Mock Version: 5.9 Mock Version: 5.9 Mock Version: 5.9 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target x86_64 --nodeps /builddir/build/SPECS/glimmer.spec'], chrootPath='/var/lib/mock/f41-build-55897710-6539452/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.v1vfqs76:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.v1vfqs76:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '7947ba40bbde451e8ca1ff7d49f0d824', '-D', '/var/lib/mock/f41-build-55897710-6539452/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.v1vfqs76:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target x86_64 --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;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721260800 Wrote: /builddir/build/SRPMS/glimmer-3.02b-27.fc41.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target x86_64 --nodeps /builddir/build/SPECS/glimmer.spec'], chrootPath='/var/lib/mock/f41-build-55897710-6539452/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.v1vfqs76:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.v1vfqs76:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '1bd54d6af13e45338052614a6b2c6ad7', '-D', '/var/lib/mock/f41-build-55897710-6539452/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.v1vfqs76:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target x86_64 --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;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721260800 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.qHad7N + umask 022 + cd /builddir/build/BUILD/glimmer-3.02b-build + test -d /builddir/build/BUILD/glimmer-3.02b-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/glimmer-3.02b-build + /usr/bin/rm -rf /builddir/build/BUILD/glimmer-3.02b-build + /usr/bin/mkdir -p /builddir/build/BUILD/glimmer-3.02b-build + /usr/bin/mkdir -p /builddir/build/BUILD/glimmer-3.02b-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.SbQTSU + umask 022 + cd /builddir/build/BUILD/glimmer-3.02b-build + cd /builddir/build/BUILD/glimmer-3.02b-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.RSW3Rh + umask 022 + cd /builddir/build/BUILD/glimmer-3.02b-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -j48 'CXXFLAGS=-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' make: Entering directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src' * Make Target is all ##### Making Directory /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common' if [ -e delcher.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc delcher.cc \ | sed '\''s/delcher\\.o[ :]*/& delcher.d/g'\'' > delcher.d' ; \ fi ; if [ -e fasta.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc fasta.cc \ | sed '\''s/fasta\\.o[ :]*/& fasta.d/g'\'' > fasta.d' ; \ fi ; if [ -e gene.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc gene.cc \ | sed '\''s/gene\\.o[ :]*/& gene.d/g'\'' > gene.d' ; \ fi ; @@@@@@@@@@@@@@@@@@@ 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/delcher.o delcher.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" delcher.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/fasta.o fasta.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" fasta.o ; \ fi ; : warning: "__cplusplus" redefined : 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/gene.o gene.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" gene.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition : warning: "__cplusplus" redefined : 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/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a a - delcher.o a - fasta.o a - gene.o make[1]: Leaving directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common' ##### Making Directory /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM' if [ -e icm.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc icm.cc \ | sed '\''s/icm\\.o[ :]*/& icm.d/g'\'' > icm.d' ; \ fi ; if [ -e build-icm.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc build-icm.cc \ | sed '\''s/build-icm\\.o[ :]*/& build-icm.d/g'\'' > build-icm.d' ; \ fi ; if [ -e build-fixed.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc build-fixed.cc \ | sed '\''s/build-fixed\\.o[ :]*/& build-fixed.d/g'\'' > build-fixed.d' ; \ fi ; if [ -e score-fixed.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc score-fixed.cc \ | sed '\''s/score-fixed\\.o[ :]*/& score-fixed.d/g'\'' > score-fixed.d' ; \ fi ; @@@@@@@@@@@@@@@@@@@ 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/icm.o icm.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" icm.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/build-icm.o build-icm.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" build-icm.o ; \ fi ; : warning: "__cplusplus" redefined : 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/build-fixed.o build-fixed.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" build-fixed.o ; \ fi ; : warning: "__cplusplus" redefined : 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/score-fixed.o score-fixed.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" score-fixed.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition : warning: "__cplusplus" redefined : 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:970, from /builddir/build/BUILD/glimmer-3.02b-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 > const&)’ at icm.cc:1412:20: /usr/include/bits/stdio2.h:111:24: warning: ‘best_info’ may be used uninitialized [-Wmaybe-uninitialized] 111 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ icm.cc: In member function ‘ICM_Training_t::Train_Model(std::vector > 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 > const&)’ at icm.cc:1412:20: /usr/include/bits/stdio2.h:111:24: warning: ‘max_pos’ may be used uninitialized [-Wmaybe-uninitialized] 111 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ icm.cc: In member function ‘ICM_Training_t::Train_Model(std::vector > const&)’: icm.cc:1343:12: note: ‘max_pos’ was declared here 1343 | int max_pos, sum; | ^~~~~~~ ################### libGLMicm.a ##################### ar: creating /builddir/build/BUILD/glimmer-3.02b-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/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/build-icm -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-icm.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ -lGLMicm ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/build-icm; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/build-icm -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-icm.