Mock Version: 3.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target s390x --nodeps /builddir/build/SPECS/glimmer.spec'], chrootPath='/var/lib/mock/fedora-rawhide-s390x-1671906161.278413/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 0x3ffb4931110>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.73ln9ocd:/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.73ln9ocd:/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', 'f32e1c065edc464380ae2504d2f28464', '-D', '/var/lib/mock/fedora-rawhide-s390x-1671906161.278413/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.73ln9ocd:/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 s390x --nodeps /builddir/build/SPECS/glimmer.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: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1658361600
Wrote: /builddir/build/SRPMS/glimmer-3.02b-22.fc38.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target s390x --nodeps /builddir/build/SPECS/glimmer.spec'], chrootPath='/var/lib/mock/fedora-rawhide-s390x-1671906161.278413/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 0x3ffb4931110>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.73ln9ocd:/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.73ln9ocd:/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', '9a86bf6cca75421c9ed277c423cfacd7', '-D', '/var/lib/mock/fedora-rawhide-s390x-1671906161.278413/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.73ln9ocd:/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 s390x --nodeps /builddir/build/SPECS/glimmer.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: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1658361600
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.E2icjU
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf glimmer3.02
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/glimmer302b.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd glimmer3.02
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ rm -f sample-run/g3-from-scratch.csh sample-run/g3-from-training.csh sample-run/g3-iterated.csh
+ sed -i s+/fs/szgenefinding/Glimmer3/bin+/usr/libexec/glimmer3+ scripts/g3-from-scratch.csh scripts/g3-from-training.csh scripts/g3-iterated.csh
+ sed -i s+/fs/szgenefinding/Glimmer3/scripts+/usr/share/glimmer3+ scripts/g3-from-scratch.csh scripts/g3-from-training.csh scripts/g3-iterated.csh
+ sed -i s+/nfshomes/adelcher/bin/elph+/usr/bin/elph+ scripts/g3-from-scratch.csh scripts/g3-from-training.csh scripts/g3-iterated.csh
+ sed -i 's/@ if/if/' src/c_make.gen
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.0S6AP7
+ 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 -march=z13 -mtune=z14 -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 -march=z13 -mtune=z14 -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 -march=z13 -mtune=z14 -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 -march=z13 -mtune=z14 -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 glimmer3.02
+ make -C src -j2 'CXXFLAGS=-std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
make: Entering directory '/builddir/build/BUILD/glimmer3.02/src'
* Make Target is all
##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Common all #####
make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Common'
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
if [ -e gene.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc gene.cc \
| sed '\''s/gene\\.o[ :]*/& gene.d/g'\'' > gene.d' ; \
fi ;
if [ -e fasta.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc fasta.cc \
| sed '\''s/fasta\\.o[ :]*/& fasta.d/g'\'' > fasta.d' ; \
fi ;
if [ -e delcher.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc delcher.cc \
| sed '\''s/delcher\\.o[ :]*/& delcher.d/g'\'' > delcher.d' ; \
fi ;
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
@@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e delcher.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/delcher.o delcher.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" delcher.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
@@@@@@@@@@@@@@@@@@@ fasta.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e fasta.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/fasta.o fasta.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" fasta.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
@@@@@@@@@@@@@@@@@@@ gene.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e gene.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/gene.o gene.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" gene.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
gene.cc: In member function 'bool PWM_t::Read(FILE*)':
gene.cc:318:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
318 | fscanf (fp, "%d", & width);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~
gene.cc:331:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
331 | fscanf (fp, "%s", tag); // skip tag in first column
| ~~~~~~~^~~~~~~~~~~~~~~
gene.cc:334:17: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
334 | fscanf (fp, "%lf", & x);
| ~~~~~~~^~~~~~~~~~~~~~~~
gene.cc: In function 'int Read_String(FILE*, char*&, long int&, char*, int)':
gene.cc:847:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
847 | fgets (Line, MAX_LINE, fp);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~
################### libGLMcommon.a #####################
