gsnap_tally-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-gsnap_tally.o -MD -MP -MF .deps/gsnap_tally-gsnap_tally.Tpo -c -o gsnap_tally-gsnap_tally.o `test -f 'gsnap_tally.c' || echo './'`gsnap_tally.c
mv -f .deps/gsnap_tally-gsnap_tally.Tpo .deps/gsnap_tally-gsnap_tally.Po
/bin/bash ../libtool --tag=CC   --mode=link gcc  -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3   -pthread  -o gsnap_tally gsnap_tally-except.o gsnap_tally-assert.o gsnap_tally-mem.o gsnap_tally-intlist.o gsnap_tally-list.o gsnap_tally-littleendian.o gsnap_tally-bigendian.o gsnap_tally-interval.o gsnap_tally-uintlist.o gsnap_tally-stopwatch.o gsnap_tally-access.o gsnap_tally-iit-read.o gsnap_tally-chrom.o gsnap_tally-genomicpos.o gsnap_tally-md5.o gsnap_tally-sequence.o gsnap_tally-genome.o gsnap_tally-gsnapread.o gsnap_tally-datadir.o gsnap_tally-getopt.o gsnap_tally-getopt1.o gsnap_tally-gsnap_tally.o  -lz -lm 
libtool: link: gcc -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -pthread -o gsnap_tally gsnap_tally-except.o gsnap_tally-assert.o gsnap_tally-mem.o gsnap_tally-intlist.o gsnap_tally-list.o gsnap_tally-littleendian.o gsnap_tally-bigendian.o gsnap_tally-interval.o gsnap_tally-uintlist.o gsnap_tally-stopwatch.o gsnap_tally-access.o gsnap_tally-iit-read.o gsnap_tally-chrom.o gsnap_tally-genomicpos.o gsnap_tally-md5.o gsnap_tally-sequence.o gsnap_tally-genome.o gsnap_tally-gsnapread.o gsnap_tally-datadir.o gsnap_tally-getopt.o gsnap_tally-getopt1.o gsnap_tally-gsnap_tally.o  -lz -lm -pthread
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/src'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
test -z "/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin" || /bin/mkdir -p "/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin"
  /bin/bash ../libtool   --mode=install /usr/bin/install -c 'gmap' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap'
libtool: install: /usr/bin/install -c gmap /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap
  /bin/bash ../libtool   --mode=install /usr/bin/install -c 'get-genome' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/get-genome'
libtool: install: /usr/bin/install -c get-genome /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/get-genome
  /bin/bash ../libtool   --mode=install /usr/bin/install -c 'gmapindex' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmapindex'
libtool: install: /usr/bin/install -c gmapindex /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmapindex
  /bin/bash ../libtool   --mode=install /usr/bin/install -c 'iit_store' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/iit_store'
libtool: install: /usr/bin/install -c iit_store /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/iit_store
  /bin/bash ../libtool   --mode=install /usr/bin/install -c 'iit_get' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/iit_get'
libtool: install: /usr/bin/install -c iit_get /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/iit_get
  /bin/bash ../libtool   --mode=install /usr/bin/install -c 'iit_dump' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/iit_dump'
libtool: install: /usr/bin/install -c iit_dump /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/iit_dump
  /bin/bash ../libtool   --mode=install /usr/bin/install -c 'gsnap' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gsnap'
libtool: install: /usr/bin/install -c gsnap /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gsnap
  /bin/bash ../libtool   --mode=install /usr/bin/install -c 'snpindex' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/snpindex'
libtool: install: /usr/bin/install -c snpindex /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/snpindex
  /bin/bash ../libtool   --mode=install /usr/bin/install -c 'cmetindex' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/cmetindex'
libtool: install: /usr/bin/install -c cmetindex /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/cmetindex
  /bin/bash ../libtool   --mode=install /usr/bin/install -c 'atoiindex' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/atoiindex'
libtool: install: /usr/bin/install -c atoiindex /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/atoiindex
  /bin/bash ../libtool   --mode=install /usr/bin/install -c 'gsnap_tally' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gsnap_tally'
libtool: install: /usr/bin/install -c gsnap_tally /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gsnap_tally
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/src'
make[2]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/src'
Making install in util
make[2]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/util'
