Mock Version: 1.4.9
Mock Version: 1.4.9
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/samtools.spec'], chrootPath='/var/lib/mock/f29-build-24936-13000/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x2001fd66a0>timeout=345600uid=998gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/samtools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'} and shell False
Building target platforms: riscv64
Building for target riscv64
Wrote: /builddir/build/SRPMS/samtools-0.1.19-16.fc29.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/samtools.spec'], chrootPath='/var/lib/mock/f29-build-24936-13000/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x2001fd66a0>timeout=345600uid=998gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/samtools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'} and shell False
Building target platforms: riscv64
Building for target riscv64
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.p7XXn9
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf samtools-0.1.19
+ /usr/bin/tar -xof -
+ /usr/bin/bzip2 -dc /builddir/build/SOURCES/samtools-0.1.19.tar.bz2
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd samtools-0.1.19
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ echo 'Patch #0 (samtools-0.1.14-soname.patch):'
Patch #0 (samtools-0.1.14-soname.patch):
+ /usr/bin/patch --no-backup-if-mismatch -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/patch --no-backup-if-mismatch -p1 -b --suffix .seq2 --fuzz=0
patching file faidx.c
+ echo 'Patch #2 (samtools-0.1.19-R-fixes.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .Rfixes --fuzz=0
Patch #2 (samtools-0.1.19-R-fixes.patch):
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.DaOjvC
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-0.1.19
+ make 'CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' 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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.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 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -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 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
BUILDSTDERR: bam_index.c: In function 'bam_index_load_core':
BUILDSTDERR: bam_index.c:335:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   fread(magic, 1, 4, fp);
BUILDSTDERR:   ^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: bam_index.c:342:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   fread(&idx->n, 4, 1, fp);
BUILDSTDERR:   ^~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: bam_index.c:355:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    fread(&size, 4, 1, fp);
BUILDSTDERR:    ^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: bam_index.c:358:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:     fread(&key, 4, 1, fp);
BUILDSTDERR:     ^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: bam_index.c:362:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:     fread(&p->n, 4, 1, fp);
BUILDSTDERR:     ^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: bam_index.c:366:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:     fread(p->list, 16, p->n, fp);
BUILDSTDERR:     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: bam_index.c:376:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    fread(&index2->n, 4, 1, fp);
BUILDSTDERR:    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: bam_index.c:380:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    fread(index2->offset, index2->n, 8, fp);
BUILDSTDERR:    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -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 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
BUILDSTDERR: razf.c: In function 'razf_flush':
BUILDSTDERR: razf.c:221:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
BUILDSTDERR:    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: razf.c:234:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:     write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
BUILDSTDERR:     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: razf.c: In function '_razf_write':
BUILDSTDERR: razf.c:201:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
BUILDSTDERR:    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: razf.c: In function 'razf_close':
BUILDSTDERR: razf.c:804:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:     write(rz->x.fpw, &rz->in, sizeof(int64_t));
BUILDSTDERR:     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: razf.c:805:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:     write(rz->x.fpw, &rz->out, sizeof(int64_t));
BUILDSTDERR:     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: razf.c:808:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:     write(rz->x.fpw, &v64, sizeof(int64_t));
BUILDSTDERR:     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: razf.c:810:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:     write(rz->x.fpw, &v64, sizeof(int64_t));
BUILDSTDERR:     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: razf.c: In function 'razf_end_flush':
BUILDSTDERR: razf.c:258:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:     write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
BUILDSTDERR:     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: razf.c: In function 'save_zindex':
BUILDSTDERR: razf.c:96:12: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   if(is_be) write(fd, &rz->index->size, sizeof(int));
BUILDSTDERR:             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: razf.c:99:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:    write(fd, &v32, sizeof(uint32_t));
BUILDSTDERR:    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: razf.c:106:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
BUILDSTDERR:   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: razf.c:107:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
BUILDSTDERR:   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
BUILDSTDERR: faidx.c: In function 'fai_load0':
BUILDSTDERR: faidx.c:309:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:      else
BUILDSTDERR:      ^~~~
BUILDSTDERR: faidx.c:312:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:   if (fp == 0) {
BUILDSTDERR:   ^~
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
BUILDSTDERR: In file included from knetfile.c:46:
BUILDSTDERR: knetfile.c: In function 'kftp_send_cmd':
BUILDSTDERR: knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:  #define netwrite(fd, ptr, len) write(fd, ptr, len)
BUILDSTDERR:                                 ^~~~~~~~~~~~~~~~~~~
BUILDSTDERR: knetfile.c:236:2: note: in expansion of macro 'netwrite'
BUILDSTDERR:   netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
BUILDSTDERR:   ^~~~~~~~
BUILDSTDERR: knetfile.c: In function 'khttp_connect_file':
BUILDSTDERR: knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:  #define netwrite(fd, ptr, len) write(fd, ptr, len)
BUILDSTDERR:                                 ^~~~~~~~~~~~~~~~~~~
BUILDSTDERR: knetfile.c:415:2: note: in expansion of macro 'netwrite'
BUILDSTDERR:   netwrite(fp->fd, buf, l);
BUILDSTDERR:   ^~~~~~~~
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -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 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -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 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC' samtools razip -j4
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -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 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -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:          ^~~
BUILDSTDERR: bcfutils.c: In function 'bcf_fix_gt':
BUILDSTDERR: bcfutils.c:254:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:      else