ar: creating /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a
a - delcher.o
a - fasta.o
a - gene.o
make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Common'
##### Making Directory /builddir/build/BUILD/glimmer3.02/src/ICM all #####
make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/ICM'
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
if [ -e score-fixed.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc score-fixed.cc \
| sed '\''s/score-fixed\\.o[ :]*/& score-fixed.d/g'\'' > score-fixed.d' ; \
fi ;
if [ -e build-fixed.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc build-fixed.cc \
| sed '\''s/build-fixed\\.o[ :]*/& build-fixed.d/g'\'' > build-fixed.d' ; \
fi ;
if [ -e build-icm.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc build-icm.cc \
| sed '\''s/build-icm\\.o[ :]*/& build-icm.d/g'\'' > build-icm.d' ; \
fi ;
if [ -e icm.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc icm.cc \
| sed '\''s/icm\\.o[ :]*/& icm.d/g'\'' > icm.d' ; \
fi ;
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
@@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e icm.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/icm.o icm.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" icm.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
icm.cc: In member function 'void Fixed_Length_ICM_t::read(const char*)':
icm.cc:1489:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1489 | fread (line, sizeof (char), ID_STRING_LEN, fp); // skip the text header line
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
icm.cc:1517:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1517 | fread (permutation, sizeof (int), length, fp);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:906,
from /builddir/build/BUILD/glimmer3.02/src/Common/delcher.hh:15,
from icm.hh:15,
from icm.cc:16:
In function 'fprintf',
inlined from 'ICM_Training_t::Train_Model(std::vector<char*, std::allocator<char*> > const&)' at icm.cc:1412:20:
/usr/include/bits/stdio2.h:79:24: warning: 'best_info' may be used uninitialized [-Wmaybe-uninitialized]
79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
icm.cc: In member function 'ICM_Training_t::Train_Model(std::vector<char*, std::allocator<char*> > const&)':
icm.cc:1342:15: note: 'best_info' was declared here
1342 | double best_info, next_info;
| ^~~~~~~~~
In function 'fprintf',
inlined from 'ICM_Training_t::Train_Model(std::vector<char*, std::allocator<char*> > const&)' at icm.cc:1412:20:
/usr/include/bits/stdio2.h:79:24: warning: 'max_pos' may be used uninitialized [-Wmaybe-uninitialized]
79 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
icm.cc: In member function 'ICM_Training_t::Train_Model(std::vector<char*, std::allocator<char*> > const&)':
icm.cc:1343:12: note: 'max_pos' was declared here
1343 | int max_pos, sum;
| ^~~~~~~
@@@@@@@@@@@@@@@@@@@ build-icm.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e build-icm.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/build-icm.o build-icm.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" build-icm.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
@@@@@@@@@@@@@@@@@@@ build-fixed.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e build-fixed.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/build-fixed.o build-fixed.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" build-fixed.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
@@@@@@@@@@@@@@@@@@@ score-fixed.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e score-fixed.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/score-fixed.o score-fixed.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" score-fixed.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
################### libGLMicm.a #####################
ar: creating /builddir/build/BUILD/glimmer3.02/lib/libGLMicm.a
a - icm.o
a - build-icm.o
a - build-fixed.o
a - score-fixed.o
++++++++++++++++++++ build-icm ++++++++++++++++++++++
if [ -z "build-icm.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/build-icm -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-icm.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
-lGLMicm ; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/build-icm; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/build-icm -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-icm.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
-lGLMicm ; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/build-icm; fi; \
fi ;
++++++++++++++++++++ build-fixed ++++++++++++++++++++++
if [ -z "build-fixed.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/build-fixed -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-fixed.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
-lGLMicm ; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/build-fixed; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/build-fixed -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-fixed.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
-lGLMicm ; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/build-fixed; fi; \
fi ;
++++++++++++++++++++ score-fixed ++++++++++++++++++++++
if [ -z "score-fixed.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/score-fixed -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib score-fixed.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
