Mock Version: 3.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64le --nodeps /builddir/build/SPECS/R-rtracklayer.spec'], chrootPath='/var/lib/mock/fedora-rawhide-ppc64le-1671760844.246070/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 0x7fff9accf610>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.6_rsg2qj:/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.6_rsg2qj:/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', 'a4838ffd7164412c910f557121cb46e7', '-D', '/var/lib/mock/fedora-rawhide-ppc64le-1671760844.246070/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.6_rsg2qj:/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-rtracklayer.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=1662249600
Wrote: /builddir/build/SRPMS/R-rtracklayer-1.56.1-1.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-rtracklayer.spec'], chrootPath='/var/lib/mock/fedora-rawhide-ppc64le-1671760844.246070/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 0x7fff9accf610>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.6_rsg2qj:/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.6_rsg2qj:/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', '9b74d7a1dbcf4583a6fffcd1a361ecf7', '-D', '/var/lib/mock/fedora-rawhide-ppc64le-1671760844.246070/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.6_rsg2qj:/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-rtracklayer.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=1662249600
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.OgPzHv
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf rtracklayer
+ /usr/bin/mkdir -p rtracklayer
+ cd rtracklayer
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/rtracklayer_1.56.1.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ sed -i -e 's|zlibbioc,||' rtracklayer/DESCRIPTION
+ sed -i -e 's|import(zlibbioc)||' rtracklayer/NAMESPACE
+ cp /builddir/build/SOURCES/rtracklayer_jimkent_license.txt .
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.89SuMr
+ 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 rtracklayer
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.UGcyAD
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le
++ dirname /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.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 rtracklayer
+ mkdir -p /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le/usr/lib64/R/library
+ /usr/bin/R CMD INSTALL rtracklayer -l /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le/usr/lib64/R/library
* installing *source* package 'rtracklayer' ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 XVector_stubs.c -o XVector_stubs.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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_rtracklayer.c -o R_init_rtracklayer.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 readGFF.c -o readGFF.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 bbiHelper.c -o bbiHelper.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 bigWig.c -o bigWig.o
bigWig.c: In function 'BWGFile_query':
bigWig.c:268:11: warning: 'ans_nhits' may be used uninitialized [-Wmaybe-uninitialized]
268 | INTEGER(ans_nhits)[i] = nqhits;
| ^~~~~~~~~~~~~~~~~~
bigWig.c:231:58: note: 'ans_nhits' was declared here
231 | SEXP ans, ans_start, ans_width, ans_score, ans_ranges, ans_nhits;
| ^~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 bigBedHelper.c -o bigBedHelper.o
In file included from /usr/include/string.h:535,
from ucsc/common.h:33,
from bigBedHelper.h:5,
from bigBedHelper.c:1:
In function 'strncpy',
inlined from 'bbNamedFileChunkKey' at bigBedHelper.c:148:3:
/usr/include/bits/string_fortified.h:95:10: warning: '__builtin_strncpy' destination unchanged after copying no bytes [-Wstringop-truncation]
95 | return __builtin___strncpy_chk (__dest, __src, __len,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
96 | __glibc_objsize (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 bigBed.c -o bigBed.o
bigBed.c: In function 'BBDFile_write':
bigBed.c:338:10: warning: variable 'extraIndexListEndOffset' set but not used [-Wunused-but-set-variable]
338 | bits64 extraIndexListEndOffset = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~
bigBed.c: In function 'BBDFile_query':
bigBed.c:195:7: warning: 'name' may be used uninitialized [-Wmaybe-uninitialized]
195 | SET_STRING_ELT(name, i, mkChar(bed->name));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:74:54: note: 'name' was declared here
74 | SEXP ans, n_qhits, ranges, chromStart, chromWidth, name, score,
| ^~~~
bigBed.c:198:7: warning: 'score' may be used uninitialized [-Wmaybe-uninitialized]
198 | INTEGER(score)[i] = bed->score;
| ^~~~~~~~~~~~~~
bigBed.c:74:60: note: 'score' was declared here
74 | SEXP ans, n_qhits, ranges, chromStart, chromWidth, name, score,
| ^~~~~
bigBed.c:205:7: warning: 'thickStart' may be used uninitialized [-Wmaybe-uninitialized]
205 | INTEGER(thickStart)[i] = bed->thickStart;
| ^~~~~~~~~~~~~~~~~~~
bigBed.c:75:26: note: 'thickStart' was declared here
75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
| ^~~~~~~~~~
bigBed.c:204:7: warning: 'thickWidth' may be used uninitialized [-Wmaybe-uninitialized]
204 | INTEGER(thickWidth)[i] = bed->thickEnd - bed->thickStart + 1;
| ^~~~~~~~~~~~~~~~~~~
