Mock Version: 3.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/primer3.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1672131962.409865/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=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.790gdkv0:/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.790gdkv0:/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', '47f56b1c5b4642f88baa4d64ee6af51b', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1672131962.409865/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.790gdkv0:/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;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/primer3.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=1658448000 Wrote: /builddir/build/SRPMS/primer3-2.4.0-8.fc38.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/primer3.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1672131962.409865/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=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.790gdkv0:/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.790gdkv0:/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', 'e19e3c51b6074712a077d7edbe99d754', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1672131962.409865/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.790gdkv0:/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;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/primer3.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=1658448000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.CiHsN7 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf primer3-2.4.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/primer3-2.4.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd primer3-2.4.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + chmod -x src/LICENSE src/Makefile src/dpal.c src/dpal.h src/format_output.c src/format_output.h src/humrep_and_simple.txt src/libprimer3.c src/libprimer3.h src/long_seq_tm_test_main.c src/masker.c src/masker.h src/masker_main.c src/ntdpal_main.c src/oligotm.c src/oligotm.h src/oligotm_main.c src/p3_seq_lib.c src/p3_seq_lib.h src/paranoid_tests.sh src/primer3_boulder_main.c src/primer3_config src/primer3_manual.htm src/print_boulder.c src/print_boulder.h src/read_boulder.c src/read_boulder.h src/release_notes.txt src/thal.c src/thal.h src/thal_main.c + chmod +x src/primer3_config + sed -i -e 's|CFLAGS = $(CC_OPTS) $(O_OPTS)|CFLAGS = $(CC_OPTS) $(O_OPTS) $(INIT_CFLAGS) -fpermissive|' src/Makefile + sed -i 's/\r//' settings_files/p3_th_settings.txt settings_files/primer3_v1_1_4_default_settings.txt settings_files/primer3web_v0_4_0_default_settings.txt settings_files/primer3web_v3_0_0_default_settings.txt settings_files/primer3web_v4_0_0_default_settings.txt + sed -i -e 's|/opt/primer3_config|/etc/primer3_config|' src/release_notes.txt src/thal_main.c src/primer3_boulder_main.c + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.tuK1pQ + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 primer3-2.4.0 + cd src + export 'INIT_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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + INIT_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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + /usr/bin/make -O -j2 V=1 VERBOSE=1 g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive primer3_boulder_main.c g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -o format_output.o format_output.c format_output.c: In function 'int print_seq(FILE*, const p3_global_settings*, const seq_args*, const p3retval*, primer_rec*, const pair_array_t*, int)': format_output.c:418:55: warning: the address of 'p3retval::rev' will never be NULL [-Waddress] 418 | if (pa->pick_right_primer && &retval->rev != NULL | ^ In file included from format_output.h:41, from format_output.c:40: libprimer3.h:860:26: note: 'p3retval::rev' declared here 860 | oligo_array fwd, intl, rev; | ^~~ format_output.c:429:54: warning: the address of 'p3retval::fwd' will never be NULL [-Waddress] 429 | if (pa->pick_left_primer && &retval->fwd != NULL | ^ libprimer3.h:860:15: note: 'p3retval::fwd' declared here 860 | oligo_array fwd, intl, rev; | ^~~ format_output.c: In function 'void format_oligos(FILE*, const p3_global_settings*, const seq_args*, const p3retval*, const char*, const pr_append_str*, int)': format_output.c:851:49: warning: the address of 'p3retval::fwd' will never be NULL [-Waddress] 851 | if ((pa->pick_left_primer) && (&retval->fwd != NULL ) | ^ libprimer3.h:860:15: note: 'p3retval::fwd' declared here 860 | oligo_array fwd, intl, rev; | ^~~ format_output.c:858:53: warning: the address of 'p3retval::intl' will never be NULL [-Waddress] 858 | if ((pa->pick_internal_oligo) && (&retval->intl != NULL ) | ^ libprimer3.h:860:20: note: 'p3retval::intl' declared here 860 | oligo_array fwd, intl, rev; | ^~~~ format_output.c:865:50: warning: the address of 'p3retval::rev' will never be NULL [-Waddress] 865 | if ((pa->pick_right_primer) && (&retval->rev != NULL ) | ^ libprimer3.h:860:26: note: 'p3retval::rev' declared here 860 | oligo_array fwd, intl, rev; | ^~~ format_output.c:888:47: warning: the address of 'p3retval::fwd' will never be NULL [-Waddress] 888 | if ((pa->pick_left_primer) && (&retval->fwd != NULL ) | ^ libprimer3.h:860:15: note: 'p3retval::fwd' declared here 860 | oligo_array fwd, intl, rev; | ^~~ format_output.c:907:51: warning: the address of 'p3retval::intl' will never be NULL [-Waddress] 907 | if ((pa->pick_internal_oligo) && (&retval->intl != NULL ) | ^ libprimer3.h:860:20: note: 'p3retval::intl' declared here 860 | oligo_array fwd, intl, rev; | ^~~~ format_output.c:926:48: warning: the address of 'p3retval::rev' will never be NULL [-Waddress] 926 | if ((pa->pick_right_primer) && (&retval->rev != NULL ) | ^ libprimer3.h:860:26: note: 'p3retval::rev' declared here 860 | oligo_array fwd, intl, rev; | ^~~ g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -o print_boulder.o print_boulder.c g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -o read_boulder.o read_boulder.c g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive masker.c g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -o p3_seq_lib.o p3_seq_lib.c p3_seq_lib.c: In function 'read_and_create_seq_lib': p3_seq_lib.c:297:1: warning: pointer 'seq_id_plus_224' may be used after 'free' [-Wuse-after-free] 297 | } | ^ p3_seq_lib.c:255:17: note: call to 'free' here 255 | free(seq_id_plus); | ~~~~^~~~~~~~~~~~~ g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -o dpal_primer.o dpal.c dpal.c: In function 'void _dpal_generic(const unsigned char*, const unsigned char*, int, int, const dpal_args*, dpal_results*)': dpal.c:368:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 368 | register int i, j, k, mg, c; | ^ dpal.c:368:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 368 | register int i, j, k, mg, c; | ^ dpal.c:368:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 368 | register int i, j, k, mg, c; | ^ dpal.c:368:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 368 | register int i, j, k, mg, c; | ^~ dpal.c:368:31: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 368 | register int i, j, k, mg, c; | ^ dpal.c:369:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 369 | register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; | ^~~ dpal.c:369:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 369 | register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; | ^~~~ dpal.c:369:50: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 369 | register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; | ^~~~~~~ dpal.c: In function 'void _dpal_long_nopath_generic(const unsigned char*, const unsigned char*, int, int, const dpal_args*, dpal_results*)': dpal.c:594:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 594 | register int i, j, k, mg, mgy, c; | ^ dpal.c:594:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 594 | register int i, j, k, mg, mgy, c; | ^ dpal.c:594:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 594 | register int i, j, k, mg, mgy, c; | ^ dpal.c:594:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 594 | register int i, j, k, mg, mgy, c; | ^~ dpal.c:594:31: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 594 | register int i, j, k, mg, mgy, c; | ^~~ dpal.c:594:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 594 | register int i, j, k, mg, mgy, c; | ^ dpal.c:595:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 595 | register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; | ^~~ dpal.c:595:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 595 | register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; | ^~~~ dpal.c:595:50: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 595 | register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; | ^~~~~~~ dpal.c: In function 'void _dpal_long_nopath_maxgap1_local(const unsigned char*, const unsigned char*, int, int, const dpal_args*, dpal_results*)': dpal.c:760:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 760 | register int i, j; | ^ dpal.c:760:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 760 | register int i, j; | ^ dpal.c:761:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 761 | register int gap = in->gap; | ^~~ dpal.c:762:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 762 | register int smax; /* The optimum score. */ | ^~~~ dpal.c:763:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 763 | register int score; /* Current score. */ | ^~~~~ dpal.c:764:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register int a; | ^ dpal.c: In function 'void _dpal_long_nopath_maxgap1_global_end(const unsigned char*, const unsigned char*, int, int, const dpal_args*, dpal_results*)': dpal.c:852:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 852 | register int i, j, k; | ^ dpal.c:852:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 852 | register int i, j, k; | ^ dpal.c:852:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 852 | register int i, j, k; | ^ dpal.c:853:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 853 | register int gap = in->gap; | ^~~ dpal.c:854:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 854 | register int smax; /* The optimum score. */ | ^~~~ dpal.c:855:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 855 | register int score; /* Current score. */ | ^~~~~ dpal.c:856:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 856 | register int a, t; | ^ dpal.c:856:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 856 | register int a, t; | ^ dpal.c: In function 'void print_align(const unsigned char*, const unsigned char*, int (*)[1600][3], int, int, const dpal_args*)': dpal.c:1036:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 1036 | for(i=j;igap; | ^~~ dpal.c:1074:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1074 | register int smax; /* The optimum score. */ | ^~~~ dpal.c:1075:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1075 | register int score; /* Current score. */ | ^~~~~ dpal.c:1076:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1076 | register int a; | ^ g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -ffloat-store -o thal_primer.o thal.c thal.c: In function 'void thal(const unsigned char*, const unsigned char*, const thal_args*, thal_results*)': thal.c:429:13: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] 429 | if ('\0' == oligo_f) { | ~~~~~^~~~~~~~~~ thal.c:434:13: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] 434 | if ('\0' == oligo_r) { | ~~~~~^~~~~~~~~~ thal.c: In function 'void tableStartATS(double, double (*)[5])': thal.c:1200:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 1200 | for (i = 0; i < 5; ++i) | ^~~ thal.c:1203:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 1203 | atpS[0][3] = atpS[3][0] = atp_value; | ^~~~ thal.c: In function 'void tableStartATH(double, double (*)[5])': thal.c:1212:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 1212 | for (i = 0; i < 5; ++i) | ^~~ thal.c:1216:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 1216 | atpH[0][3] = atpH[3][0] = atp_value; | ^~~~ thal.c: In function 'int symmetry_thermo(const unsigned char*)': thal.c:2438:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2438 | register char s; | ^ thal.c:2439:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2439 | register char e; | ^ In file included from /usr/include/string.h:535, from thal.c:43: In function 'strcpy', inlined from 'safe_malloc(unsigned long, thal_results*)' at thal.c:708:7, inlined from 'calc_hairpin(int, int, double*, int)' at thal.c:1753:30: /usr/include/bits/string_fortified.h:79:33: warning: argument 1 null where non-null expected [-Wnonnull] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/bits/string_fortified.h:79:33: note: in a call to built-in function '__memcpy_chk' In function 'strcpy', inlined from 'safe_malloc(unsigned long, thal_results*)' at thal.c:708:7, inlined from 'calc_bulge_internal(int, int, int, int, double*, int, int) [clone .isra.0]' at thal.c:1831:30: /usr/include/bits/string_fortified.h:79:33: warning: argument 1 null where non-null expected [-Wnonnull] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/bits/string_fortified.h:79:33: note: in a call to built-in function '__memcpy_chk' In function 'strcpy', inlined from 'safe_malloc(unsigned long, thal_results*)' at thal.c:708:7, inlined from 'maxTM(int, int)' at thal.c:1373:30, inlined from 'fillMatrix(int, thal_results*)' at thal.c:1304:14, inlined from 'thal(unsigned char const*, unsigned char const*, thal_args const*, thal_results*)' at thal.c:550:17: /usr/include/bits/string_fortified.h:79:33: warning: argument 1 null where non-null expected [-Wnonnull] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/bits/string_fortified.h:79:33: note: in a call to built-in function '__memcpy_chk' gcc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -c -o oligotm.o oligotm.c cc1: warning: command-line option '-fpermissive' is valid for C++/ObjC++ but not for C oligotm.c: In function 'oligotm': oligotm.c:424:44: warning: comparison between pointer and zero character constant [-Wpointer-compare] 424 | for(i = 0; i <= len && d != NULL && d != '\0';) { | ^~ oligotm.c:424:42: note: did you mean to dereference the pointer? 424 | for(i = 0; i <= len && d != NULL && d != '\0';) { | ^ ar rv libmasker.a masker.o a - masker.o ranlib libmasker.a ar: creating libmasker.a g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -o ntdpal_main.o ntdpal_main.c g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -Wno-deprecated -o libprimer3.o libprimer3.c g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -o thal_main.o thal_main.c g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -o dpal.o dpal.c dpal.c: In function 'void _dpal_generic(const unsigned char*, const unsigned char*, int, int, const dpal_args*, dpal_results*)': dpal.c:368:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 368 | register int i, j, k, mg, c; | ^ dpal.c:368:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 368 | register int i, j, k, mg, c; | ^ dpal.c:368:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 368 | register int i, j, k, mg, c; | ^ dpal.c:368:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 368 | register int i, j, k, mg, c; | ^~ dpal.c:368:31: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 368 | register int i, j, k, mg, c; | ^ dpal.c:369:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 369 | register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; | ^~~ dpal.c:369:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 369 | register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; | ^~~~ dpal.c:369:50: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 369 | register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; | ^~~~~~~ dpal.c: In function 'void _dpal_long_nopath_generic(const unsigned char*, const unsigned char*, int, int, const dpal_args*, dpal_results*)': dpal.c:594:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 594 | register int i, j, k, mg, mgy, c; | ^ dpal.c:594:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 594 | register int i, j, k, mg, mgy, c; | ^ dpal.c:594:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 594 | register int i, j, k, mg, mgy, c; | ^ dpal.c:594:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 594 | register int i, j, k, mg, mgy, c; | ^~ dpal.c:594:31: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 594 | register int i, j, k, mg, mgy, c; | ^~~ dpal.c:594:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 594 | register int i, j, k, mg, mgy, c; | ^ dpal.c:595:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 595 | register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; | ^~~ dpal.c:595:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 595 | register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; | ^~~~ dpal.c:595:50: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 595 | register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; | ^~~~~~~ dpal.c: In function 'void _dpal_long_nopath_maxgap1_local(const unsigned char*, const unsigned char*, int, int, const dpal_args*, dpal_results*)': dpal.c:760:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 760 | register int i, j; | ^ dpal.c:760:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 760 | register int i, j; | ^ dpal.c:761:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 761 | register int gap = in->gap; | ^~~ dpal.c:762:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 762 | register int smax; /* The optimum score. */ | ^~~~ dpal.c:763:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 763 | register int score; /* Current score. */ | ^~~~~ dpal.c:764:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register int a; | ^ dpal.c: In function 'void _dpal_long_nopath_maxgap1_global_end(const unsigned char*, const unsigned char*, int, int, const dpal_args*, dpal_results*)': dpal.c:852:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 852 | register int i, j, k; | ^ dpal.c:852:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 852 | register int i, j, k; | ^ dpal.c:852:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 852 | register int i, j, k; | ^ dpal.c:853:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 853 | register int gap = in->gap; | ^~~ dpal.c:854:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 854 | register int smax; /* The optimum score. */ | ^~~~ dpal.c:855:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 855 | register int score; /* Current score. */ | ^~~~~ dpal.c:856:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 856 | register int a, t; | ^ dpal.c:856:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 856 | register int a, t; | ^ dpal.c: In function 'void print_align(const unsigned char*, const unsigned char*, int (*)[1600][3], int, int, const dpal_args*)': dpal.c:1036:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 1036 | for(i=j;igap; | ^~~ dpal.c:1074:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1074 | register int smax; /* The optimum score. */ | ^~~~ dpal.c:1075:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1075 | register int score; /* Current score. */ | ^~~~~ dpal.c:1076:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1076 | register int a; | ^ g++ -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm ar rv libprimer3.a libprimer3.o p3_seq_lib.o a - libprimer3.o a - p3_seq_lib.o ranlib libprimer3.a ar: creating libprimer3.a ar rv libdpal.a dpal_primer.o a - dpal_primer.o ranlib libdpal.a ar: creating libdpal.a ar rv libthal.a thal_primer.o a - thal_primer.o ranlib libthal.a ar: creating libthal.a ar rv liboligotm.a oligotm.o a - oligotm.o ranlib liboligotm.a ar: creating liboligotm.a g++ -g -o ntdpal ntdpal_main.o dpal.o g++ -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -o oligotm oligotm_main.c liboligotm.a -lm g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -ffloat-store -o thal.o thal.c thal.c: In function 'void thal(const unsigned char*, const unsigned char*, const thal_args*, thal_results*)': thal.c:429:13: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] 429 | if ('\0' == oligo_f) { | ~~~~~^~~~~~~~~~ thal.c:434:13: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] 434 | if ('\0' == oligo_r) { | ~~~~~^~~~~~~~~~ thal.c: In function 'void tableStartATS(double, double (*)[5])': thal.c:1200:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 1200 | for (i = 0; i < 5; ++i) | ^~~ thal.c:1203:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 1203 | atpS[0][3] = atpS[3][0] = atp_value; | ^~~~ thal.c: In function 'void tableStartATH(double, double (*)[5])': thal.c:1212:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 1212 | for (i = 0; i < 5; ++i) | ^~~ thal.c:1216:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 1216 | atpH[0][3] = atpH[3][0] = atp_value; | ^~~~ thal.c: In function 'int symmetry_thermo(const unsigned char*)': thal.c:2438:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2438 | register char s; | ^ thal.c:2439:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2439 | register char e; | ^ In file included from /usr/include/string.h:535, from thal.c:43: In function 'strcpy', inlined from 'safe_malloc(unsigned long, thal_results*)' at thal.c:708:7, inlined from 'calc_hairpin(int, int, double*, int)' at thal.c:1753:30: /usr/include/bits/string_fortified.h:79:33: warning: argument 1 null where non-null expected [-Wnonnull] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/bits/string_fortified.h:79:33: note: in a call to built-in function '__memcpy_chk' In function 'strcpy', inlined from 'safe_malloc(unsigned long, thal_results*)' at thal.c:708:7, inlined from 'calc_bulge_internal(int, int, int, int, double*, int, int) [clone .isra.0]' at thal.c:1831:30: /usr/include/bits/string_fortified.h:79:33: warning: argument 1 null