Mock Version: 5.6
Mock Version: 5.6
Mock Version: 5.6
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target aarch64 --nodeps /builddir/build/SPECS/R-GenomicAlignments.spec'], chrootPath='/var/lib/mock/f40-build-55023886-6531822/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 0xffffa9d7f410>timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.i5osstlf:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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=False)
Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.i5osstlf:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', 'cefb39106fba426f9c4c0fcd99df6e7d', '-D', '/var/lib/mock/f40-build-55023886-6531822/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.i5osstlf:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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 --noclean --target aarch64 --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: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1714003200
Wrote: /builddir/build/SRPMS/R-GenomicAlignments-1.32.1-8.fc40.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target aarch64 --nodeps /builddir/build/SPECS/R-GenomicAlignments.spec'], chrootPath='/var/lib/mock/f40-build-55023886-6531822/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 0xffffa9d7f410>timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.i5osstlf:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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=False)
Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.i5osstlf:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', '7404a8ca8ab941008d09c3fdce84e8ac', '-D', '/var/lib/mock/f40-build-55023886-6531822/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.i5osstlf:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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 --noclean --target aarch64 --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: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1714003200
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.fi0zXw
+ 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 ']'
+ rm -rf /builddir/build/BUILD/GenomicAlignments-SPECPARTS
+ /usr/bin/mkdir -p /builddir/build/BUILD/GenomicAlignments-SPECPARTS
+ /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.FZDTI6
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ 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.OuiJh3
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-8.fc40.aarch64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-8.fc40.aarch64
++ dirname /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-8.fc40.aarch64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-8.fc40.aarch64
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ 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-1.32.1-8.fc40.aarch64/usr/lib64/R/library
+ R CMD INSTALL GenomicAlignments -l /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-8.fc40.aarch64/usr/lib64/R/library
* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -c cigar_utils.c -o cigar_utils.o
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:534:25: warning: ‘range_buf1’ may be used uninitialized [-Wmaybe-uninitialized]
  534 |                         new_IRanges_from_IntPairAE("IRanges", range_buf));
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cigar_utils.c: In function ‘cigar_ranges’:
cigar_utils.c:590:20: note: ‘range_buf1’ was declared here
  590 |         IntPairAE *range_buf1;
      |                    ^~~~~~~~~~
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 ‘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));
      |                                               ~~~~~~~~~~~~~~~~~~
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;
      |                   ^~~~~~~~~~~~~~~
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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
coordinate_mapping_methods.c: In function ‘to_query’:
coordinate_mapping_methods.c:64:26: 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 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -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-1.32.1-8.fc40.aarch64/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-1.32.1-8.fc40.aarch64/usr/lib64/R/library/R.css
+ /usr/bin/find-debuginfo -j12 --strict-build-id -m -i --build-id-seed 1.32.1-8.fc40 --unique-debug-suffix -1.32.1-8.fc40.aarch64 --unique-debug-src-base R-GenomicAlignments-1.32.1-8.fc40.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/GenomicAlignments
find-debuginfo: starting
Extracting debug info from 1 files
DWARF-compressing 1 files
sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/R-GenomicAlignments-1.32.1-8.fc40.aarch64
121 blocks
find-debuginfo: done
+ /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
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j12
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.c5Fj5P
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ 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
Processing files: R-GenomicAlignments-1.32.1-8.fc40.aarch64
Provides: R(GenomicAlignments) = 1.32.1 R-GenomicAlignments = 1.32.1-8.fc40 R-GenomicAlignments(aarch-64) = 1.32.1-8.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: R(ABI) = 4.4 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 ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) rtld(GNU_HASH)
Suggests: R(BSgenome) R(RUnit) R(rtracklayer)
Processing files: R-GenomicAlignments-debugsource-1.32.1-8.fc40.aarch64
Provides: R-GenomicAlignments-debugsource = 1.32.1-8.fc40 R-GenomicAlignments-debugsource(aarch-64) = 1.32.1-8.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-GenomicAlignments-debuginfo-1.32.1-8.fc40.aarch64
Provides: R-GenomicAlignments-debuginfo = 1.32.1-8.fc40 R-GenomicAlignments-debuginfo(aarch-64) = 1.32.1-8.fc40 debuginfo(build-id) = 5832e31d2e61a6a1e9bed6408cdbce2bdf551cbe
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-GenomicAlignments-debugsource(aarch-64) = 1.32.1-8.fc40
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-GenomicAlignments-1.32.1-8.fc40.aarch64
Wrote: /builddir/build/RPMS/R-GenomicAlignments-debugsource-1.32.1-8.fc40.aarch64.rpm
Wrote: /builddir/build/RPMS/R-GenomicAlignments-debuginfo-1.32.1-8.fc40.aarch64.rpm
Wrote: /builddir/build/RPMS/R-GenomicAlignments-1.32.1-8.fc40.aarch64.rpm
Child return code was: 0