cp gmap_compress.pl gmap_compress
chmod +x gmap_compress
cp gmap_uncompress.pl gmap_uncompress
chmod +x gmap_uncompress
cp gmap_process.pl gmap_process
chmod +x gmap_process
cp gmap_setup.pl gmap_setup
chmod +x gmap_setup
cp gmap_build.pl gmap_build
chmod +x gmap_build
cp gmap_reassemble.pl gmap_reassemble
chmod +x gmap_reassemble
cp md_coords.pl md_coords
chmod +x md_coords
cp fa_coords.pl fa_coords
chmod +x fa_coords
cp psl_splicesites.pl psl_splicesites
chmod +x psl_splicesites
cp psl_introns.pl psl_introns
chmod +x psl_introns
cp psl_genes.pl psl_genes
chmod +x psl_genes
cp gtf_splicesites.pl gtf_splicesites
chmod +x gtf_splicesites
cp gtf_introns.pl gtf_introns
chmod +x gtf_introns
cp gtf_genes.pl gtf_genes
chmod +x gtf_genes
cp gff3_splicesites.pl gff3_splicesites
chmod +x gff3_splicesites
cp gff3_introns.pl gff3_introns
chmod +x gff3_introns
cp gff3_genes.pl gff3_genes
chmod +x gff3_genes
cp dbsnp_iit.pl dbsnp_iit
chmod +x dbsnp_iit
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/util'
test -z "/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin" || /bin/mkdir -p "/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin"
 /usr/bin/install -c 'gmap_compress' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap_compress'
 /usr/bin/install -c 'gmap_uncompress' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap_uncompress'
 /usr/bin/install -c 'gmap_process' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap_process'
 /usr/bin/install -c 'gmap_setup' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap_setup'
 /usr/bin/install -c 'gmap_build' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap_build'
 /usr/bin/install -c 'gmap_reassemble' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap_reassemble'
 /usr/bin/install -c 'md_coords' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/md_coords'
 /usr/bin/install -c 'fa_coords' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/fa_coords'
 /usr/bin/install -c 'psl_splicesites' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/psl_splicesites'
 /usr/bin/install -c 'psl_introns' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/psl_introns'
 /usr/bin/install -c 'psl_genes' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/psl_genes'
 /usr/bin/install -c 'gtf_splicesites' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gtf_splicesites'
 /usr/bin/install -c 'gtf_introns' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gtf_introns'
 /usr/bin/install -c 'gtf_genes' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gtf_genes'
 /usr/bin/install -c 'gff3_splicesites' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gff3_splicesites'
 /usr/bin/install -c 'gff3_introns' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gff3_introns'
 /usr/bin/install -c 'gff3_genes' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gff3_genes'
 /usr/bin/install -c 'dbsnp_iit' '/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/dbsnp_iit'
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/util'
make[2]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/util'
Making install in tests
make[2]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/tests'
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/tests'
make[4]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
make[4]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/tests'
make[2]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/tests'
make[2]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
make[3]: Entering directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
make[3]: Nothing to be done for `install-exec-am'.
/bin/bash /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/config/install-sh -d /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share
make[3]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
make[2]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
make[1]: Leaving directory `/home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap'
installing to /home/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/gmapR/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function from function ‘directory’ in package ‘gmapR’
Creating a generic function for ‘bamPaths’ from package ‘Rsamtools’ in package ‘gmapR’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘gmapR.Rnw’ 
** testing if installed package can be loaded
* DONE (gmapR)

name	user	system	elapsed
GmapGenome-class	0.752	0.008	0.783
GmapGenomeDirectory-class	0.012	0.004	0.020
TP53Genome	0.012	0.004	0.035
gmap_build-methods	0.012	0.000	0.010
makeGmapGenomePackage	0.032	0.000	0.033