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###
### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL gmapR
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘gmapR’ ...
** using staged installation
** libs
cd gstruct/; \
CFLAGS="-g -O3" \
./configure --enable-static --disable-shared \
--prefix=/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr --includedir=/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include/gstruct \
--libdir=/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/lib \
--with-samtools-lib=/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/samtools \
--disable-maintainer-mode \
--disable-binaries
checking package version... 2017-01-01
checking whether to enable maintainer-specific portions of Makefiles... no
loading default site script ./config.site
checking CFLAGS... -g -O3
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
checking target system type... aarch64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking whether make supports nested variables... yes
checking dependency style of gcc... gcc3
checking bindir... /home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/bin
checking whether to link statically... not specified so disabled by default
checking for a working version of perl... /usr/bin/perl
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for X... libraries , headers
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for qsub... no
checking gmap program directory...
checking for get-genome... false
checking for iit_store... false
checking for iit_get... false
checking for gmap_build... false
checking for gmap... false
checking for gsnap... false
checking for sam_sort... false
checking for uniqscan... false
checking for rint in -lm... yes
checking for pthreads feature... not specified so enabled by default
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... gcc
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for working volatile... yes
checking for size_t... yes
checking for off_t... yes
checking for caddr_t... yes
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking size of off_t... 8
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for working mmap with MAP_FIXED... yes
checking for working mmap with MAP_VARIABLE... no
checking for MAP_FILE in mmap... yes
checking for MAP_VARIABLE in mmap... no
checking for MAP_SHARED in mmap... yes
checking for MAP_PRIVATE in mmap... yes
checking for MAP_FAILED in mmap... yes
checking for MADV_DONTNEED in madvise... yes
checking for MADV_WILLNEED in madvise... yes
checking for MADV_RANDOM in madvise... yes
checking for MADV_SEQUENTIAL in madvise... yes
checking for ceil... yes
checking for floor... yes
checking for index... yes
checking for log... yes
checking for madvise... yes
checking for memcpy... yes
checking for memmove... yes
checking for memset... yes
checking for munmap... yes
checking for pow... yes
checking for rint... yes
checking for stat64... yes
checking for strtoul... yes
checking for sysconf... yes
checking for sysctl... no
checking for sigaction... yes
checking for struct stat64... no
checking for pagesize via sysconf... yes
checking for pagesize via sysctl... no
checking whether fopen accepts "b" mode... yes
checking whether fopen accepts "t" mode... yes
checking for builtin popcount/clz/ctz features... not specified so enabled by default
./configure: line 16917: ACX_BUILTIN_POPCOUNT: command not found
checking for bsr instruction in assembly... yes
checking whether sse2 is enabled... not specified so enabled by default
checking compiler is defective and requires an immediate in sse2 shift commands... yes
checking whether ssse3 is enabled... not specified so enabled by default
checking whether sse4.1 is enabled... not specified so enabled by default
checking whether sse4.2 is enabled... not specified so enabled by default
checking whether avx is enabled... not specified so enabled by default
checking whether avx2 is enabled... not specified so enabled by default
checking whether simd is enabled... not specified so enabled by default
checking gmapdb... /home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share
checking whether to make binaries... disabled
checking for zlib support... enabled
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzopen in -lz... yes
checking for gzeof in -lz... yes
checking for gzgetc in -lz... yes
checking for gzgets in -lz... yes
checking for gzclose in -lz... yes
checking if zlib package is complete... working
checking for gzbuffer in -lz... yes
checking for samtools program... checking for samtools library... provided by --with-samtools-lib
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating lib/gstruct-1.0.pc
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING:
WARNING: You don't seem to have gsnap specified.
checking Standard compiler and flags to be used... gcc -g -O3
checking Standard linker flags to be used...
checking pthread compiler flags to be used...
checking popcnt compiler flags to be used...
checking SIMD features available on computer...
checking SIMD compiler flags to be used...