-lGLMicm ; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/score-fixed; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/score-fixed -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib score-fixed.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
-lGLMicm ; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/score-fixed; fi; \
fi ;
make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/ICM'
##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Glimmer'
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
if [ -e test.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc test.cc \
| sed '\''s/test\\.o[ :]*/& test.d/g'\'' > test.d' ; \
fi ;
if [ -e long-orfs.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc long-orfs.cc \
| sed '\''s/long-orfs\\.o[ :]*/& long-orfs.d/g'\'' > long-orfs.d' ; \
fi ;
if [ -e glimmer3.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc glimmer3.cc \
| sed '\''s/glimmer3\\.o[ :]*/& glimmer3.d/g'\'' > glimmer3.d' ; \
fi ;
if [ -e anomaly.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc anomaly.cc \
| sed '\''s/anomaly\\.o[ :]*/& anomaly.d/g'\'' > anomaly.d' ; \
fi ;
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
@@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e anomaly.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/anomaly.o anomaly.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" anomaly.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
anomaly.cc: In function 'int main(int, char**)':
anomaly.cc:82:27: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
82 | if (Start < End && End - Start <= Len / 2 || Start - End > Len / 2)
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
@@@@@@@@@@@@@@@@@@@ glimmer3.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e glimmer3.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/glimmer3.o glimmer3.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" glimmer3.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
glimmer3.cc: In function 'void Score_Orfs(std::vector<Orf_t>&, std::vector<Gene_t>&, FILE*)':
glimmer3.cc:2861:20: warning: variable 'max_rate' set but not used [-Wunused-but-set-variable]
2861 | double max, max_rate;
| ^~~~~~~~
glimmer3.cc:2867:23: warning: variable 'max_j' set but not used [-Wunused-but-set-variable]
2867 | int fr, frame, max_j, orf_start, frame_score;
| ^~~~~
glimmer3.cc: In function 'void Read_Entropy_Profiles(const char*, bool&)':
glimmer3.cc:2608:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
2608 | fgets (line, MAX_LINE, fp); // skip header line
| ~~~~~~^~~~~~~~~~~~~~~~~~~~
glimmer3.cc: In function 'Score_Orfs(std::vector<Orf_t, std::allocator<Orf_t> >&, std::vector<Gene_t, std::allocator<Gene_t> >&, _IO_FILE*)':
glimmer3.cc:3010:26: warning: 'first_score' may be used uninitialized [-Wmaybe-uninitialized]
3010 | gene_score = 100.0 * best_score / (best_j - 2);
| ~~~~~~^~~~~~~~~~~~
glimmer3.cc:2855:15: note: 'first_score' was declared here
2855 | double first_score, best_score = - DBL_MAX;
| ^~~~~~~~~~~
In function 'Find_Orfs(std::vector<Orf_t, std::allocator<Orf_t> >&)',
inlined from 'main' at glimmer3.cc:250:20:
glimmer3.cc:896:12: warning: 'ignore_ct' may be used uninitialized [-Wmaybe-uninitialized]
896 | if (ignore_sub >= ignore_ct)
| ^~
glimmer3.cc: In function 'main':
glimmer3.cc:830:9: note: 'ignore_ct' was declared here
830 | int ignore_ct;
| ^~~~~~~~~
glimmer3.cc:907:24: warning: 'orf_stop' may be used uninitialized [-Wmaybe-uninitialized]
907 | int which, orf_stop;
| ^~~~~~~~
In function 'Trace_Back(_IO_FILE*, Event_Node_t const&)',
inlined from 'main' at glimmer3.cc:263:21:
glimmer3.cc:3442:29: warning: 'prev_score' may be used uninitialized [-Wmaybe-uninitialized]
3442 | gene . Set_Score (prev_score - p -> score);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
glimmer3.cc: In function 'main':
glimmer3.cc:3411:12: note: 'prev_score' was declared here
3411 | double prev_score;
| ^~~~~~~~~~
In function 'Trace_Back(_IO_FILE*, Event_Node_t const&)',
inlined from 'main' at glimmer3.cc:263:21:
glimmer3.cc:3441:32: warning: 'rev_start' may be used uninitialized [-Wmaybe-uninitialized]
3441 | gene . Set_Gene_Len (rev_start - p -> pos);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
glimmer3.cc: In function 'main':
glimmer3.cc:3412:21: note: 'rev_start' was declared here
3412 | int f, i, j, n, rev_start;
| ^~~~~~~~~
@@@@@@@@@@@@@@@@@@@ long-orfs.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e long-orfs.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/long-orfs.o long-orfs.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" long-orfs.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
long-orfs.cc: In function 'void Find_Orfs(std::vector<Orf_t>&)':
long-orfs.cc:585:9: warning: variable 'first_fwd_stop' set but not used [-Wunused-but-set-variable]
585 | int first_fwd_stop [3] = {0};
| ^~~~~~~~~~~~~~
long-orfs.cc: In function 'void Read_Entropy_Profiles(const char*, bool&)':
long-orfs.cc:1317:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1317 | fgets (line, MAX_LINE, fp); // skip header line
| ~~~~~~^~~~~~~~~~~~~~~~~~~~
In function 'Find_Orfs(std::vector<Orf_t, std::allocator<Orf_t> >&)',
inlined from 'main' at long-orfs.cc:141:17:
long-orfs.cc:655:12: warning: 'ignore_ct' may be used uninitialized [-Wmaybe-uninitialized]
655 | if (ignore_sub >= ignore_ct)
| ^~
long-orfs.cc: In function 'main':
