Mock Version: 6.5 Mock Version: 6.5 Mock Version: 6.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target riscv64 --nodeps /builddir/build/SPECS/seaview.spec'], chrootPath='/var/lib/mock/f45-build-35877-699/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=864000uid=995gid=135user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fuaglavz:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fuaglavz:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '40f038dfe284445c9f04f8c8a2fc601b', '-D', '/var/lib/mock/f45-build-35877-699/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fuaglavz:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target riscv64 --nodeps /builddir/build/SPECS/seaview.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: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1784246400 Wrote: /builddir/build/SRPMS/seaview-5.1-5.fc45.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target riscv64 --nodeps /builddir/build/SPECS/seaview.spec'], chrootPath='/var/lib/mock/f45-build-35877-699/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=864000uid=995gid=135user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fuaglavz:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fuaglavz:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'cc89c2fbcc6b49e28b86c5373882fc75', '-D', '/var/lib/mock/f45-build-35877-699/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.fuaglavz:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target riscv64 --nodeps /builddir/build/SPECS/seaview.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: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1784246400 Executing(mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.OZ0XGI Creating(rpmbuild.env): /builddir/build/BUILD/seaview-5.1-build/rpmbuild.env RPM_SOURCE_DIR="/builddir/build/SOURCES" RPM_BUILD_DIR="/builddir/build/BUILD/seaview-5.1-build" RPM_OPT_FLAGS="-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer" RPM_LD_FLAGS="-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes " RPM_ARCH="riscv64" RPM_OS="linux" RPM_BUILD_NCPUS="8" RPM_SPECPARTS_DIR="/builddir/build/BUILD/seaview-5.1-build/SPECPARTS" export RPM_SOURCE_DIR RPM_BUILD_DIR RPM_OPT_FLAGS RPM_ARCH RPM_OS RPM_BUILD_NCPUS RPM_SPECPARTS_DIR RPM_LD_FLAGS RPM_DOC_DIR="/usr/share/doc" export RPM_DOC_DIR RPM_PACKAGE_NAME="seaview" RPM_PACKAGE_VERSION="5.1" RPM_PACKAGE_RELEASE="5.fc45" export RPM_PACKAGE_NAME RPM_PACKAGE_VERSION RPM_PACKAGE_RELEASE LANG=C.UTF-8 export LANG unset CDPATH DISPLAY ||: unset DEBUGINFOD_URLS ||: unset RPM_CONFIG_DIR ||: RPM_BUILD_ROOT="/builddir/build/BUILD/seaview-5.1-build/BUILDROOT" export RPM_BUILD_ROOT PKG_CONFIG_PATH="${PKG_CONFIG_PATH}:/usr/lib64/pkgconfig:/usr/share/pkgconfig" export PKG_CONFIG_PATH CONFIG_SITE=${CONFIG_SITE:-NONE} export CONFIG_SITE Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.UtXfDJ + umask 022 + cd /builddir/build/BUILD/seaview-5.1-build + cd /builddir/build/BUILD/seaview-5.1-build + rm -rf seaview + /usr/bin/rpmuncompress -x /builddir/build/SOURCES/seaview_5.1.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd seaview + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (seaview-chris.patch): + echo 'Patch #0 (seaview-chris.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .chris --fuzz=0 patching file Makefile + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.Je9C3m + umask 022 + cd /builddir/build/BUILD/seaview-5.1-build + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 seaview + make -j8 c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" seaview.cxx c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" custom.cxx c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" use_mase_files.cxx c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" regions.cxx c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" load_seq.cxx c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" align.cxx c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" xfmatpt.cxx c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" comlines.cxx regions.cxx: In function ‘void save_active_region(SEA_VIEW*)’: regions.cxx:503:10: warning: variable ‘taille’ set but not used [-Wunused-but-set-variable=] 503 | int tmp, taille; | ^~~~~~ regions.cxx: In function ‘int create_gblocks_mask(SEA_VIEW*, region*, int, int, int, int, int)’: regions.cxx:314:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 314 | system(cmd); | ~~~~~~^~~~~ use_mase_files.cxx: In function ‘int read_mase_seqs_header(const char*, char***, char***, char***, char**, char**)’: use_mase_files.cxx:215:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 215 | while((line[l-1] == ' ' || line[l-1] == '\n') && l>0 ) l--; line[l] = 0; | ^~~~~ use_mase_files.cxx:215:69: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 215 | while((line[l-1] == ' ' || line[l-1] == '\n') && l>0 ) l--; line[l] = 0; | ^~~~ use_mase_files.cxx: In function ‘int read_clustal_align(const char*, char***, char***, char***, char**, char**)’: use_mase_files.cxx:623:17: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 623 | while(*p==' ') p--; *(p+1)=0; | ^~~~~ use_mase_files.cxx:623:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 623 | while(*p==' ') p--; *(p+1)=0; | ^ align.cxx: In function ‘void replace_stars(char*)’: align.cxx:1310:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1310 | fread(all, 1, l, in); | ~~~~~^~~~~~~~~~~~~~~ seaview.cxx: In function ‘int delete_selected_seqs(SEA_VIEW*)’: seaview.cxx:1759:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 1759 | for(i = 0, j = 0; i< view->tot_seqs; i++) | ^~~ seaview.cxx:1762:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1762 | memcpy(view->col_rank , temp_data, new_tot_seqs * sizeof(char *) ); | ^~~~~~ seaview.cxx: In function ‘void colors_callback(Fl_Widget*, void*)’: seaview.cxx:1913:15: warning: variable ‘item’ set but not used [-Wunused-but-set-variable=] 1913 | Fl_Menu_Item *item; | ^~~~ seaview.cxx: In function ‘void delete_tmp_filename(const char*)’: seaview.cxx:638:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 638 | system(fname); | ~~~~~~^~~~~~~ seaview.cxx: In function ‘char* run_and_close_native_file_chooser(Fl_Native_File_Chooser*, int)’: seaview.cxx:2908:45: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2908 | if( *last_visited_directory )chdir(last_visited_directory); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ regions.cxx:291:40: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 496 [-Wformat-truncation=] 291 | snprintf(cmd, sizeof(cmd), "\"%s\" \"%s\" -p=s -t=%c", q, fname, view->protein?'p':'d'); | ^~ ~~~~~ In file included from /usr/include/stdio.h:974, from seaview.h:3, from regions.cxx:1: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘int create_gblocks_mask(SEA_VIEW*, region*, int, int, int, int, int)’ at regions.cxx:291:11: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output 16 or more bytes (assuming 4111) into a destination of size 500 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ regions.cxx: In function ‘int create_gblocks_mask(SEA_VIEW*, region*, int, int, int, int, int)’: regions.cxx:344:42: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized] 344 | memmove(cmd, last, l + 1 - (last - cmd)); | ~~~~~^~~~~ regions.cxx:246:56: note: ‘last’ was declared here 246 | char base_fname[PATH_MAX], fname[PATH_MAX], *p, *q, *last; | ^~~~ align.cxx: In function ‘void edit_align_callback(Fl_Widget*, void*)’: align.cxx:952:48: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 952 | snprintf(resname, sizeof(resname), "msa_name_%d", view->alignment_algorithm + 1); | ^ In file included from /usr/include/stdio.h:974, from seaview.h:3, from align.cxx:1: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void edit_align_callback(Fl_Widget*, void*)’ at align.cxx:952:9: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 11 and 21 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘void edit_align_callback(Fl_Widget*, void*)’: align.cxx:999:37: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size 7 [-Wformat-truncation=] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~ In function ‘char* get_opt_resname(int)’, inlined from ‘char* get_algo_opts(int, char**)’ at align.cxx:990:32, inlined from ‘void edit_align_callback(Fl_Widget*, void*)’ at align.cxx:954:21: align.cxx:999:23: note: directive argument in the range [-2147483647, 2147483647] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* get_opt_resname(int)’ at align.cxx:999:9, inlined from ‘char* get_algo_opts(int, char**)’ at align.cxx:990:32, inlined from ‘void edit_align_callback(Fl_Widget*, void*)’ at align.cxx:954:21: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 15 and 25 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘void align_opt_callback(Fl_Widget*, long int)’: align.cxx:999:37: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 7 [-Wformat-truncation=] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~ In function ‘char* get_opt_resname(int)’, inlined from ‘char* get_algo_opts(int, char**)’ at align.cxx:990:32, inlined from ‘void align_opt_callback(Fl_Widget*, long int)’ at align.cxx:976:22: align.cxx:999:23: note: directive argument in the range [1, 2147483647] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* get_opt_resname(int)’ at align.cxx:999:9, inlined from ‘char* get_algo_opts(int, char**)’ at align.cxx:990:32, inlined