Mock Version: 1.4.15 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/msisensor.spec'], chrootPath='/var/lib/mock/915389-epel-7-x86_64-1558721106.027813/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.lu32fhk9:/etc/resolv.conf']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.lu32fhk9:/etc/resolv.conf'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'bbd3a93f5fc94255927cb7ac9b0a6feb', '-D', '/var/lib/mock/915389-epel-7-x86_64-1558721106.027813/root', '-a', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.lu32fhk9:/etc/resolv.conf', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=en_US.UTF-8', '-u', 'mockbuild', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/msisensor.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/msisensor-0.6-1.el7.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/msisensor.spec'], chrootPath='/var/lib/mock/915389-epel-7-x86_64-1558721106.027813/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.lu32fhk9:/etc/resolv.conf']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.lu32fhk9:/etc/resolv.conf'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '61c976ed5a1e47bd86d26583efa20d60', '-D', '/var/lib/mock/915389-epel-7-x86_64-1558721106.027813/root', '-a', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.lu32fhk9:/etc/resolv.conf', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=en_US.UTF-8', '-u', 'mockbuild', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/msisensor.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.SwqIr9 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf msisensor-0.6 + /usr/bin/gzip -dc /builddir/build/SOURCES/msisensor-0.6.tar.gz + /usr/bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + cd msisensor-0.6 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.CB6Inw + umask 022 + cd /builddir/build/BUILD + cd msisensor-0.6 + make make -C vendor/samtools-0.1.19 make[1]: Entering directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19' make[2]: Entering directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19' make[3]: Entering directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o BUILDSTDERR: bgzf.c: In function 'worker_aux': BUILDSTDERR: bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] BUILDSTDERR: int i, tmp, stop = 0; BUILDSTDERR: ^ BUILDSTDERR: bgzf.c: In function 'bgzf_close': BUILDSTDERR: bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable] BUILDSTDERR: int ret, count, block_length; BUILDSTDERR: ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -g -Wall -O2 -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 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -Wall -O2 -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 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o BUILDSTDERR: bam_pileup.c: In function 'resolve_cigar2': BUILDSTDERR: bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable] BUILDSTDERR: int k, is_head = 0; BUILDSTDERR: ^ gcc -c -g -Wall -O2 -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 -g -Wall -O2 -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 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o gcc -c -g -Wall -O2 -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 -g -Wall -O2 -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 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o BUILDSTDERR: bam_reheader.c: In function 'bam_reheader': BUILDSTDERR: bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable] BUILDSTDERR: bam_header_t *old; BUILDSTDERR: ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o BUILDSTDERR: kprobaln.c: In function 'kpa_glocal': BUILDSTDERR: kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable] BUILDSTDERR: int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; BUILDSTDERR: ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o 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[3]: Leaving directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19' make[3]: Entering directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19/bcftools' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o BUILDSTDERR: bcf.c: In function 'bcf_fmt_core': BUILDSTDERR: bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable] BUILDSTDERR: int iPL = -1; BUILDSTDERR: ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o BUILDSTDERR: bcfutils.c: In function 'bcf_fit_alt': BUILDSTDERR: bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable] BUILDSTDERR: int ipl=-1, igt=-1; BUILDSTDERR: ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o BUILDSTDERR: em.c: In function 'bcf_em1': BUILDSTDERR: em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable] BUILDSTDERR: int i, n, n2; BUILDSTDERR: ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.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[3]: Leaving directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19/bcftools' make[3]: Entering directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19/misc' make[3]: Nothing to be done for `lib'. make[3]: Leaving directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19/misc' gcc -c -g -Wall -O2 -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 -g -Wall -O2 -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 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -Wall -O2 -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 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -Wall -O2 -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 -g -Wall -O2 -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 -g -Wall -O2 -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 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o BUILDSTDERR: cut_target.c: In function 'main_cut_target': BUILDSTDERR: cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable] BUILDSTDERR: int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l; BUILDSTDERR: ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o gcc -c -g -Wall -O2 -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 -g -Wall -O2 -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 -g -Wall -O2 -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 -lncurses -ltinfo -lm -lz -lpthread make[2]: Leaving directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19' make[2]: Entering directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19/bcftools' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[2]: Leaving directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19/bcftools' make[2]: Entering directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19/misc' gcc -c -g -Wall -O2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c BUILDSTDERR: md5.c: In function 'MD5Final': BUILDSTDERR: md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] BUILDSTDERR: ((uint32_t *) ctx->in)[14] = ctx->bits[0]; BUILDSTDERR: ^ BUILDSTDERR: md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] BUILDSTDERR: ((uint32_t *) ctx->in)[15] = ctx->bits[1]; BUILDSTDERR: ^ BUILDSTDERR: 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] BUILDSTDERR: memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ BUILDSTDERR: ^ gcc -g -Wall -O2 -o md5sum-lite md5sum-lite.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o BUILDSTDERR: md5.c: In function 'MD5Final': BUILDSTDERR: md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] BUILDSTDERR: ((uint32_t *) ctx->in)[14] = ctx->bits[0]; BUILDSTDERR: ^ BUILDSTDERR: md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] BUILDSTDERR: ((uint32_t *) ctx->in)[15] = ctx->bits[1]; BUILDSTDERR: ^ BUILDSTDERR: 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] BUILDSTDERR: memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ BUILDSTDERR: ^ gcc -g -Wall -O2 -c -I.. -o md5fa.o md5fa.c gcc -g -Wall -O2 -o md5fa md5.o md5fa.o -lz gcc -g -Wall -O2 -o maq2sam-short maq2sam.c -lz gcc -g -Wall -O2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz gcc -g -Wall -O2 -c -I.. -o ace2sam.o ace2sam.c gcc -g -Wall -O2 -o ace2sam ace2sam.o -lz gcc -g -Wall -O2 -c -I.. -o wgsim.o wgsim.c gcc -g -Wall -O2 -o wgsim wgsim.o -lm -lz gcc -g -Wall -O2 -c -I.. -o bamcheck.o bamcheck.c gcc -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz make[2]: Leaving directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19/misc' make[1]: Leaving directory `/builddir/build/BUILD/msisensor-0.6/vendor/samtools-0.1.19' g++ -O2 -fopenmp -Ivendor/samtools-0.1.19 -c cmds.cpp -o cmds.o g++ -O2 -fopenmp -Ivendor/samtools-0.1.19 -c scan.cpp -o scan.o g++ -O2 -fopenmp -Ivendor/samtools-0.1.19 -c distribution.cpp -o distribution.o g++ -O2 -fopenmp -Ivendor/samtools-0.1.19 -c refseq.cpp -o refseq.o g++ -O2 -fopenmp -Ivendor/samtools-0.1.19 -c polyscan.cpp -o polyscan.o g++ -O2 -fopenmp -Ivendor/samtools-0.1.19 -c param.cpp -o param.o g++ -O2 -fopenmp -Ivendor/samtools-0.1.19 -c utilities.cpp -o utilities.o g++ -O2 -fopenmp -Ivendor/samtools-0.1.19 -c homo.cpp -o homo.o g++ -O2 -fopenmp -Ivendor/samtools-0.1.19 -c window.cpp -o window.o g++ -O2 -fopenmp -Ivendor/samtools-0.1.19 -c bamreader.cpp -o bamreader.o g++ -O2 -fopenmp -Ivendor/samtools-0.1.19 -c sample.cpp -o sample.o g++ -O2 -fopenmp -Ivendor/samtools-0.1.19 -c chi.cpp -o chi.o g++ -O2 -fopenmp -Ivendor/samtools-0.1.19 -c somatic.cpp -o somatic.o g++ cmds.o scan.o distribution.o refseq.o polyscan.o param.o utilities.o homo.o window.o bamreader.o sample.o chi.o somatic.o -O2 -fopenmp -Lvendor/samtools-0.1.19 -lm -lbam -lz -lpthread -o msisensor + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.yqQ4Qj + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/msisensor-0.6-1.el7.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/msisensor-0.6-1.el7.x86_64 BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/msisensor-0.6-1.el7.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/msisensor-0.6-1.el7.x86_64 + cd msisensor-0.6 + mkdir -p /builddir/build/BUILDROOT/msisensor-0.6-1.el7.x86_64/usr/bin + install -m 0755 -p msisensor /builddir/build/BUILDROOT/msisensor-0.6-1.el7.x86_64/usr/bin/msisensor + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 /builddir/build/BUILD/msisensor-0.6 extracting debug info from /builddir/build/BUILDROOT/msisensor-0.6-1.el7.x86_64/usr/bin/msisensor BUILDSTDERR: dwz: Too few files for multifile optimization /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. BUILDSTDERR: 379 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: msisensor-0.6-1.el7.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.cpRV37 + umask 022 + cd /builddir/build/BUILD + cd msisensor-0.6 + DOCDIR=/builddir/build/BUILDROOT/msisensor-0.6-1.el7.x86_64/usr/share/doc/msisensor-0.6 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/msisensor-0.6-1.el7.x86_64/usr/share/doc/msisensor-0.6 + cp -pr README.md /builddir/build/BUILDROOT/msisensor-0.6-1.el7.x86_64/usr/share/doc/msisensor-0.6 + cp -pr vendor/samtools-0.1.19/examples/00README.txt /builddir/build/BUILDROOT/msisensor-0.6-1.el7.x86_64/usr/share/doc/msisensor-0.6 + cp -pr LICENSE /builddir/build/BUILDROOT/msisensor-0.6-1.el7.x86_64/usr/share/doc/msisensor-0.6 + exit 0 Provides: msisensor = 0.6-1.el7 msisensor(x86-64) = 0.6-1.el7 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.7)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libpthread.so.0(GLIBC_2.3.2)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) libz.so.1(ZLIB_1.2.3.3)(64bit) rtld(GNU_HASH) Processing files: msisensor-debuginfo-0.6-1.el7.x86_64 Provides: msisensor-debuginfo = 0.6-1.el7 msisensor-debuginfo(x86-64) = 0.6-1.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/msisensor-0.6-1.el7.x86_64 Wrote: /builddir/build/RPMS/msisensor-0.6-1.el7.x86_64.rpm Wrote: /builddir/build/RPMS/msisensor-debuginfo-0.6-1.el7.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.icjMKz + umask 022 + cd /builddir/build/BUILD + cd msisensor-0.6 + rm -rf /builddir/build/BUILDROOT/msisensor-0.6-1.el7.x86_64 + exit 0 Child return code was: 0