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ -lGLMicm ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/build-icm; fi; \ fi ; ++++++++++++++++++++ build-fixed ++++++++++++++++++++++ if [ -z "build-fixed.o" ] ; then \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/build-fixed -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-fixed.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ -lGLMicm ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/build-fixed; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/build-fixed -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib build-fixed.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ -lGLMicm ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/build-fixed; fi; \ fi ; ++++++++++++++++++++ score-fixed ++++++++++++++++++++++ if [ -z "score-fixed.o" ] ; then \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/score-fixed -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib score-fixed.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ -lGLMicm ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/score-fixed; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/score-fixed -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib score-fixed.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ -lGLMicm ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/score-fixed; fi; \ fi ; make[1]: Leaving directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM' ##### Making Directory /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer' if [ -e anomaly.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc anomaly.cc \ | sed '\''s/anomaly\\.o[ :]*/& anomaly.d/g'\'' > anomaly.d' ; \ fi ; if [ -e glimmer3.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc glimmer3.cc \ | sed '\''s/glimmer3\\.o[ :]*/& glimmer3.d/g'\'' > glimmer3.d' ; \ fi ; if [ -e long-orfs.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc long-orfs.cc \ | sed '\''s/long-orfs\\.o[ :]*/& long-orfs.d/g'\'' > long-orfs.d' ; \ fi ; if [ -e test.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc test.cc \ | sed '\''s/test\\.o[ :]*/& test.d/g'\'' > test.d' ; \ fi ; @@@@@@@@@@@@@@@@@@@ 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/anomaly.o anomaly.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" anomaly.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/glimmer3.o glimmer3.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" glimmer3.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition @@@@@@@@@@@@@@@@@@@ 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/long-orfs.o long-orfs.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" long-orfs.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition @@@@@@@@@@@@@@@@@@@ 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/test.o test.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" test.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition : warning: "__cplusplus" redefined : 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) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ long-orfs.cc: In function ‘void Find_Orfs(std::vector&)’: 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}; | ^~~~~~~~~~~~~~ glimmer3.cc: In function ‘void Score_Orfs(std::vector&, std::vector&, 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; | ^~~~~ 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 | ~~~~~~^~~~~~~~~~~~~~~~~~~~ ++++++++++++++++++++ test ++++++++++++++++++++++ if [ -z "test.o" ] ; then \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/test -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib test.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/test; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/test -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib test.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/test; fi; \ fi ; 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 | ~~~~~~^~~~~~~~~~~~~~~~~~~~ ++++++++++++++++++++ anomaly ++++++++++++++++++++++ if [ -z "anomaly.o" ] ; then \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/anomaly -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib anomaly.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/anomaly; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/anomaly -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib anomaly.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/anomaly; fi; \ fi ; In function ‘Find_Orfs(std::vector >&)’, 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; | ^~~~~~~~~ glimmer3.cc: In function ‘Find_Orfs(std::vector >&)’: glimmer3.cc:896:12: warning: ‘ignore_ct’ may be used uninitialized [-Wmaybe-uninitialized] 896 | if (ignore_sub >= ignore_ct) | ^~ 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; | ^~~~~~~~ ++++++++++++++++++++ long-orfs ++++++++++++++++++++++ if [ -z "long-orfs.o" ] ; then \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/long-orfs -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib long-orfs.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/long-orfs; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/long-orfs -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib long-orfs.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/long-orfs; fi; \ fi ; glimmer3.cc: In function ‘Score_Orfs(std::vector >&, std::vector >&, _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 ‘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; | ^~~~~~~~~ ++++++++++++++++++++ glimmer3 ++++++++++++++++++++++ if [ -z "glimmer3.o" ] ; then \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/glimmer3 -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib glimmer3.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMicm.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/glimmer3; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/glimmer3 -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib glimmer3.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMicm.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/glimmer3; fi; \ fi ; make[1]: Leaving directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer' ##### Making Directory /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util' if [ -e entropy-profile.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc entropy-profile.cc \ | sed '\''s/entropy-profile\\.o[ :]*/& entropy-profile.d/g'\'' > entropy-profile.d' ; \ fi ; if [ -e entropy-score.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc entropy-score.cc \ | sed '\''s/entropy-score\\.o[ :]*/& entropy-score.d/g'\'' > entropy-score.d' ; \ fi ; if [ -e extract.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc extract.cc \ | sed '\''s/extract\\.o[ :]*/& extract.d/g'\'' > extract.d' ; \ fi ; if [ -e multi-extract.