Mock Version: 3.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64le --nodeps /builddir/build/SPECS/R-GenomicAlignments.spec'], chrootPath='/var/lib/mock/fedora-rawhide-ppc64le-1671754479.045306/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': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fff8fd952d0>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fx6ja7r5:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fx6ja7r5:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'bed7e69707b1419b8c8bf7130a169a62', '-D', '/var/lib/mock/fedora-rawhide-ppc64le-1671754479.045306/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fx6ja7r5:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--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;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64le --nodeps /builddir/build/SPECS/R-GenomicAlignments.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': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1662163200
Wrote: /builddir/build/SRPMS/R-GenomicAlignments-1.32.1-1.fc38.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64le --nodeps /builddir/build/SPECS/R-GenomicAlignments.spec'], chrootPath='/var/lib/mock/fedora-rawhide-ppc64le-1671754479.045306/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': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fff8fd952d0>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fx6ja7r5:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fx6ja7r5:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '6017e083b0b648c9a328031018af3c5a', '-D', '/var/lib/mock/fedora-rawhide-ppc64le-1671754479.045306/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fx6ja7r5:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--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;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64le --nodeps /builddir/build/SPECS/R-GenomicAlignments.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': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1662163200
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.hEBBiK
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf GenomicAlignments
+ /usr/bin/mkdir -p GenomicAlignments
+ cd GenomicAlignments
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/GenomicAlignments_1.32.1.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.CwqXri
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd GenomicAlignments
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.3zHuv3
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-1.fc38.ppc64le '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-1.fc38.ppc64le
++ dirname /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-1.fc38.ppc64le
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-1.fc38.ppc64le
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd GenomicAlignments
+ mkdir -p /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-1.fc38.ppc64le/usr/lib64/R/library
+ R CMD INSTALL GenomicAlignments -l /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-1.fc38.ppc64le/usr/lib64/R/library
* installing *source* package 'GenomicAlignments' ...
** using staged installation
** libs
gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I/usr/local/include -fPIC -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I/usr/local/include -fPIC -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I/usr/local/include -fPIC -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I/usr/local/include -fPIC -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:658:48: warning: 'range_buf2' may be used uninitialized [-Wmaybe-uninitialized]
658 | range_buf1 = range_buf2->elts[*f_elt - 1];
| ~~~~~~~~~~^~~~~~
cigar_utils.c:591:22: note: 'range_buf2' was declared here
591 | IntPairAEAE *range_buf2;
| ^~~~~~~~~~
cigar_utils.c:674:37: warning: 'breakpoint' may be used uninitialized [-Wmaybe-uninitialized]
674 | *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
| ~~~~~~~~~~~^~~
cigar_utils.c:588:62: note: 'breakpoint' was declared here
588 | int cigar_len, space0, pos_len, f_is_NULL, ans_len, *breakpoint,
| ^~~~~~~~~~
cigar_utils.c:626:29: warning: 'flag_elt' may be used uninitialized [-Wmaybe-uninitialized]
626 | if (*flag_elt == NA_INTEGER) {
| ^~~~~~~~~
cigar_utils.c:593:20: note: 'flag_elt' was declared here
593 | const int *flag_elt, *pos_elt, *f_elt;
| ^~~~~~~~