long-orfs.cc:590:9: note: 'ignore_ct' was declared here
590 | int ignore_ct;
| ^~~~~~~~~
@@@@@@@@@@@@@@@@@@@ test.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e test.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/test.o test.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" test.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
++++++++++++++++++++ anomaly ++++++++++++++++++++++
if [ -z "anomaly.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/anomaly -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib anomaly.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/anomaly; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/anomaly -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib anomaly.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/anomaly; fi; \
fi ;
++++++++++++++++++++ glimmer3 ++++++++++++++++++++++
if [ -z "glimmer3.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/glimmer3 -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib glimmer3.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a /builddir/build/BUILD/glimmer3.02/lib/libGLMicm.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/glimmer3; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/glimmer3 -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib glimmer3.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a /builddir/build/BUILD/glimmer3.02/lib/libGLMicm.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/glimmer3; fi; \
fi ;
++++++++++++++++++++ long-orfs ++++++++++++++++++++++
if [ -z "long-orfs.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/long-orfs -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib long-orfs.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/long-orfs; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/long-orfs -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib long-orfs.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/long-orfs; fi; \
fi ;
++++++++++++++++++++ test ++++++++++++++++++++++
if [ -z "test.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/test -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib test.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/test; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/test -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib test.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/test; fi; \
fi ;
make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Glimmer'
##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Util all #####
make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Util'
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
if [ -e window-acgt.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc window-acgt.cc \
| sed '\''s/window-acgt\\.o[ :]*/& window-acgt.d/g'\'' > window-acgt.d' ; \
fi ;
if [ -e uncovered.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc uncovered.cc \
| sed '\''s/uncovered\\.o[ :]*/& uncovered.d/g'\'' > uncovered.d' ; \
fi ;
if [ -e start-codon-distrib.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc start-codon-distrib.cc \
| sed '\''s/start-codon-distrib\\.o[ :]*/& start-codon-distrib.d/g'\'' > start-codon-distrib.d' ; \
fi ;
if [ -e multi-extract.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc multi-extract.cc \
| sed '\''s/multi-extract\\.o[ :]*/& multi-extract.d/g'\'' > multi-extract.d' ; \
fi ;
if [ -e extract.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc extract.cc \
| sed '\''s/extract\\.o[ :]*/& extract.d/g'\'' > extract.d' ; \
fi ;
if [ -e entropy-score.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc entropy-score.cc \
| sed '\''s/entropy-score\\.o[ :]*/& entropy-score.d/g'\'' > entropy-score.d' ; \
fi ;
if [ -e entropy-profile.cc ] ; then \
/bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc entropy-profile.cc \
| sed '\''s/entropy-profile\\.o[ :]*/& entropy-profile.d/g'\'' > entropy-profile.d' ; \
fi ;
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
@@@@@@@@@@@@@@@@@@@ entropy-profile.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e entropy-profile.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/entropy-profile.o entropy-profile.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" entropy-profile.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
In file included from /usr/include/c++/13/string:42,
from /builddir/build/BUILD/glimmer3.02/src/Common/delcher.hh:26,
from entropy-profile.hh:15,
from entropy-profile.cc:16:
In function 'std::char_traits<char>::length(char const*)',
inlined from 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::assign(char const*)' at /usr/include/c++/13/bits/basic_string.h:1647:19,
inlined from 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::operator=(char const*)' at /usr/include/c++/13/bits/basic_string.h:815:28,
inlined from 'main' at entropy-profile.cc:62:22:
/usr/include/c++/13/bits/char_traits.h:389:32: warning: 'seq' may be used uninitialized [-Wmaybe-uninitialized]
389 | return __builtin_strlen(__s);
| ~~~~~~~~~~~~~~~~^~~~~
entropy-profile.cc: In function 'main':
entropy-profile.cc:54:21: note: 'seq' was declared here
54 | const char * seq, * rev_seq;
| ^~~
@@@@@@@@@@@@@@@@@@@ entropy-score.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e entropy-score.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/entropy-score.o entropy-score.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" entropy-score.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