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c: In function ‘worker_aux’:
samtools/bgzf.c:412:16: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
412 | int i, tmp, stop = 0;
| ^~~
samtools/bgzf.c: In function ‘bgzf_close’:
samtools/bgzf.c:592:18: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
592 | int ret, count, block_length;
| ^~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/kstring.c -o samtools/kstring.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam.c -o samtools/bam.o
samtools/bam.c: In function ‘bam_header_write’:
samtools/bam.c:128:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
128 | strncpy(buf, "BAM\001", 4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_import.c -o samtools/bam_import.o
In file included from /usr/include/aarch64-linux-gnu/bits/libc-header-start.h:33,
from /usr/include/limits.h:26,
from /usr/lib/gcc/aarch64-linux-gnu/11/include/limits.h:203,
from /usr/lib/gcc/aarch64-linux-gnu/11/include/syslimits.h:7,
from /usr/lib/gcc/aarch64-linux-gnu/11/include/limits.h:34,
from /usr/include/zconf.h:418,
from /usr/include/zlib.h:34,
from samtools/bam_import.c:3:
/usr/include/features.h:194:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
194 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/sam.c -o samtools/sam.o
In file included from /usr/include/aarch64-linux-gnu/bits/libc-header-start.h:33,
from /usr/include/string.h:26,
from samtools/sam.c:3:
/usr/include/features.h:194:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
194 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_index.c -o samtools/bam_index.o
samtools/bam_index.c: In function ‘bam_index_core’:
samtools/bam_index.c:178:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow]
178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
| ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_md.c -o samtools/bam_md.o
samtools/bam_md.c: In function ‘bam_prob_realn_core’:
samtools/bam_md.c:214:35: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
214 | *(bq - 3) = 'Z';
| ~~~~~~~~~~^~~~~
samtools/bam_md.c:198:19: note: at offset -2 into destination object of size [0, 9223372036854775807] allocated by ‘bam_aux_get’
198 | if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq;
| ^~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function ‘razf_open_w’:
samtools/razf.c:178:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
178 | strncpy((char*)rz->header->extra, "RAZF", 4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/faidx.c -o samtools/faidx.o
samtools/faidx.c: In function ‘fai_load0’:
samtools/faidx.c:309:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
309 | else
| ^~~~
samtools/faidx.c:312:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
312 | if (fp == 0) {
| ^~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/knetfile.c -o samtools/knetfile.o
In file included from /usr/include/time.h:25,
from samtools/knetfile.c:33:
/usr/include/features.h:194:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
194 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_sort.c -o samtools/bam_sort.o
In file included from /usr/include/aarch64-linux-gnu/bits/libc-header-start.h:33,
from /usr/include/stdlib.h:26,
from samtools/bam_sort.c:3:
/usr/include/features.h:194:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
194 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/sam_header.c -o samtools/sam_header.o
In file included from /usr/include/aarch64-linux-gnu/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from samtools/sam_header.c:3:
/usr/include/features.h:194:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
194 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_reheader.c -o samtools/bam_reheader.o
samtools/bam_reheader.c: In function ‘bam_reheader’:
samtools/bam_reheader.c:12:23: warning: variable ‘old’ set but not used [-Wunused-but-set-variable]
12 | bam_header_t *old;
| ^~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/kprobaln.c -o samtools/kprobaln.o
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:28: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
78 | int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/samtools_patch.c -o samtools/samtools_patch.o
ar -crus samtools/libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools/samtools_patch.o
ar: `u' modifier ignored since `D' is the default (see `U')
cd gstruct; \
make install
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/gstruct'
Making install in src
make[2]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/gstruct/src'
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c -o libgstruct_1.0_la-except.lo `test -f 'except.c' || echo './'`except.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c except.c -o libgstruct_1.0_la-except.o