cigar_utils.c:656:29: warning: 'f_elt' may be used uninitialized [-Wmaybe-uninitialized]
656 | if (*f_elt == NA_INTEGER)
| ^~~~~~
cigar_utils.c:593:41: note: 'f_elt' was declared here
593 | const int *flag_elt, *pos_elt, *f_elt;
| ^~~~~
In function 'parse_cigar_ranges',
inlined from 'cigar_ranges' at cigar_utils.c:660:12:
cigar_utils.c:213:21: warning: 'range_buf1' may be used uninitialized [-Wmaybe-uninitialized]
213 | buf_nelt0 = IntPairAE_get_nelt(range_buf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:590:20: note: 'range_buf1' was declared here
590 | IntPairAE *range_buf1;
| ^~~~~~~~~~
In file included from /usr/include/R/Rdefines.h:41,
from GenomicAlignments.h:1,
from cigar_utils.c:1:
In function 'make_CompressedIRangesList',
inlined from 'cigar_ranges' at cigar_utils.c:680:2:
cigar_utils.c:542:25: warning: 'ans_breakpoints' may be used uninitialized [-Wmaybe-uninitialized]
542 | new_PartitioningByEnd("PartitioningByEnd",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
543 | breakpoints, NULL));
| ~~~~~~~~~~~~~~~~~~
/usr/include/R/Rinternals.h:367:36: note: in definition of macro 'PROTECT'
367 | #define PROTECT(s) Rf_protect(s)
| ^
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:587:19: note: 'ans_breakpoints' was declared here
587 | SEXP ans, ans_breakpoints, f_levels, cigar_elt;
| ^~~~~~~~~~~~~~~
In function 'make_list_of_IRanges',
inlined from 'cigar_ranges' at cigar_utils.c:679:10:
/usr/include/R/Rinternals.h:891:33: warning: 'f_levels' may be used uninitialized [-Wmaybe-uninitialized]
891 | #define duplicate Rf_duplicate
/usr/include/R/Rinternals.h:367:36: note: in definition of macro 'PROTECT'
367 | #define PROTECT(s) Rf_protect(s)
| ^
cigar_utils.c:522:29: note: in expansion of macro 'duplicate'
522 | PROTECT(ans_names = duplicate(names));
| ^~~~~~~~~
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:587:36: note: 'f_levels' was declared here
587 | SEXP ans, ans_breakpoints, f_levels, cigar_elt;
| ^~~~~~~~
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:708:29: warning: 'flag_elt' may be used uninitialized [-Wmaybe-uninitialized]
708 | if (*flag_elt == NA_INTEGER) {
| ^~~~~~~~~
cigar_utils.c:698:20: note: 'flag_elt' was declared here
698 | const int *flag_elt;
| ^~~~~~~~
In function 'narrow_cigar_string',
inlined from 'cigar_narrow' at cigar_utils.c:920:12:
cigar_utils.c:872:12: warning: 'Loffset' may be used uninitialized [-Wmaybe-uninitialized]
872 | if (Roffset < Loffset) {
| ^
cigar_utils.c: In function 'cigar_narrow':
cigar_utils.c:854:13: note: 'Loffset' was declared here
854 | int Loffset, Roffset, buf_offset;
| ^~~~~~~
In function 'narrow_cigar_string',
inlined from 'cigar_narrow' at cigar_utils.c:920:12:
cigar_utils.c:872:12: warning: 'Roffset' may be used uninitialized [-Wmaybe-uninitialized]
872 | if (Roffset < Loffset) {
| ^
cigar_utils.c: In function 'cigar_narrow':
cigar_utils.c:854:22: note: 'Roffset' was declared here
854 | int Loffset, Roffset, buf_offset;
| ^~~~~~~
In function 'qnarrow_cigar_string',
inlined from 'cigar_qnarrow' at cigar_utils.c:1116:12:
cigar_utils.c:1063:12: warning: 'Loffset' may be used uninitialized [-Wmaybe-uninitialized]
1063 | if (Roffset < Loffset) {
| ^
cigar_utils.c: In function 'cigar_qnarrow':
cigar_utils.c:1045:13: note: 'Loffset' was declared here
1045 | int Loffset, Roffset, buf_offset;
| ^~~~~~~
In function 'qnarrow_cigar_string',
inlined from 'cigar_qnarrow' at cigar_utils.c:1116:12:
cigar_utils.c:1063:12: warning: 'Roffset' may be used uninitialized [-Wmaybe-uninitialized]
1063 | if (Roffset < Loffset) {
| ^
cigar_utils.c: In function 'cigar_qnarrow':
cigar_utils.c:1045:22: note: 'Roffset' was declared here
1045 | int Loffset, Roffset, buf_offset;
| ^~~~~~~
gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I/usr/local/include -fPIC -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
coordinate_mapping_methods.c: In function 'to_query':
coordinate_mapping_methods.c:64:21: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized]
64 | if (query_loc < 0 || n == 0)
| ~~~~~~~~~~~~~~^~~~~~~~~
coordinate_mapping_methods.c:17:7: note: 'n' was declared here
17 | int n, offset = 0, OPL, query_consumed = 0;
| ^
coordinate_mapping_methods.c: In function 'to_ref':
coordinate_mapping_methods.c:219:6: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized]
219 | if (n == 0)
| ^
coordinate_mapping_methods.c:172:7: note: 'n' was declared here
172 | int n, offset = 0, OPL, query_consumed = 0;