entropy-score.cc: In function 'int main(int, char**)':
entropy-score.cc:157:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
157 | if (line [n - 1] == '\n');
| ^~
entropy-score.cc:158:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
158 | line [n - 1] = '\0';
| ^~~~
entropy-score.cc: In function 'void Read_Entropy_Profiles(const char*, bool&)':
entropy-score.cc:327:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
327 | fgets (line, MAX_LINE, fp); // skip header line
| ~~~~~~^~~~~~~~~~~~~~~~~~~~
@@@@@@@@@@@@@@@@@@@ extract.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e extract.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/extract.o extract.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" extract.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
@@@@@@@@@@@@@@@@@@@ multi-extract.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e multi-extract.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/multi-extract.o multi-extract.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" multi-extract.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
@@@@@@@@@@@@@@@@@@@ start-codon-distrib.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e start-codon-distrib.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/start-codon-distrib.o start-codon-distrib.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" start-codon-distrib.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
@@@@@@@@@@@@@@@@@@@ uncovered.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e uncovered.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/uncovered.o uncovered.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" uncovered.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
@@@@@@@@@@@@@@@@@@@ window-acgt.cc @@@@@@@@@@@@@@@@@@@@@
if [ -e window-acgt.cc ] ; then \
g++ -D__cplusplus -std=c++14 -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 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -c \
-I/builddir/build/BUILD/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer3.02/inc -o /builddir/build/BUILD/glimmer3.02/obj/window-acgt.o window-acgt.cc ; \
else \
/cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer3.02/obj \
" :/builddir/build/BUILD/glimmer3.02/obj" window-acgt.o ; \
fi ;
<command-line>: warning: "__cplusplus" redefined
<built-in>: note: this is the location of the previous definition
++++++++++++++++++++ entropy-profile ++++++++++++++++++++++
if [ -z "entropy-profile.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/entropy-profile -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-profile.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/entropy-profile; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/entropy-profile -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-profile.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/entropy-profile; fi; \
fi ;
++++++++++++++++++++ entropy-score ++++++++++++++++++++++
if [ -z "entropy-score.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/entropy-score -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-score.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/entropy-score; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/entropy-score -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-score.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/entropy-score; fi; \
fi ;
++++++++++++++++++++ extract ++++++++++++++++++++++
if [ -z "extract.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/extract -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib extract.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/extract; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/extract -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib extract.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/extract; fi; \
fi ;
++++++++++++++++++++ multi-extract ++++++++++++++++++++++
if [ -z "multi-extract.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/multi-extract -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib multi-extract.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/multi-extract; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/multi-extract -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib multi-extract.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/multi-extract; fi; \
fi ;
++++++++++++++++++++ start-codon-distrib ++++++++++++++++++++++
if [ -z "start-codon-distrib.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/start-codon-distrib -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib start-codon-distrib.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/start-codon-distrib; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/start-codon-distrib -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib start-codon-distrib.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/start-codon-distrib; fi; \
fi ;
++++++++++++++++++++ uncovered ++++++++++++++++++++++
if [ -z "uncovered.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/uncovered -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib uncovered.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/uncovered; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/uncovered -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib uncovered.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/uncovered; fi; \