where non-null expected [-Wnonnull] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/bits/string_fortified.h:79:33: note: in a call to built-in function '__memcpy_chk' In function 'strcpy', inlined from 'safe_malloc(unsigned long, thal_results*)' at thal.c:708:7, inlined from 'maxTM(int, int)' at thal.c:1373:30, inlined from 'fillMatrix(int, thal_results*)' at thal.c:1304:14, inlined from 'thal(unsigned char const*, unsigned char const*, thal_args const*, thal_results*)' at thal.c:550:17: /usr/include/bits/string_fortified.h:79:33: warning: argument 1 null where non-null expected [-Wnonnull] 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/bits/string_fortified.h:79:33: note: in a call to built-in function '__memcpy_chk' g++ -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fpermissive -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a liboligotm.a libmasker.a -lm g++ -g -o ntthal thal_main.o thal.o -lm g++ -g -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o masker.o libprimer3.a libdpal.a libthal.a liboligotm.a libmasker.a -lm + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.SebeaX + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64 ++ dirname /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64 + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 primer3-2.4.0 + mkdir -p /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/bin + install -p -m 0755 src/primer3_core /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/bin/primer3_core + install -p -m 0755 src/oligotm /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/bin/oligotm + install -p -m 0755 src/ntdpal /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/bin/ntdpal + mkdir -p /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/etc/primer3_config + cp -r src/primer3_config /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/etc/ + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 2.4.0-8.fc38 --unique-debug-suffix -2.4.0-8.fc38.x86_64 --unique-debug-src-base primer3-2.4.0-8.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/primer3-2.4.0 extracting debug info from /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/bin/ntdpal extracting debug info from /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/bin/oligotm extracting debug info from /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/bin/primer3_core original debug info size: 1068kB, size after compression: 964kB /usr/bin/sepdebugcrcfix: Updated 3 CRC32s, 0 CRC32s did match. 1417 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.1Z2gkQ + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 primer3-2.4.0 + pushd src ~/build/BUILD/primer3-2.4.0/src ~/build/BUILD/primer3-2.4.0 ~/build/BUILD/primer3-2.4.0 + popd + RPM_EC=0 ++ jobs -p + exit 0 Processing files: primer3-2.4.0-8.fc38.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.K3rlMv + umask 022 + cd /builddir/build/BUILD + cd primer3-2.4.0 + DOCDIR=/builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/share/doc/primer3 + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/share/doc/primer3 + cp -pr README.md /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/share/doc/primer3 + cp -pr example /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/share/doc/primer3 + cp -pr settings_files/p3_th_settings.txt settings_files/primer3_v1_1_4_default_settings.txt settings_files/primer3web_v0_4_0_default_settings.txt settings_files/primer3web_v3_0_0_default_settings.txt settings_files/primer3web_v4_0_0_default_settings.txt /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/share/doc/primer3 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.cc745v + umask 022 + cd /builddir/build/BUILD + cd primer3-2.4.0 + LICENSEDIR=/builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/share/licenses/primer3 + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/share/licenses/primer3 + cp -pr LICENSE /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64/usr/share/licenses/primer3 + RPM_EC=0 ++ jobs -p + exit 0 Provides: primer3 = 2.4.0-8.fc38 primer3(x86-64) = 2.4.0-8.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(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_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) rtld(GNU_HASH) Processing files: primer3-debugsource-2.4.0-8.fc38.x86_64 Provides: primer3-debugsource = 2.4.0-8.fc38 primer3-debugsource(x86-64) = 2.4.0-8.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: primer3-debuginfo-2.4.0-8.fc38.x86_64 Provides: debuginfo(build-id) = 589f67419ab52b8c4351fc32bf99765e92a80552 debuginfo(build-id) = 59661449e80789eca71f5ac81faad4991258947e debuginfo(build-id) = d89c607f7b1032c802558770ff8dd39c7eebb164 primer3-debuginfo = 2.4.0-8.fc38 primer3-debuginfo(x86-64) = 2.4.0-8.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: primer3-debugsource(x86-64) = 2.4.0-8.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64 Wrote: /builddir/build/RPMS/primer3-debugsource-2.4.0-8.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/primer3-debuginfo-2.4.0-8.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/primer3-2.4.0-8.fc38.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.iIj6kc + umask 022 + cd /builddir/build/BUILD + cd primer3-2.4.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/primer3-2.4.0-8.fc38.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.ChJ8Ts + umask 022 + cd /builddir/build/BUILD + rm -rf primer3-2.4.0 primer3-2.4.0.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0