mv -f .deps/libgstruct_1.0_la-except.Tpo .deps/libgstruct_1.0_la-except.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c -o libgstruct_1.0_la-assert.lo `test -f 'assert.c' || echo './'`assert.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c assert.c -o libgstruct_1.0_la-assert.o
mv -f .deps/libgstruct_1.0_la-assert.Tpo .deps/libgstruct_1.0_la-assert.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c -o libgstruct_1.0_la-mem.lo `test -f 'mem.c' || echo './'`mem.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c mem.c -o libgstruct_1.0_la-mem.o
mv -f .deps/libgstruct_1.0_la-mem.Tpo .deps/libgstruct_1.0_la-mem.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c -o libgstruct_1.0_la-intlist.lo `test -f 'intlist.c' || echo './'`intlist.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c intlist.c -o libgstruct_1.0_la-intlist.o
mv -f .deps/libgstruct_1.0_la-intlist.Tpo .deps/libgstruct_1.0_la-intlist.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c -o libgstruct_1.0_la-list.lo `test -f 'list.c' || echo './'`list.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c list.c -o libgstruct_1.0_la-list.o
mv -f .deps/libgstruct_1.0_la-list.Tpo .deps/libgstruct_1.0_la-list.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c -o libgstruct_1.0_la-littleendian.lo `test -f 'littleendian.c' || echo './'`littleendian.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c littleendian.c -o libgstruct_1.0_la-littleendian.o
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
17 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
mv -f .deps/libgstruct_1.0_la-littleendian.Tpo .deps/libgstruct_1.0_la-littleendian.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c -o libgstruct_1.0_la-bigendian.lo `test -f 'bigendian.c' || echo './'`bigendian.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c bigendian.c -o libgstruct_1.0_la-bigendian.o
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
296 | write(fd,buf,4);
| ^~~~~~~~~~~~~~~
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
457 | read(fd,buf,4);
| ^~~~~~~~~~~~~~
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
758 | read(fd,buf,8);
| ^~~~~~~~~~~~~~
mv -f .deps/libgstruct_1.0_la-bigendian.Tpo .deps/libgstruct_1.0_la-bigendian.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c -o libgstruct_1.0_la-interval.lo `test -f 'interval.c' || echo './'`interval.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c interval.c -o libgstruct_1.0_la-interval.o
mv -f .deps/libgstruct_1.0_la-interval.Tpo .deps/libgstruct_1.0_la-interval.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c -o libgstruct_1.0_la-uintlist.lo `test -f 'uintlist.c' || echo './'`uintlist.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c uintlist.c -o libgstruct_1.0_la-uintlist.o
mv -f .deps/libgstruct_1.0_la-uintlist.Tpo .deps/libgstruct_1.0_la-uintlist.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c -o libgstruct_1.0_la-stopwatch.lo `test -f 'stopwatch.c' || echo './'`stopwatch.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c stopwatch.c -o libgstruct_1.0_la-stopwatch.o
mv -f .deps/libgstruct_1.0_la-stopwatch.Tpo .deps/libgstruct_1.0_la-stopwatch.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c -o libgstruct_1.0_la-access.lo `test -f 'access.c' || echo './'`access.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c access.c -o libgstruct_1.0_la-access.o
access.c: In function ‘Access_file_exists_p’:
access.c:59:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration]
59 | if (stat64(filename,&sb) == 0) {
| ^~~~~~
| stat
In file included from access.c:39:
access.c: In function ‘Access_allocated’:
littleendian.h:18:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
18 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(unsigned int),n,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:125:3: note: in expansion of macro ‘FREAD_UINTS’
125 | FREAD_UINTS(memory,(*len)/eltsize,fp);
| ^~~~~~~~~~~
mv -f .deps/libgstruct_1.0_la-access.Tpo .deps/libgstruct_1.0_la-access.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c -o libgstruct_1.0_la-iit-read.lo `test -f 'iit-read.c' || echo './'`iit-read.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c iit-read.c -o libgstruct_1.0_la-iit-read.o
In file included from iit-read.c:12:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:15:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
15 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2353:5: note: in expansion of macro ‘FREAD_INT’
2353 | FREAD_INT(&version,fp);
| ^~~~~~~~~
iit-read.c: In function ‘IIT_read’:
littleendian.h:15:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
15 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2619:5: note: in expansion of macro ‘FREAD_INT’
2619 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function ‘read_tree’:
iit-read.c:1731:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1731 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1732:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1732 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1733:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1733 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1734:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1734 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1735:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1735 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function ‘read_intervals’:
iit-read.c:1816:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1816 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1817:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1817 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1819:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1819 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1823:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1823 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from iit-read.c:12:
iit-read.c: In function ‘read_words’:
littleendian.h:20:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
20 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1907:5: note: in expansion of macro ‘FREAD_UINT8’
1907 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
littleendian.h:16:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
16 | #define FREAD_UINT(p,fp) fread(p,sizeof(unsigned int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT’
1913 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
iit-read.c: In function ‘read_annotations’:
iit-read.c:2257:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2257 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2263:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2263 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2268:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2268 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(unsigned int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2279:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2279 | read(new->fd,new->labels,new->label_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2285:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2285 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2290:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2290 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(unsigned int));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2301:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2301 | read(new->fd,new->annotations,new->annot_length*sizeof(char));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from iit-read.c:12:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:15:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
15 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:3019:5: note: in expansion of macro ‘FREAD_INT’
3019 | FREAD_INT(&new->version,fp);
| ^~~~~~~~~
iit-read.c: In function ‘read_words_debug’:
littleendian.h:20:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
20 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2030:5: note: in expansion of macro ‘FREAD_UINT8’
2030 | FREAD_UINT8(&length8,fp);
| ^~~~~~~~~~~
littleendian.h:16:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
16 | #define FREAD_UINT(p,fp) fread(p,sizeof(unsigned int),1,fp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2035:5: note: in expansion of macro ‘FREAD_UINT’
2035 | FREAD_UINT(&length,fp);
| ^~~~~~~~~~
mv -f .deps/libgstruct_1.0_la-iit-read.Tpo .deps/libgstruct_1.0_la-iit-read.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c -o libgstruct_1.0_la-chrom.lo `test -f 'chrom.c' || echo './'`chrom.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c chrom.c -o libgstruct_1.0_la-chrom.o
chrom.c: In function ‘Chrom_from_string’:
chrom.c:108:12: warning: comparison between pointer and zero character constant [-Wpointer-compare]
108 | while (p != '\0' && *p >= '0' && *p <= '9') {
| ^~
chrom.c:108:10: note: did you mean to dereference the pointer?
108 | while (p != '\0' && *p >= '0' && *p <= '9') {
| ^
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. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c -o libgstruct_1.0_la-genomicpos.lo `test -f 'genomicpos.c' || echo './'`genomicpos.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c genomicpos.c -o libgstruct_1.0_la-genomicpos.o
