Mock Version: 1.2.13 ENTER do(['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/samtools.spec'], chrootPath='/var/lib/mock/epel-1-armhfp-588422776f2765478d24a2d81d5dd3911fe28fbd/root'shell=FalseprintOutput=Falseenv={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0logger=uid=996) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/samtools.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'} and shell False Building target platforms: armv7hl Building for target armv7hl Wrote: /builddir/build/SRPMS/samtools-0.1.19-7.el7.src.rpm Child return code was: 0 LEAVE do --> ENTER do(['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/samtools.spec '], chrootPath='/var/lib/mock/epel-1-armhfp-588422776f2765478d24a2d81d5dd3911fe28fbd/root'shell=Falseuid=996env={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0private_network=Truelogger=printOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/samtools.spec '] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'} and shell False Building target platforms: armv7hl Building for target armv7hl Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.9yW9Vg + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf samtools-0.1.19 + /usr/bin/bzip2 -dc /builddir/build/SOURCES/samtools-0.1.19.tar.bz2 + /usr/bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + cd samtools-0.1.19 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (samtools-0.1.14-soname.patch): + echo 'Patch #0 (samtools-0.1.14-soname.patch):' + /usr/bin/cat /builddir/build/SOURCES/samtools-0.1.14-soname.patch + /usr/bin/patch -p1 -b --suffix .soname --fuzz=0 patching file Makefile Hunk #1 succeeded at 84 (offset 6 lines). Patch #1 (samtools-0.1.19-faidx_fetch_seq2.patch): + echo 'Patch #1 (samtools-0.1.19-faidx_fetch_seq2.patch):' + /usr/bin/cat /builddir/build/SOURCES/samtools-0.1.19-faidx_fetch_seq2.patch + /usr/bin/patch -p1 -b --suffix .seq2 --fuzz=0 patching file faidx.c Patch #2 (samtools-0.1.19-R-fixes.patch): + echo 'Patch #2 (samtools-0.1.19-R-fixes.patch):' + /usr/bin/cat /builddir/build/SOURCES/samtools-0.1.19-R-fixes.patch + /usr/bin/patch -p1 -b --suffix .Rfixes --fuzz=0 patching file faidx.c patching file faidx.h + perl -pi -e 's[/software/bin/python][/usr/bin/python]' misc/varfilter.py + sed -i 's/\r//' misc/export2sam.pl + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.3xIJbF + umask 022 + cd /builddir/build/BUILD + cd samtools-0.1.19 + make 'CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard' dylib -j4 make[1]: Entering directory `/builddir/build/BUILD/samtools-0.1.19' rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib make[1]: Leaving directory `/builddir/build/BUILD/samtools-0.1.19' make[1]: Entering directory `/builddir/build/BUILD/samtools-0.1.19' gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o bgzf.c: In function 'worker_aux': bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] int i, tmp, stop = 0; ^ bgzf.c: In function 'bgzf_close': bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable] int ret, count, block_length; ^ gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o bam_import.c: In function 'append_text': bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"realloc failed to alloc %ld bytes\n", y); ^ bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat=] fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y); ^ bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=] bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat=] gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o bam_index.c: In function 'bam_index_load_core': bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(magic, 1, 4, fp); ^ bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&idx->n, 4, 1, fp); ^ bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&size, 4, 1, fp); ^ bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&key, 4, 1, fp); ^ bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&p->n, 4, 1, fp); ^ bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p->list, 16, p->n, fp); ^ bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&index2->n, 4, 1, fp); ^ bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(index2->offset, index2->n, 8, fp); ^ bam_pileup.c: In function 'resolve_cigar2': bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable] int k, is_head = 0; ^ gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o razf.c: In function 'razf_flush': razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^ razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^ razf.c: In function '_razf_write': razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^ razf.c: In function 'razf_close': razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->in, sizeof(int64_t)); ^ razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->out, sizeof(int64_t)); ^ razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^ razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^ razf.c: In function 'razf_end_flush': razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^ razf.c: In function 'save_zindex': razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] if(is_be) write(fd, &rz->index->size, sizeof(int)); ^ razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, &v32, sizeof(uint32_t)); ^ razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); ^ razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); ^ gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o In file included from knetfile.c:46:0: knetfile.c: In function 'kftp_send_cmd': knetfile.h:9:37: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^ knetfile.c:236:2: note: in expansion of macro 'netwrite' netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); ^ knetfile.c: In function 'khttp_connect_file': knetfile.h:9:37: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^ knetfile.c:415:2: note: in expansion of macro 'netwrite' netwrite(fp->fd, buf, l); ^ gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o bam_reheader.c: In function 'bam_reheader': bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable] bam_header_t *old; ^ gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o kprobaln.c: In function 'kpa_glocal': kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable] int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; ^ gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o gcc -shared -Wl,-soname,libbam.so.1 -o libbam.so.1 bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o -lc -lz make[1]: Leaving directory `/builddir/build/BUILD/samtools-0.1.19' + make 'CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC' samtools razip -j4 gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o make[1]: Entering directory `/builddir/build/BUILD/samtools-0.1.19' ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o make[1]: Leaving directory `/builddir/build/BUILD/samtools-0.1.19' make[1]: Entering directory `/builddir/build/BUILD/samtools-0.1.19/bcftools' gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o bcf.c: In function 'bcf_fmt_core': bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable] int iPL = -1; ^ gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o bcfutils.c: In function 'bcf_fit_alt': bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable] int ipl=-1, igt=-1; ^ gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o em.c: In function 'bcf_em1': em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable] int i, n, n2; ^ gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o make[1]: Leaving directory `/builddir/build/BUILD/samtools-0.1.19/bcftools' make[1]: Entering directory `/builddir/build/BUILD/samtools-0.1.19/misc' make[1]: Nothing to be done for `lib'. make[1]: Leaving directory `/builddir/build/BUILD/samtools-0.1.19/misc' gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o cut_target.c: In function 'main_cut_target': cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable] int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l; ^ gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o padding.c: In function 'bam_pad2unpad': padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=] fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l); ^ gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o razip.c: In function 'main': razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(f_dst, buffer, c); ^ razip.c: In function 'write_open': razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] scanf("%c", &c); ^ gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -o razip razip.o razf.o knetfile.o -lz gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread + cd misc/ + make 'CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC' -j4 gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -I.. md5.c -o md5.o gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -c -I.. -o md5fa.o md5fa.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -o maq2sam-short maq2sam.c -lz md5.c: In function 'MD5Final': md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((uint32_t *) ctx->in)[14] = ctx->bits[0]; ^ md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((uint32_t *) ctx->in)[15] = ctx->bits[1]; ^ md5.c:155:26: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess] memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ^ md5.c: In function 'MD5Final': md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((uint32_t *) ctx->in)[14] = ctx->bits[0]; ^ md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] ((uint32_t *) ctx->in)[15] = ctx->bits[1]; ^ md5.c:155:26: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess] memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ^ gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -c -I.. -o ace2sam.o ace2sam.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -c -I.. -o wgsim.o wgsim.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -c -I.. -o bamcheck.o bamcheck.c ace2sam.c: In function 'main': ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat=] fprintf(stderr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line ^ gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -o md5sum-lite md5sum-lite.o gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -o md5fa md5.o md5fa.o -lz gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -o wgsim wgsim.o -lm -lz gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -o ace2sam ace2sam.o -lz gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz + cd ../bcftools + make 'CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC' -j4 make[1]: Entering directory `/builddir/build/BUILD/samtools-0.1.19/bcftools' gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I.. call1.c -o call1.o gcc -c -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I.. main.c -o main.o gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[1]: Leaving directory `/builddir/build/BUILD/samtools-0.1.19/bcftools' + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.oj1Gse + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm '!=' / ']' + rm -rf /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm ++ dirname /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm + cd samtools-0.1.19 + rm -rf /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm + mkdir -p /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/bin + install -p samtools razip /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/bin + mkdir -p /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/include/samtools + install -p -m 644 bam.h bam2bcf.h bam_endian.h bam_tview.h bgzf.h errmod.h faidx.h kaln.h khash.h klist.h knetfile.h kprobaln.h kseq.h ksort.h kstring.h razf.h sam.h sam_header.h sample.h /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/include/samtools + mkdir -p /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/lib + strip libbam.so.1 + install -p -m 755 libbam.so.1 /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/lib + ln -sf libbam.so.1 /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/lib/libbam.so + mkdir -p /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/share/man/man1/ + cp -p samtools.1 /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/share/man/man1/ + cd misc/ + install -p blast2sam.pl bowtie2sam.pl export2sam.pl interpolate_sam.pl maq2sam-long maq2sam-short md5fa md5sum-lite novo2sam.pl psl2sam.pl sam2vcf.pl samtools.pl soap2sam.pl varfilter.py wgsim wgsim_eval.pl zoom2sam.pl /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/bin + cd ../bcftools/ + install -p bcftools vcfutils.pl /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/bin + mv README README.bcftools + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 /builddir/build/BUILD/samtools-0.1.19 extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/bin/md5fa extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/bin/samtools extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/bin/maq2sam-long extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/bin/maq2sam-short extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/bin/bcftools extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/bin/wgsim extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/bin/md5sum-lite extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/bin/razip /usr/lib/rpm/sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match. 1407 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-compress + /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/lib/rpm/redhat/brp-java-repack-jars Processing files: samtools-0.1.19-7.el7.armv7hl Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.OepAdg + umask 022 + cd /builddir/build/BUILD + cd samtools-0.1.19 + DOCDIR=/builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/share/doc/samtools-0.1.19 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/share/doc/samtools-0.1.19 + cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/share/doc/samtools-0.1.19 + cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/share/doc/samtools-0.1.19 + cp -pr COPYING /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/share/doc/samtools-0.1.19 + cp -pr INSTALL /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/share/doc/samtools-0.1.19 + cp -pr NEWS /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/share/doc/samtools-0.1.19 + cp -pr examples/ /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/share/doc/samtools-0.1.19 + cp -pr bcftools/README.bcftools /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/share/doc/samtools-0.1.19 + cp -pr bcftools/bcf.tex /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm/usr/share/doc/samtools-0.1.19 + exit 0 Provides: samtools = 0.1.19-7.el7 samtools(armv7hl-32) = 0.1.19-7.el7 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/env /usr/bin/perl /usr/bin/python ld-linux-armhf.so.3 ld-linux-armhf.so.3(GLIBC_2.4) libc.so.6 libc.so.6(GLIBC_2.15) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libgcc_s.so.1 libgcc_s.so.1(GCC_3.5) libm.so.6 libm.so.6(GLIBC_2.4) libncurses.so.5 libpthread.so.0 libpthread.so.0(GLIBC_2.4) libtinfo.so.5 libz.so.1 libz.so.1(ZLIB_1.2.0) libz.so.1(ZLIB_1.2.2) libz.so.1(ZLIB_1.2.3.3) perl(Carp) perl(Data::Dumper) perl(File::Spec) perl(Getopt::Long) perl(Getopt::Std) perl(List::Util) perl(constant) perl(strict) perl(warnings) rtld(GNU_HASH) Processing files: samtools-devel-0.1.19-7.el7.armv7hl Provides: samtools-devel = 0.1.19-7.el7 samtools-devel(armv7hl-32) = 0.1.19-7.el7 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libbam.so.1 Processing files: samtools-libs-0.1.19-7.el7.armv7hl Provides: libbam.so.1 samtools-libs = 0.1.19-7.el7 samtools-libs(armv7hl-32) = 0.1.19-7.el7 Requires(interp): /sbin/ldconfig /sbin/ldconfig Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires(post): /sbin/ldconfig Requires(postun): /sbin/ldconfig Requires: ld-linux-armhf.so.3 ld-linux-armhf.so.3(GLIBC_2.4) libc.so.6 libc.so.6(GLIBC_2.15) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libgcc_s.so.1 libgcc_s.so.1(GCC_3.5) libz.so.1 libz.so.1(ZLIB_1.2.0) libz.so.1(ZLIB_1.2.2) libz.so.1(ZLIB_1.2.3.3) rtld(GNU_HASH) Processing files: samtools-debuginfo-0.1.19-7.el7.armv7hl Provides: samtools-debuginfo = 0.1.19-7.el7 samtools-debuginfo(armv7hl-32) = 0.1.19-7.el7 Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm Wrote: /builddir/build/RPMS/samtools-0.1.19-7.el7.armv7hl.rpm Wrote: /builddir/build/RPMS/samtools-devel-0.1.19-7.el7.armv7hl.rpm Wrote: /builddir/build/RPMS/samtools-libs-0.1.19-7.el7.armv7hl.rpm Wrote: /builddir/build/RPMS/samtools-debuginfo-0.1.19-7.el7.armv7hl.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.qopgN3 + umask 022 + cd /builddir/build/BUILD + cd samtools-0.1.19 + rm -rf /builddir/build/BUILDROOT/samtools-0.1.19-7.el7.arm + exit 0 Child return code was: 0 LEAVE do -->