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc multi-extract.cc \ | sed '\''s/multi-extract\\.o[ :]*/& multi-extract.d/g'\'' > multi-extract.d' ; \ fi ; if [ -e start-codon-distrib.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-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 uncovered.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc uncovered.cc \ | sed '\''s/uncovered\\.o[ :]*/& uncovered.d/g'\'' > uncovered.d' ; \ fi ; if [ -e window-acgt.cc ] ; then \ /bin/sh -ec 'g++ -M -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc window-acgt.cc \ | sed '\''s/window-acgt\\.o[ :]*/& window-acgt.d/g'\'' > window-acgt.d' ; \ fi ; @@@@@@@@@@@@@@@@@@@ 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/entropy-profile.o entropy-profile.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" entropy-profile.o ; \ fi ; @@@@@@@@@@@@@@@@@@@ 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/entropy-score.o entropy-score.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" entropy-score.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition @@@@@@@@@@@@@@@@@@@ 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/extract.o extract.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" extract.o ; \ fi ; : warning: "__cplusplus" redefined : 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/multi-extract.o multi-extract.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" multi-extract.o ; \ fi ; : warning: "__cplusplus" redefined : 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/start-codon-distrib.o start-codon-distrib.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" start-codon-distrib.o ; \ fi ; : warning: "__cplusplus" redefined : 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/uncovered.o uncovered.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" uncovered.o ; \ fi ; : warning: "__cplusplus" redefined : 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 -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c \ -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -I/../SYS/inc -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util -I/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/inc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj/window-acgt.o window-acgt.cc ; \ else \ /cm/cmtools/bin/links.pl /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj \ " :/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj" window-acgt.o ; \ fi ; : warning: "__cplusplus" redefined : note: this is the location of the previous definition : warning: "__cplusplus" redefined : 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 | ~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:42, from /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common/delcher.hh:26, from entropy-profile.hh:15, from entropy-profile.cc:16: In function ‘std::char_traits::length(char const*)’, inlined from ‘std::__cxx11::basic_string, std::allocator >::assign(char const*)’ at /usr/include/c++/14/bits/basic_string.h:1695:19, inlined from ‘std::__cxx11::basic_string, std::allocator >::operator=(char const*)’ at /usr/include/c++/14/bits/basic_string.h:829:28, inlined from ‘main’ at entropy-profile.cc:62:22: /usr/include/c++/14/bits/char_traits.h:391:32: warning: ‘seq’ may be used uninitialized [-Wmaybe-uninitialized] 391 | 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; | ^~~ ++++++++++++++++++++ extract ++++++++++++++++++++++ if [ -z "extract.o" ] ; then \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/extract -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib extract.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/extract; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/extract -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib extract.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/extract; fi; \ fi ; ++++++++++++++++++++ entropy-profile ++++++++++++++++++++++ if [ -z "entropy-profile.o" ] ; then \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/entropy-profile -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-profile.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/entropy-profile; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/entropy-profile -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-profile.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/entropy-profile; fi; \ fi ; ++++++++++++++++++++ entropy-score ++++++++++++++++++++++ if [ -z "entropy-score.o" ] ; then \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/entropy-score -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-score.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/entropy-score; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/entropy-score -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib entropy-score.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/entropy-score; fi; \ fi ; ++++++++++++++++++++ window-acgt ++++++++++++++++++++++ if [ -z "window-acgt.o" ] ; then \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/window-acgt -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib window-acgt.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/window-acgt; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/window-acgt -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib window-acgt.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/window-acgt; fi; \ fi ; ++++++++++++++++++++ start-codon-distrib ++++++++++++++++++++++ if [ -z "start-codon-distrib.o" ] ; then \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/start-codon-distrib -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib start-codon-distrib.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/start-codon-distrib; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/start-codon-distrib -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib start-codon-distrib.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/start-codon-distrib; fi; \ fi ; ++++++++++++++++++++ multi-extract ++++++++++++++++++++++ if [ -z "multi-extract.o" ] ; then \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/multi-extract -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib multi-extract.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/multi-extract; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/multi-extract -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib multi-extract.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/multi-extract; fi; \ fi ; ++++++++++++++++++++ uncovered ++++++++++++++++++++++ if [ -z "uncovered.o" ] ; then \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if gcc -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/uncovered -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib uncovered.