BUILDSTDERR:      ^~~~
BUILDSTDERR: bcfutils.c:256:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:   b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
BUILDSTDERR:   ^
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -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 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -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 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
BUILDSTDERR: bam2bcf.c: In function 'bcf_call2bcf':
BUILDSTDERR: bam2bcf.c:428:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:      if (bc->read_pos_bias != -1 )
BUILDSTDERR:      ^~
BUILDSTDERR: bam2bcf.c:430:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
BUILDSTDERR:   kputc('\0', &s);
BUILDSTDERR:   ^~~~~
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
BUILDSTDERR: bam2bcf_indel.c: In function 'bcf_call_add_rg':
BUILDSTDERR: bam2bcf_indel.c:32:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:     for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
BUILDSTDERR:     ^~~
BUILDSTDERR: bam2bcf_indel.c:32:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
BUILDSTDERR:     for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
BUILDSTDERR:                                                       ^~
BUILDSTDERR: bam2bcf_indel.c:33:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:     for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
BUILDSTDERR:     ^~~
BUILDSTDERR: bam2bcf_indel.c:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
BUILDSTDERR:     for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
BUILDSTDERR:                                                       ^~
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
BUILDSTDERR: errmod.c: In function 'errmod_cal':
BUILDSTDERR: errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare]
BUILDSTDERR:   if (m > m) return -1;
BUILDSTDERR:         ^
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.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'
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:                                     ^~~~~~~
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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
BUILDSTDERR: bam2depth.c: In function 'main_depth':
BUILDSTDERR: bam2depth.c:85:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:      else
BUILDSTDERR:      ^~~~
BUILDSTDERR: bam2depth.c:87:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:   data = calloc(n, sizeof(void*)); // data[i] for the i-th input
BUILDSTDERR:   ^~~~
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
BUILDSTDERR: razip.c: In function 'main':
BUILDSTDERR: razip.c:131:5: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:      write(f_dst, buffer, c);
BUILDSTDERR:      ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: razip.c: In function 'write_open':
BUILDSTDERR: razip.c:32:4: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:     scanf("%c", &c);
BUILDSTDERR:     ^~~~~~~~~~~~~~~
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -o razip razip.o razf.o knetfile.o -lz
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC' -j4
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -I.. md5.c -o md5.o
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -o maq2sam-short maq2sam.c -lz
BUILDSTDERR: md5.c: In function 'MD5Final':
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:                           ^
BUILDSTDERR: md5.c: In function 'MD5Final':
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 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -c -I.. -o ace2sam.o ace2sam.c
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -c -I.. -o wgsim.o wgsim.c
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -c -I.. -o bamcheck.o bamcheck.c
BUILDSTDERR: ace2sam.c: In function 'main':
BUILDSTDERR: ace2sam.c:162:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:     if (write_cns) puts(t[4].s); t[4].l = 0;
BUILDSTDERR:     ^~
BUILDSTDERR: ace2sam.c:162:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
BUILDSTDERR:     if (write_cns) puts(t[4].s); t[4].l = 0;
BUILDSTDERR:                                  ^
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -o md5sum-lite md5sum-lite.o
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -o md5fa md5.o md5fa.o -lz
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -o wgsim wgsim.o -lm -lz
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -o ace2sam ace2sam.o -lz
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+ cd ../bcftools
+ make 'CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC' -j4
make[1]: Entering directory '/builddir/build/BUILD/samtools-0.1.19/bcftools'
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I..  call1.c -o call1.o
gcc -c -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I..  main.c -o main.o
BUILDSTDERR: call1.c: In function 'write_header':
BUILDSTDERR: call1.c:303:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:      if (!strstr(str.s, "##FORMAT=<ID=GL,"))
BUILDSTDERR:      ^~
BUILDSTDERR: call1.c:305:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
BUILDSTDERR:   if (!strstr(str.s, "##FORMAT=<ID=DP,"))
BUILDSTDERR:   ^~
gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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.RMz6HE
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64
BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64
+ cd samtools-0.1.19
+ rm -rf /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64
+ mkdir -p /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin
+ install -p samtools razip /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin
+ mkdir -p /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/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-0.1.19-16.fc29.riscv64/usr/include/samtools
+ mkdir -p /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/lib64
+ strip libbam.so.1
+ install -p -m 755 libbam.so.1 /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/lib64
+ ln -sf libbam.so.1 /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/lib64/libbam.so
+ mkdir -p /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/share/man/man1/
+ cp -p samtools.1 /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/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-0.1.19-16.fc29.riscv64/usr/bin
+ cd ../bcftools/
+ install -p bcftools vcfutils.pl /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin
+ mv README README.bcftools
+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 0.1.19-16.fc29 --unique-debug-suffix -0.1.19-16.fc29.riscv64 --unique-debug-src-base samtools-0.1.19-16.fc29.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/samtools-0.1.19
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/maq2sam-short
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/samtools
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/razip
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/maq2sam-long
extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/maq2sam-short
extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/razip
extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/samtools
extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/maq2sam-long
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/md5fa
extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/md5fa
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/bcftools
extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/bcftools
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/wgsim
extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/wgsim
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/md5sum-lite
extracting debug info from /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/bin/md5sum-lite
/usr/lib/rpm/sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match.