bigBed.c:75:38: note: 'thickWidth' was declared here
75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
| ^~~~~~~~~~
bigBed.c:209:7: warning: 'itemRgb' may be used uninitialized [-Wmaybe-uninitialized]
209 | SET_STRING_ELT(itemRgb, i, mkChar(rgbBuf));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:75:50: note: 'itemRgb' was declared here
75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
| ^~~~~~~
bigBed.c:218:7: warning: 'blocks' may be used uninitialized [-Wmaybe-uninitialized]
218 | SET_VECTOR_ELT(blocks, i, new_IRanges("IRanges", bstart, bwidth, R_NilValue));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bigBed.c:75:59: note: 'blocks' was declared here
75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks,
| ^~~~~~
bigBed.c:236:13: warning: 'lengthIndex' may be used uninitialized [-Wmaybe-uninitialized]
236 | INTEGER(lengthIndex)[efIndex] = index + 1;
| ^~~~~~~~~~~~~~~~~~~~
bigBed.c:76:31: note: 'lengthIndex' was declared here
76 | extraFields = R_NilValue, lengthIndex;
| ^~~~~~~~~~~
bigBed.c:226:22: warning: 'typeId' may be used uninitialized [-Wmaybe-uninitialized]
226 | switch(typeId[efIndex]) {
| ^
bigBed.c:141:13: note: 'typeId' was declared here
141 | SEXPTYPE *typeId;
| ^~~~~~
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 chain_io.c -o chain_io.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 twoBit.c -o twoBit.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 handlers.c -o handlers.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 utils.c -o utils.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/memgfx.c -o ucsc/memgfx.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/aliType.c -o ucsc/aliType.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/binRange.c -o ucsc/binRange.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/htmlColor.c -o ucsc/htmlColor.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/sqlList.c -o ucsc/sqlList.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/tokenizer.c -o ucsc/tokenizer.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/asParse.c -o ucsc/asParse.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/basicBed.c -o ucsc/basicBed.o
ucsc/basicBed.c: In function 'bedParseRgb':
ucsc/basicBed.c:997:1: warning: '__builtin_strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
997 | strncpy(dupe, itemRgb, sizeof(dupe));
| ^
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/bigBed.c -o ucsc/bigBed.o
ucsc/bigBed.c: In function 'extractField':
ucsc/bigBed.c:314:52: warning: '%s' directive argument is null [-Wformat-overflow=]
314 | warn("Not enough fields in extractField of %s", line);
| ^~
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/bbiRead.c -o ucsc/bbiRead.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/bwgQuery.c:187:25: warning: variable 'blockEnd' set but not used [-Wunused-but-set-variable]
187 | char *blockPt, *blockEnd;
| ^~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/common.c -o ucsc/common.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/dnautil.c -o ucsc/dnautil.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:331:5: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
331 | write(STDERR_FILENO, errMsg, strlen(errMsg));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/hash.c -o ucsc/hash.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/linefile.c -o ucsc/linefile.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/localmem.c -o ucsc/localmem.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/dystring.c -o ucsc/dystring.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/obscure.c -o ucsc/obscure.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/rbTree.c -o ucsc/rbTree.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/dlist.c -o ucsc/dlist.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/hex.c -o ucsc/hex.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/filePath.c -o ucsc/filePath.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/htmlPage.c -o ucsc/htmlPage.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/udc.c -o ucsc/udc.o
In file included from ucsc/udc.c:41:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
|
ucsc/udc.c: In function 'djb2_hash':
ucsc/udc.c:1088:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
1088 | while (c = *str++)
| ^
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/net.c -o ucsc/net.o
In file included from ucsc/net.c:19:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
|
ucsc/net.c: In function 'netConnectWithTimeout':
ucsc/net.c:148:38: warning: passing argument 3 to 'restrict'-qualified parameter aliases with argument 4 [-Wrestrict]
148 | res = select(sd+1, NULL, &mySet, &mySet, &tempTime);
| ^~~~~~ ~~~~~~
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/bits.c -o ucsc/bits.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/twoBit.c -o ucsc/twoBit.o
In file included from ucsc/twoBit.c:15:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
|
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/internet.c -o ucsc/internet.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/https.c -o ucsc/https.o
In file included from ucsc/https.c:17:
ucsc/net.h:178:1: warning: "/*" within comment [-Wcomment]
178 | /* Use byteRange as a work-around alternate method to get file size (content-length).