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/uncovered; fi; \ else \ cd /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/obj; \ if g++ -o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/uncovered -g -lm \ -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib -L/usr/lib -L/usr/shlib -L/usr/X11R6/lib -L/lib uncovered.o /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/lib/libGLMcommon.a \ ; then \ true; else rm -f /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/bin/uncovered; fi; \ fi ; make[1]: Leaving directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util' * Make Target is all ##### Making Directory /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common' ##### Making Directory /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM' ##### Making Directory /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer' ##### Making Directory /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util' * Make Target is all ##### Making Directory /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Common' ##### Making Directory /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/ICM' ##### Making Directory /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Glimmer' ##### Making Directory /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util all ##### make[1]: Entering directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src/Util' make: Leaving directory '/builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/src' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.pyaV10 + umask 022 + cd /builddir/build/BUILD/glimmer-3.02b-build + '[' /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT ++ dirname /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT + mkdir -p /builddir/build/BUILD/glimmer-3.02b-build + mkdir /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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/BUILD/glimmer-3.02b-build/BUILDROOT + mkdir -p /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT/usr/libexec/glimmer3 + mkdir -p /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT/usr/share/glimmer3 + mkdir -p /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT/usr/bin + install -m 755 scripts/g3-from-scratch.csh scripts/g3-from-training.csh scripts/g3-iterated.csh /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT//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/BUILD/glimmer-3.02b-build/BUILDROOT/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/BUILD/glimmer-3.02b-build/BUILDROOT/usr/share/glimmer3 + ln -s ../libexec/glimmer3/glimmer3 /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT//usr/bin/glimmer3 + /usr/bin/find-debuginfo -j48 --strict-build-id -m -i --build-id-seed 3.02b-27.fc41 --unique-debug-suffix -3.02b-27.fc41.x86_64 --unique-debug-src-base glimmer-3.02b-27.fc41.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02 find-debuginfo: starting Extracting debug info from 13 files DWARF-compressing 13 files sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/glimmer-3.02b-27.fc41.x86_64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/share/glimmer3/get-motif-counts.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/match-list-col.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/upstream-coords.awk from /bin/awk -f to #!/usr/bin/awk -f mangling shebang in /usr/bin/g3-from-scratch.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-iterated.csh from /bin/csh to #!/usr/bin/csh + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j48 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j48 /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT Scanned 22 directories and 65 files, processed 0 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/glimmer-3.02b-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.qqUHwj + umask 022 + cd /builddir/build/BUILD/glimmer-3.02b-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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-27.fc41.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.SurxB3 + umask 022 + cd /builddir/build/BUILD/glimmer-3.02b-build + cd glimmer3.02 + DOCDIR=/builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT/usr/share/doc/glimmer + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT/usr/share/doc/glimmer + cp -pr /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/LICENSE /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT/usr/share/doc/glimmer + cp -pr /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/glim302notes.pdf /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT/usr/share/doc/glimmer + cp -pr /builddir/build/BUILD/glimmer-3.02b-build/glimmer3.02/sample-run /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT/usr/share/doc/glimmer + RPM_EC=0 ++ jobs -p + exit 0 Provides: glimmer = 3.02b-27.fc41 glimmer(x86-64) = 3.02b-27.fc41 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_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(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_2.2.5)(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_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH) Processing files: glimmer-debugsource-3.02b-27.fc41.x86_64 Provides: glimmer-debugsource = 3.02b-27.fc41 glimmer-debugsource(x86-64) = 3.02b-27.fc41 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-27.fc41.x86_64 Provides: debuginfo(build-id) = 09a0c2dc5f45372892affc1f2a1a1a84de0371ef debuginfo(build-id) = 19fcceef47fbdbae8ddfecbd9f0bbb5436df12c9 debuginfo(build-id) = 47e06fffc23e90039ea7a8a03891a30dd5437537 debuginfo(build-id) = 4aabccae1a77a637385d3e41c3a09729e86db396 debuginfo(build-id) = 61cffd55fd9b9dc055007fa0c1566e65c5d713fe debuginfo(build-id) = 6b36f0e2b85ab06a9f9c5b5081de28a49ab5d139 debuginfo(build-id) = 6c7195ca3a15c7690af21ec0d9292708164ed987 debuginfo(build-id) = 86e40c1cc1d97bc9bb1bd889c266aea2801fd830 debuginfo(build-id) = 91534b1c6ba0b187d365116a5ca0a3f689c42ef1 debuginfo(build-id) = c26069559bde25313911e8deeca7bb01c09297c6 debuginfo(build-id) = d017cf43bd1932a774e19867da9ed14ffce46975 debuginfo(build-id) = f084600ed551b9fd6d894557d033bc9f44f282e7 debuginfo(build-id) = f1e1da5f422ea85cef366ea94a8de1777ac14a37 glimmer-debuginfo = 3.02b-27.fc41 glimmer-debuginfo(x86-64) = 3.02b-27.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: glimmer-debugsource(x86-64) = 3.02b-27.fc41 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/glimmer-3.02b-build/BUILDROOT Wrote: /builddir/build/RPMS/glimmer-debugsource-3.02b-27.fc41.x86_64.rpm Wrote: /builddir/build/RPMS/glimmer-debuginfo-3.02b-27.fc41.x86_64.rpm Wrote: /builddir/build/RPMS/glimmer-3.02b-27.fc41.x86_64.rpm Child return code was: 0