BUILDSTDERR: 1407 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
BUILDSTDERR: /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 1
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
mangling shebang in /usr/bin/export2sam.pl from /usr/bin/env perl to #!/usr/bin/perl
BUILDSTDERR: *** WARNING: mangling shebang in /usr/bin/varfilter.py from #!/usr/bin/python to #!/usr/bin/python2. This will become an ERROR, fix it manually!
Processing files: samtools-0.1.19-16.fc29.riscv64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.fgR50p
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-0.1.19
+ DOCDIR=/builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/share/doc/samtools
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/share/doc/samtools
+ cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/share/doc/samtools
+ cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/share/doc/samtools
+ cp -pr COPYING /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/share/doc/samtools
+ cp -pr INSTALL /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/share/doc/samtools
+ cp -pr NEWS /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/share/doc/samtools
+ cp -pr examples/ /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/share/doc/samtools
+ cp -pr bcftools/README.bcftools /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/share/doc/samtools
+ cp -pr bcftools/bcf.tex /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64/usr/share/doc/samtools
+ exit 0
Provides: samtools = 0.1.19-16.fc29 samtools(riscv-64) = 0.1.19-16.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl /usr/bin/python2 ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libncurses.so.6()(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.27)(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) libz.so.1(ZLIB_1.2.2)(64bit) libz.so.1(ZLIB_1.2.3.3)(64bit) 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-0.1.19-16.fc29.riscv64
Provides: samtools-devel = 0.1.19-16.fc29 samtools-devel(riscv-64) = 0.1.19-16.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libbam.so.1()(64bit)
Processing files: samtools-libs-0.1.19-16.fc29.riscv64
Provides: libbam.so.1()(64bit) samtools-libs = 0.1.19-16.fc29 samtools-libs(riscv-64) = 0.1.19-16.fc29
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-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) libz.so.1(ZLIB_1.2.2)(64bit) libz.so.1(ZLIB_1.2.3.3)(64bit) rtld(GNU_HASH)
Processing files: samtools-debugsource-0.1.19-16.fc29.riscv64
Provides: samtools-debugsource = 0.1.19-16.fc29 samtools-debugsource(riscv-64) = 0.1.19-16.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: samtools-debuginfo-0.1.19-16.fc29.riscv64
Provides: debuginfo(build-id) = 066cccdd6d6965a50da9caa7c08364747ba573f5 debuginfo(build-id) = 08d8b11d23ba4ee6a651ab138db875ea065a8dca debuginfo(build-id) = 090a2d635d9bc39e4601fe935b7f0b6ca3e32ca4 debuginfo(build-id) = 1d58c1c56ac18ec41ec274c4565351fe25d118a5 debuginfo(build-id) = 2c0eb7dd525d4b11ad3a3ff4160d839dccaece35 debuginfo(build-id) = 5c5623f8ce6a97854a20a576804454a4c8d58d95 debuginfo(build-id) = 72a06e0d085e7d000ce4941e51ac70a4f4670600 debuginfo(build-id) = e65295c12e66710a058748df758daff7e7ab9afd samtools-debuginfo = 0.1.19-16.fc29 samtools-debuginfo(riscv-64) = 0.1.19-16.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: samtools-debugsource(riscv-64) = 0.1.19-16.fc29
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64
Wrote: /builddir/build/RPMS/samtools-0.1.19-16.fc29.riscv64.rpm
Wrote: /builddir/build/RPMS/samtools-devel-0.1.19-16.fc29.riscv64.rpm
Wrote: /builddir/build/RPMS/samtools-libs-0.1.19-16.fc29.riscv64.rpm
Wrote: /builddir/build/RPMS/samtools-debugsource-0.1.19-16.fc29.riscv64.rpm
Wrote: /builddir/build/RPMS/samtools-debuginfo-0.1.19-16.fc29.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.epA99E
+ umask 022
+ cd /builddir/build/BUILD
+ cd samtools-0.1.19
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-0.1.19-16.fc29.riscv64
+ exit 0
Child return code was: 0