|
ucsc/https.c: In function 'openSslInit':
ucsc/https.c:76:5: warning: 'ERR_load_SSL_strings' is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations]
76 | ERR_load_SSL_strings();
| ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/openssl/sslerr.h:17,
from /usr/include/openssl/ssl.h:43,
from ucsc/https.c:8:
/usr/include/openssl/sslerr_legacy.h:29:27: note: declared here
29 | OSSL_DEPRECATEDIN_3_0 int ERR_load_SSL_strings(void);
| ^~~~~~~~~~~~~~~~~~~~
ucsc/https.c: At top level:
ucsc/https.c:27:13: warning: 'openssl_locking_callback' defined but not used [-Wunused-function]
27 | static void openssl_locking_callback(int mode, int n, const char * file, int line)
| ^~~~~~~~~~~~~~~~~~~~~~~~
ucsc/https.c:22:22: warning: 'openssl_id_callback' defined but not used [-Wunused-function]
22 | static unsigned long openssl_id_callback(void)
| ^~~~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/base64.c -o ucsc/base64.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/verbose.c -o ucsc/verbose.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/os.c -o ucsc/os.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 ucsc/_portimpl.c -o ucsc/_portimpl.o
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 rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bbiHelper.o bigWig.o bigBedHelper.o bigBed.o chain_io.o twoBit.o handlers.o utils.o ucsc/memgfx.o ucsc/aliType.o ucsc/binRange.o ucsc/htmlColor.o ucsc/sqlList.o ucsc/tokenizer.o ucsc/asParse.o ucsc/basicBed.o ucsc/bigBed.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/hex.o ucsc/filePath.o ucsc/htmlPage.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -lssl -lcrypto -L/usr/lib64/R/lib -lR
installing to /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le/usr/lib64/R/library/00LOCK-rtracklayer/00new/rtracklayer/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer'
** help
*** installing help indices
converting help for package 'rtracklayer'
finding HTML links ... done
BEDFile-class html
BamFile-methods html
Bed15TrackLine-class html
BigBedFile html
finding level-2 HTML links ... done
BigBedSelection html
BigWigFile html
BigWigSelection-class html
BrowserViewList-class html
Chain-class html
FastaFile-class html
GFFFile-class html
GRangesForUCSCGenome html
GenomicData html
GenomicSelection html
IntegerRangesList-methods html
Quickload-class html
QuickloadGenome-class html
TabixFile-methods html
TrackDb-class html
TrackHub-class html
TrackHubGenome-class html
TwoBitFile-class html
UCSCData-class html
UCSCFile-class html
UCSCSchema-class html
UCSCTableQuery-class html
WIGFile-class html
activeView-methods html
asBED html
asGFF html
basicTrackLine-class html
blocks-methods html
browseGenome html
browserSession-class html
browserSession-methods html
browserView-class html
browserView-methods html
browserViews-methods html
cpneTrack html
genomeBrowsers html
laySequence-methods html
layTrack-methods html
liftOver html
readGFF html
targets html
tracks-methods html
ucscGenomes html
ucscSession-class html
ucscTrackLine-class html
ucscTrackModes-class html
ucscTrackModes-methods html
ucscView-class html
wigToBigWig html
wigTrackLine-class 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 (rtracklayer)
+ test -d rtracklayer/src
+ cd rtracklayer/src
+ rm -f IRanges_stubs.o R_init_rtracklayer.o S4Vectors_stubs.o XVector_stubs.o bbiHelper.o bigBed.o bigBedHelper.o bigWig.o chain_io.o handlers.o readGFF.o twoBit.o utils.o rtracklayer.so
+ rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le/usr/lib64/R/library/R.css
+ rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le/usr/lib64/R/library/rtracklayer/tests/quickload/T_species_Oct_2011/bedGraphData.bw
+ /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 1.56.1-1.fc38 --unique-debug-suffix -1.56.1-1.fc38.ppc64le --unique-debug-src-base R-rtracklayer-1.56.1-1.fc38.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/rtracklayer
extracting debug info from /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le/usr/lib64/R/library/rtracklayer/libs/rtracklayer.so
original debug info size: 1664kB, size after compression: 1536kB
/usr/bin/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
2226 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.p6ZtKI
+ 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 rtracklayer
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: R-rtracklayer-1.56.1-1.fc38.ppc64le
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.uH8xZc
+ umask 022
+ cd /builddir/build/BUILD
+ cd rtracklayer
+ LICENSEDIR=/builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le/usr/share/licenses/R-rtracklayer
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le/usr/share/licenses/R-rtracklayer
+ cp -pr rtracklayer_jimkent_license.txt /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le/usr/share/licenses/R-rtracklayer
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: R(rtracklayer) = 1.56.1 R-rtracklayer = 1.56.1-1.fc38 R-rtracklayer(ppc-64) = 1.56.1-1.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) >= 0.35.3 R(BiocIO) R(Biostrings) >= 2.47.6 R(GenomeInfoDb) >= 1.15.2 R(GenomicAlignments) >= 1.15.6 R(GenomicRanges) >= 1.37.2 R(IRanges) >= 2.13.13 R(RCurl) >= 1.4.2 R(Rsamtools) >= 1.31.2 R(S4Vectors) >= 0.23.18 R(XML) >= 1.98.0 R(XVector) >= 0.19.7 R(methods) R(restfulr) >= 0.0.13 R(tools) R-core >= 3.5.0 libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.28)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libcrypto.so.3()(64bit) libcrypto.so.3(OPENSSL_3.0.0)(64bit) libssl.so.3()(64bit) libssl.so.3(OPENSSL_3.0.0)(64bit) libz.so.1()(64bit) rtld(GNU_HASH)
Suggests: R(BSgenome) >= 1.33.4 R(RUnit)
Processing files: R-rtracklayer-debugsource-1.56.1-1.fc38.ppc64le
Provides: R-rtracklayer-debugsource = 1.56.1-1.fc38 R-rtracklayer-debugsource(ppc-64) = 1.56.1-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-rtracklayer-debuginfo-1.56.1-1.fc38.ppc64le
Provides: R-rtracklayer-debuginfo = 1.56.1-1.fc38 R-rtracklayer-debuginfo(ppc-64) = 1.56.1-1.fc38 debuginfo(build-id) = 36b8939583d56f0b14455307bb22422859a795bf
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-rtracklayer-debugsource(ppc-64) = 1.56.1-1.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le
Wrote: /builddir/build/RPMS/R-rtracklayer-debugsource-1.56.1-1.fc38.ppc64le.rpm
Wrote: /builddir/build/RPMS/R-rtracklayer-debuginfo-1.56.1-1.fc38.ppc64le.rpm
Wrote: /builddir/build/RPMS/R-rtracklayer-1.56.1-1.fc38.ppc64le.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.EBu6vA
+ umask 022
+ cd /builddir/build/BUILD
+ cd rtracklayer
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-rtracklayer-1.56.1-1.fc38.ppc64le
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.Y2LUlf
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf rtracklayer rtracklayer.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0