mv -f .deps/libgstruct_1.0_la-genomicpos.Tpo .deps/libgstruct_1.0_la-genomicpos.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c -o libgstruct_1.0_la-md5.lo `test -f 'md5.c' || echo './'`md5.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c md5.c -o libgstruct_1.0_la-md5.o
mv -f .deps/libgstruct_1.0_la-md5.Tpo .deps/libgstruct_1.0_la-md5.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c -o libgstruct_1.0_la-sequence.lo `test -f 'sequence.c' || echo './'`sequence.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c sequence.c -o libgstruct_1.0_la-sequence.o
mv -f .deps/libgstruct_1.0_la-sequence.Tpo .deps/libgstruct_1.0_la-sequence.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c -o libgstruct_1.0_la-genome.lo `test -f 'genome.c' || echo './'`genome.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c genome.c -o libgstruct_1.0_la-genome.o
genome.c: In function ‘fill_buffer’:
genome.c:1218:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1218 | read(this->fd,gbuffer1,length);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘genomecomp_read_current’:
genome.c:329:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
329 | read(this->fd,buffer,4);
| ^~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:1374:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1374 | read(this->fd,gbuffer1,length);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:1451:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1451 | read(this->fd,gbuffer1,length);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘Genome_get_char’:
genome.c:1554:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1554 | read(this->fd,gbuffer1,/*length*/1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘Genome_ntcounts’:
genome.c:1710:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1710 | read(this->fd,gbuffer,length);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mv -f .deps/libgstruct_1.0_la-genome.Tpo .deps/libgstruct_1.0_la-genome.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c -o libgstruct_1.0_la-uinttable.lo `test -f 'uinttable.c' || echo './'`uinttable.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c uinttable.c -o libgstruct_1.0_la-uinttable.o
mv -f .deps/libgstruct_1.0_la-uinttable.Tpo .deps/libgstruct_1.0_la-uinttable.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c -o libgstruct_1.0_la-table.lo `test -f 'table.c' || echo './'`table.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c table.c -o libgstruct_1.0_la-table.o
mv -f .deps/libgstruct_1.0_la-table.Tpo .deps/libgstruct_1.0_la-table.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c -o libgstruct_1.0_la-chrnum.lo `test -f 'chrnum.c' || echo './'`chrnum.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c chrnum.c -o libgstruct_1.0_la-chrnum.o
mv -f .deps/libgstruct_1.0_la-chrnum.Tpo .deps/libgstruct_1.0_la-chrnum.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c -o libgstruct_1.0_la-bamread.lo `test -f 'bamread.c' || echo './'`bamread.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c bamread.c -o libgstruct_1.0_la-bamread.o
mv -f .deps/libgstruct_1.0_la-bamread.Tpo .deps/libgstruct_1.0_la-bamread.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c -o libgstruct_1.0_la-samread.lo `test -f 'samread.c' || echo './'`samread.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c samread.c -o libgstruct_1.0_la-samread.o
mv -f .deps/libgstruct_1.0_la-samread.Tpo .deps/libgstruct_1.0_la-samread.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c -o libgstruct_1.0_la-parserange.lo `test -f 'parserange.c' || echo './'`parserange.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c parserange.c -o libgstruct_1.0_la-parserange.o
mv -f .deps/libgstruct_1.0_la-parserange.Tpo .deps/libgstruct_1.0_la-parserange.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c -o libgstruct_1.0_la-tableuint.lo `test -f 'tableuint.c' || echo './'`tableuint.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c tableuint.c -o libgstruct_1.0_la-tableuint.o
mv -f .deps/libgstruct_1.0_la-tableuint.Tpo .deps/libgstruct_1.0_la-tableuint.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c -o libgstruct_1.0_la-iit-write.lo `test -f 'iit-write.c' || echo './'`iit-write.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c iit-write.c -o libgstruct_1.0_la-iit-write.o
mv -f .deps/libgstruct_1.0_la-iit-write.Tpo .deps/libgstruct_1.0_la-iit-write.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-ucharlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-ucharlist.Tpo -c -o libgstruct_1.0_la-ucharlist.lo `test -f 'ucharlist.c' || echo './'`ucharlist.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-ucharlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-ucharlist.Tpo -c ucharlist.c -o libgstruct_1.0_la-ucharlist.o
