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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f9fd79a54d0>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;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target 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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: 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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f9fd79a54d0>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;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target 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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: 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;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n");
      |     ^~~
dpal.c:1036:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1036 |     for(i=j;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n");
      |                                                      ^~~~~~~
dpal.c: In function 'int illegal_char(const unsigned char*, const int (*)[256], char*)':
dpal.c:1049:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
 1049 |   register const unsigned char *p;
      |                                 ^
dpal.c: In function 'void _dpal_long_nopath_maxgap1_local_end(const unsigned char*, const unsigned char*, int, int, const dpal_args*, dpal_results*)':
dpal.c:1072:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
 1072 |   register int i, j;
      |                ^
dpal.c:1072:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
 1072 |   register int i, j;
      |                   ^
dpal.c:1073:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
 1073 |   register int gap = in->gap;
      |                ^~~
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;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n");
      |     ^~~
dpal.c:1036:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1036 |     for(i=j;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n");
      |                                                      ^~~~~~~
dpal.c: In function 'int illegal_char(const unsigned char*, const int (*)[256], char*)':
dpal.c:1049:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
 1049 |   register const unsigned char *p;
      |                                 ^
dpal.c: In function 'void _dpal_long_nopath_maxgap1_local_end(const unsigned char*, const unsigned char*, int, int, const dpal_args*, dpal_results*)':
dpal.c:1072:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
 1072 |   register int i, j;
      |                ^
dpal.c:1072:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
 1072 |   register int i, j;
      |                   ^
dpal.c:1073:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
 1073 |   register int gap = in->gap;
      |                ^~~
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