from ‘void align_opt_callback(Fl_Widget*, long int)’ at align.cxx:976:22: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 15 and 24 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘void align_opt_callback(Fl_Widget*, long int)’: align.cxx:981:21: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 5 [-Wformat-truncation=] 981 | snprintf(tmp, 5, "%d", reponse); | ^~ align.cxx:981:20: note: directive argument in the range [0, 2147483646] 981 | snprintf(tmp, 5, "%d", reponse); | ^~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void align_opt_callback(Fl_Widget*, long int)’ at align.cxx:981:11: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 2 and 11 bytes into a destination of size 5 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" resource.cxx align.cxx: In function ‘void delete_align_callback(Fl_Widget*, void*)’: align.cxx:829:50: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 829 | snprintf(msa_name, sizeof(msa_name), "msa_name_%d", view->alignment_algorithm + 1); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:829:9: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 11 and 21 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘void delete_align_callback(Fl_Widget*, void*)’: align.cxx:839:58: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 839 | snprintf(msa_name, sizeof(msa_name), "msa_name_%d", num + 1); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:839:10: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 11 and 21 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘void delete_align_callback(Fl_Widget*, void*)’: align.cxx:841:58: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 841 | snprintf(msa_name, sizeof(msa_name), "msa_name_%d", num); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:841:10: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 11 and 21 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘void delete_align_callback(Fl_Widget*, void*)’: align.cxx:844:58: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 844 | snprintf(msa_name, sizeof(msa_name), "msa_args_%d", num + 1); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:844:10: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 11 and 21 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘void delete_align_callback(Fl_Widget*, void*)’: align.cxx:846:58: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 846 | snprintf(msa_name, sizeof(msa_name), "msa_args_%d", num); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:846:10: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 11 and 21 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘void delete_align_callback(Fl_Widget*, void*)’: align.cxx:999:37: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size 7 [-Wformat-truncation=] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~ In function ‘char* get_opt_resname(int)’, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:849:24: align.cxx:999:23: note: directive argument in the range [-2147483646, 2147483647] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* get_opt_resname(int)’ at align.cxx:999:9, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:849:24: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 15 and 25 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘void delete_align_callback(Fl_Widget*, void*)’: align.cxx:999:37: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size 7 [-Wformat-truncation=] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~ In function ‘char* get_opt_resname(int)’, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:857:39: align.cxx:999:23: note: directive argument in the range [-2147483647, 2147483646] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* get_opt_resname(int)’ at align.cxx:999:9, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:857:39: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 15 and 25 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘void delete_align_callback(Fl_Widget*, void*)’: align.cxx:999:37: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size 7 [-Wformat-truncation=] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~ In function ‘char* get_opt_resname(int)’, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:853:26: align.cxx:999:23: note: directive argument in the range [-2147483647, 2147483646] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* get_opt_resname(int)’ at align.cxx:999:9, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:853:26: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 15 and 25 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘void delete_align_callback(Fl_Widget*, void*)’: align.cxx:999:37: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size 