| ^
gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I/usr/local/include -fPIC -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
In function 'unsafe_overlap_encoding',
inlined from 'overlap_encoding' at encodeOverlaps_methods.c:209:2:
encodeOverlaps_methods.c:182:9: warning: 'out_nelt0' may be used uninitialized [-Wmaybe-uninitialized]
182 | CharAE_delete_at(out, out_nelt0, j1 * nrow);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
encodeOverlaps_methods.c: In function 'overlap_encoding':
encodeOverlaps_methods.c:99:13: note: 'out_nelt0' was declared here
99 | int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
| ^~~~~~~~~
gcc -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/usr/lib64/R/lib -lR
installing to /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-1.fc38.ppc64le/usr/lib64/R/library/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GenomicAlignments'
finding HTML links ... done
GAlignmentPairs-class html
finding level-2 HTML links ... done
GAlignments-class html
GAlignmentsList-class html
GappedReads-class html
OverlapEncodings-class html
cigar-utils html
coordinate-mapping-methods html
coverage-methods html
encodeOverlaps-methods html
findCompatibleOverlaps-methods html
findMateAlignment html
findOverlaps-methods html
findSpliceOverlaps-methods html
intra-range-methods html
junctions-methods html
pileLettersAt html
readGAlignments html
sequenceLayer html
setops-methods html
stackStringsFromGAlignments html
summarizeOverlaps-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicAlignments)
+ test -d GenomicAlignments/src
+ cd GenomicAlignments/src
+ rm -f IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o GenomicAlignments.so
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-1.fc38.ppc64le/usr/lib64/R/library/R.css
+ /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 1.32.1-1.fc38 --unique-debug-suffix -1.32.1-1.fc38.ppc64le --unique-debug-src-base R-GenomicAlignments-1.32.1-1.fc38.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/GenomicAlignments
extracting debug info from /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-1.fc38.ppc64le/usr/lib64/R/library/GenomicAlignments/libs/GenomicAlignments.so
original debug info size: 256kB, size after compression: 256kB
/usr/bin/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
121 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.3fFvn4
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd GenomicAlignments
+ RPM_EC=0
Processing files: R-GenomicAlignments-1.32.1-1.fc38.ppc64le
++ jobs -p
+ exit 0
Provides: R(GenomicAlignments) = 1.32.1 R-GenomicAlignments = 1.32.1-1.fc38 R-GenomicAlignments(ppc-64) = 1.32.1-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: R(ABI) = 4.2 R(BiocGenerics) >= 0.37.0 R(BiocParallel) R(Biostrings) >= 2.55.7 R(GenomeInfoDb) >= 1.13.1 R(GenomicRanges) >= 1.41.5 R(IRanges) >= 2.23.9 R(Rsamtools) >= 1.31.2 R(S4Vectors) >= 0.27.12 R(SummarizedExperiment) >= 1.9.13 R(methods) R(stats) R(utils) R-core >= 4.0.0 libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) rtld(GNU_HASH)
Suggests: R(BSgenome) R(RUnit) R(rtracklayer)
Processing files: R-GenomicAlignments-debugsource-1.32.1-1.fc38.ppc64le
Provides: R-GenomicAlignments-debugsource = 1.32.1-1.fc38 R-GenomicAlignments-debugsource(ppc-64) = 1.32.1-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-GenomicAlignments-debuginfo-1.32.1-1.fc38.ppc64le
Provides: R-GenomicAlignments-debuginfo = 1.32.1-1.fc38 R-GenomicAlignments-debuginfo(ppc-64) = 1.32.1-1.fc38 debuginfo(build-id) = 95abfce898b9df830374ec446accb380e0112b85
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-GenomicAlignments-debugsource(ppc-64) = 1.32.1-1.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-1.fc38.ppc64le
Wrote: /builddir/build/RPMS/R-GenomicAlignments-debugsource-1.32.1-1.fc38.ppc64le.rpm
Wrote: /builddir/build/RPMS/R-GenomicAlignments-debuginfo-1.32.1-1.fc38.ppc64le.rpm
Wrote: /builddir/build/RPMS/R-GenomicAlignments-1.32.1-1.fc38.ppc64le.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.RpYVvj
+ umask 022
+ cd /builddir/build/BUILD
+ cd GenomicAlignments
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-1.fc38.ppc64le
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.9AKZ6S
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf GenomicAlignments GenomicAlignments.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0