mv -f .deps/libgstruct_1.0_la-ucharlist.Tpo .deps/libgstruct_1.0_la-ucharlist.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c -o libgstruct_1.0_la-matchpool.lo `test -f 'matchpool.c' || echo './'`matchpool.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c matchpool.c -o libgstruct_1.0_la-matchpool.o
mv -f .deps/libgstruct_1.0_la-matchpool.Tpo .deps/libgstruct_1.0_la-matchpool.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c -o libgstruct_1.0_la-mismatchpool.lo `test -f 'mismatchpool.c' || echo './'`mismatchpool.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c mismatchpool.c -o libgstruct_1.0_la-mismatchpool.o
mv -f .deps/libgstruct_1.0_la-mismatchpool.Tpo .deps/libgstruct_1.0_la-mismatchpool.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c -o libgstruct_1.0_la-tally.lo `test -f 'tally.c' || echo './'`tally.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c tally.c -o libgstruct_1.0_la-tally.o
mv -f .deps/libgstruct_1.0_la-tally.Tpo .deps/libgstruct_1.0_la-tally.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c -o libgstruct_1.0_la-translation.lo `test -f 'translation.c' || echo './'`translation.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c translation.c -o libgstruct_1.0_la-translation.o
mv -f .deps/libgstruct_1.0_la-translation.Tpo .deps/libgstruct_1.0_la-translation.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c -o libgstruct_1.0_la-expr.lo `test -f 'expr.c' || echo './'`expr.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c expr.c -o libgstruct_1.0_la-expr.o
mv -f .deps/libgstruct_1.0_la-expr.Tpo .deps/libgstruct_1.0_la-expr.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c -o libgstruct_1.0_la-bamtally.lo `test -f 'bamtally.c' || echo './'`bamtally.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c bamtally.c -o libgstruct_1.0_la-bamtally.o
bamtally.c:7453:14: error: unknown type name ‘__m128i’
7453 | __m128i *passing_counts, int nreps, int nmult) {
| ^~~~~~~
bamtally.c:8190:21: error: unknown type name ‘__m128i’
8190 | get_passing_counts (__m128i *passing_counts, int readlength, Bamline_T *bamlines, int nreps, int minimum_quality_score) {
| ^~~~~~~
bamtally.c: In function ‘Bamtally_run’:
bamtally.c:8372:3: error: unknown type name ‘__m128i’
8372 | __m128i *passing_counts;
| ^~~~~~~
bamtally.c:8543:13: warning: implicit declaration of function ‘revise_read’; did you mean ‘revise_read_lh’? [-Wimplicit-function-declaration]
8543 | revise_read(alloc_tallies,chrstart,chrend,chrpos_low,chrpos_high,Bamline_flag(bamline_rep),
| ^~~~~~~~~~~
| revise_read_lh
bamtally.c:8551:31: error: ‘__m128i’ undeclared (first use in this function)
8551 | passing_counts = (__m128i *) _mm_malloc((nvectors + 1) * sizeof(__m128i),16);
| ^~~~~~~
bamtally.c:8551:31: note: each undeclared identifier is reported only once for each function it appears in
bamtally.c:8551:40: error: expected expression before ‘)’ token
8551 | passing_counts = (__m128i *) _mm_malloc((nvectors + 1) * sizeof(__m128i),16);
| ^
bamtally.c:8552:13: warning: implicit declaration of function ‘get_passing_counts’ [-Wimplicit-function-declaration]
8552 | get_passing_counts(passing_counts,readlength,&(bamlines[linei_start]),nreps,minimum_quality_score);
| ^~~~~~~~~~~~~~~~~~
bamtally.c:8559:13: warning: implicit declaration of function ‘_mm_free’; did you mean ‘Mem_free’? [-Wimplicit-function-declaration]
8559 | _mm_free(passing_counts);
| ^~~~~~~~
| Mem_free
bamtally.c:8792:40: error: expected expression before ‘)’ token
8792 | passing_counts = (__m128i *) _mm_malloc((nvectors + 1) * sizeof(__m128i),16);
| ^
bamtally.c: In function ‘Bamtally_expr’:
bamtally.c:8986:3: error: unknown type name ‘__m128i’
8986 | __m128i *passing_counts;
| ^~~~~~~
bamtally.c:9152:31: error: ‘__m128i’ undeclared (first use in this function)
9152 | passing_counts = (__m128i *) _mm_malloc((nvectors + 1) * sizeof(__m128i),16);
| ^~~~~~~
bamtally.c:9152:40: error: expected expression before ‘)’ token
9152 | passing_counts = (__m128i *) _mm_malloc((nvectors + 1) * sizeof(__m128i),16);
| ^
bamtally.c:9381:40: error: expected expression before ‘)’ token
9381 | passing_counts = (__m128i *) _mm_malloc((nvectors + 1) * sizeof(__m128i),16);
| ^
make[2]: *** [Makefile:1014: libgstruct_1.0_la-bamtally.lo] Error 1
make[2]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/gstruct/src'
make[1]: *** [Makefile:440: install-recursive] Error 1
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/gmapR/src/gstruct'
make: *** [Makefile:50: gstruct] Error 2
ERROR: compilation failed for package ‘gmapR’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/gmapR’