fi ;
++++++++++++++++++++ window-acgt ++++++++++++++++++++++
if [ -z "window-acgt.o" ] ; then \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if gcc -o /builddir/build/BUILD/glimmer3.02/bin/window-acgt -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib window-acgt.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/window-acgt; fi; \
else \
cd /builddir/build/BUILD/glimmer3.02/obj; \
if g++ -o /builddir/build/BUILD/glimmer3.02/bin/window-acgt -g -lm \
-L/builddir/build/BUILD/glimmer3.02/lib -L/builddir/build/BUILD/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib window-acgt.o /builddir/build/BUILD/glimmer3.02/lib/libGLMcommon.a \
; then \
true; else rm -f /builddir/build/BUILD/glimmer3.02/bin/window-acgt; fi; \
fi ;
make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Util'
* Make Target is all
##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Common all #####
make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Common'
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Common'
##### Making Directory /builddir/build/BUILD/glimmer3.02/src/ICM all #####
make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/ICM'
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/ICM'
##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Glimmer'
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Glimmer'
##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Util all #####
make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Util'
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Util'
* Make Target is all
##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Common all #####
make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Common'
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Common'
##### Making Directory /builddir/build/BUILD/glimmer3.02/src/ICM all #####
make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/ICM'
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/ICM'
##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Glimmer'
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Glimmer'
##### Making Directory /builddir/build/BUILD/glimmer3.02/src/Util all #####
make[1]: Entering directory '/builddir/build/BUILD/glimmer3.02/src/Util'
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/builddir/build/BUILD/glimmer3.02/src/Util'
make: Leaving directory '/builddir/build/BUILD/glimmer3.02/src'
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.ZC2FfB
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x
++ dirname /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x
+ 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 -march=z13 -mtune=z14 -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 -march=z13 -mtune=z14 -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 -march=z13 -mtune=z14 -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 -march=z13 -mtune=z14 -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 glimmer3.02
+ rm -rf /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x
+ mkdir -p /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3
+ mkdir -p /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/share/glimmer3
+ mkdir -p /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/bin
+ install -m 755 scripts/g3-from-scratch.csh scripts/g3-from-training.csh scripts/g3-iterated.csh /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x//usr/bin
+ install -m 755 bin/anomaly bin/build-fixed bin/build-icm bin/entropy-profile bin/entropy-score bin/extract bin/glimmer3 bin/long-orfs bin/multi-extract bin/score-fixed bin/start-codon-distrib bin/uncovered bin/window-acgt /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3
+ install -m 755 scripts/get-motif-counts.awk scripts/glim-diff.awk scripts/match-list-col.awk scripts/not-acgt.awk scripts/upstream-coords.awk /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/share/glimmer3
+ ln -s ../libexec/glimmer3/glimmer3 /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x//usr/bin/glimmer3
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 3.02b-22.fc38 --unique-debug-suffix -3.02b-22.fc38.s390x --unique-debug-src-base glimmer-3.02b-22.fc38.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/glimmer3.02
extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3/anomaly
extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3/build-fixed
extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3/build-icm
extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3/entropy-profile
extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3/entropy-score
extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3/extract
extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3/glimmer3
extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3/long-orfs
extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3/multi-extract
extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3/score-fixed
extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3/start-codon-distrib
extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3/uncovered
extracting debug info from /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/libexec/glimmer3/window-acgt
original debug info size: 5356kB, size after compression: 3028kB
/usr/bin/sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match.
748 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
mangling shebang in /usr/bin/g3-iterated.csh from /bin/csh to #!/usr/bin/csh
mangling shebang in /usr/bin/g3-from-training.csh from /bin/csh to #!/usr/bin/csh
mangling shebang in /usr/bin/g3-from-scratch.csh from /bin/csh to #!/usr/bin/csh
mangling shebang in /usr/share/glimmer3/upstream-coords.awk from /bin/awk -f to #!/usr/bin/awk -f
mangling shebang in /usr/share/glimmer3/not-acgt.awk from /bin/awk -f to #!/usr/bin/awk -f
mangling shebang in /usr/share/glimmer3/match-list-col.awk from /bin/awk -f to #!/usr/bin/awk -f
mangling shebang in /usr/share/glimmer3/glim-diff.awk from /bin/awk -f to #!/usr/bin/awk -f
mangling shebang in /usr/share/glimmer3/get-motif-counts.awk from /bin/awk -f to #!/usr/bin/awk -f
+ /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.8qLQsE
+ 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 -march=z13 -mtune=z14 -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 -march=z13 -mtune=z14 -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 -march=z13 -mtune=z14 -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 -march=z13 -mtune=z14 -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 glimmer3.02
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: glimmer-3.02b-22.fc38.s390x
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.g4FJ7f
+ umask 022
+ cd /builddir/build/BUILD
+ cd glimmer3.02
+ DOCDIR=/builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/share/doc/glimmer
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/share/doc/glimmer
+ cp -pr LICENSE /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/share/doc/glimmer
+ cp -pr glim302notes.pdf /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/share/doc/glimmer
+ cp -pr sample-run /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x/usr/share/doc/glimmer
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: glimmer = 3.02b-22.fc38 glimmer(s390-64) = 3.02b-22.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/awk /usr/bin/csh libc.so.6()(64bit) libc.so.6(GLIBC_2.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2)(64bit) libm.so.6(GLIBC_2.27)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH)
Processing files: glimmer-debugsource-3.02b-22.fc38.s390x
Provides: glimmer-debugsource = 3.02b-22.fc38 glimmer-debugsource(s390-64) = 3.02b-22.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: glimmer-debuginfo-3.02b-22.fc38.s390x
Provides: debuginfo(build-id) = 0e6b9728e22439fde41dd5d0757988a76e98c52b debuginfo(build-id) = 11874e7a378291268984c8bc734a98c8ad7979e3 debuginfo(build-id) = 1d6cd7a1bba4d050a6db0f8e92716f2602e5e7b3 debuginfo(build-id) = 324a000f5912eb67b9b2f31eb0cc4c6993cb8776 debuginfo(build-id) = 7cf98b9b4670411016e5635bf21d395f21081a6a debuginfo(build-id) = 8824a3297282fc6df539796318224a86112fdc03 debuginfo(build-id) = 895ea30e4a20d3c929c3cfa1ab8894be0cbf9da8 debuginfo(build-id) = a0e7cbdf98f753ee00b23a70af4e32c59c022549 debuginfo(build-id) = c5c9b4dbdaf1485d339f470e0be8706b5cd6f414 debuginfo(build-id) = c6670de741dc0ee07bc4eada84bd47cdc9feb150 debuginfo(build-id) = e53455b8871adaf2b56c1b7b76929dc229e9840b debuginfo(build-id) = e5e4d961faf2506ff7bc34e23eefcb904c9f2826 debuginfo(build-id) = f5245b1b2e0213fbd3e92dc24e94102a789958b2 glimmer-debuginfo = 3.02b-22.fc38 glimmer-debuginfo(s390-64) = 3.02b-22.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: glimmer-debugsource(s390-64) = 3.02b-22.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x
Wrote: /builddir/build/RPMS/glimmer-debuginfo-3.02b-22.fc38.s390x.rpm
Wrote: /builddir/build/RPMS/glimmer-debugsource-3.02b-22.fc38.s390x.rpm
Wrote: /builddir/build/RPMS/glimmer-3.02b-22.fc38.s390x.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.xDrbzi
+ umask 022
+ cd /builddir/build/BUILD
+ cd glimmer3.02
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/glimmer-3.02b-22.fc38.s390x
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.iH97l4
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf glimmer3.02 glimmer3.02.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0