7 [-Wformat-truncation=] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~ In function ‘char* get_opt_resname(int)’, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:865:23: align.cxx:999:23: note: directive argument in the range [-2147483647, 2147483647] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* get_opt_resname(int)’ at align.cxx:999:9, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:865:23: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 15 and 25 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘void delete_align_callback(Fl_Widget*, void*)’: align.cxx:999:37: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size 7 [-Wformat-truncation=] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~ In function ‘char* get_opt_resname(int)’, inlined from ‘char* get_algo_opts(int, char**)’ at align.cxx:990:32, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:877:21: align.cxx:999:23: note: directive argument in the range [-2147483647, 2147483647] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* get_opt_resname(int)’ at align.cxx:999:9, inlined from ‘char* get_algo_opts(int, char**)’ at align.cxx:990:32, inlined from ‘void delete_align_callback(Fl_Widget*, void*)’ at align.cxx:877:21: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 15 and 25 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ xfmatpt.cxx: In function ‘void change_comput_params(Fl_Widget*, void*)’: xfmatpt.cxx:750:29: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 750 | snprintf(tmp, 10,"%d", fdui->identites); | ^ In file included from /usr/include/stdio.h:974, from seaview.h:3, from matpt.h:3, from xfmatpt.cxx:1: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void change_comput_params(Fl_Widget*, void*)’ at xfmatpt.cxx:750:10: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 2 and 11 bytes into a destination of size 10 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ regions.cxx: In function ‘const char* site_mask_creation_dialog(SEA_VIEW*, position_mask*)’: regions.cxx:746:10: warning: ‘retval’ may be used uninitialized [-Wmaybe-uninitialized] 746 | return retval; | ^~~~~~ regions.cxx:688:15: note: ‘retval’ was declared here 688 | const char *retval; | ^~~~~~ align.cxx: In function ‘char* calc_msa_command(SEA_VIEW*, char*, void (*)(const char*, ...))’: align.cxx:999:37: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size 7 [-Wformat-truncation=] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~ In function ‘char* get_opt_resname(int)’, inlined from ‘char* get_algo_opts(int, char**)’ at align.cxx:990:32, inlined from ‘char* calc_msa_command(SEA_VIEW*, char*, void (*)(const char*, ...))’ at align.cxx:615:24: align.cxx:999:23: note: directive argument in the range [-2147483647, 2147483647] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* get_opt_resname(int)’ at align.cxx:999:9, inlined from ‘char* get_algo_opts(int, char**)’ at align.cxx:990:32, inlined from ‘char* calc_msa_command(SEA_VIEW*, char*, void (*)(const char*, ...))’ at align.cxx:615:24: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 15 and 25 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘void cre_align_menu(SEA_VIEW*)’: align.cxx:999:37: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size 7 [-Wformat-truncation=] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~ In function ‘char* get_opt_resname(int)’, inlined from ‘char* get_algo_opts(int, char**)’ at align.cxx:990:32, inlined from ‘void cre_align_menu(SEA_VIEW*)’ at align.cxx:752:23: align.cxx:999:23: note: directive argument in the range [-2147483647, 2147483647] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* get_opt_resname(int)’ at align.cxx:999:9, inlined from ‘char* get_algo_opts(int, char**)’ at align.cxx:990:32, inlined from ‘void cre_align_menu(SEA_VIEW*)’ at align.cxx:752:23: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 15 and 25 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘char* get_algo_opts(int, char**)’: align.cxx:999:37: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size 7 [-Wformat-truncation=] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~ In function ‘char* get_opt_resname(int)’, inlined from ‘char* get_algo_opts(int, char**)’ at align.cxx:990:32: align.cxx:999:23: note: directive argument in the range [-2147483647, 2147483647] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* get_opt_resname(int)’ at align.cxx:999:9, inlined from ‘char* get_algo_opts(int, char**)’ at align.cxx:990:32: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 15 and 25 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" nexus.cxx align.cxx: In function ‘char* get_opt_resname(int)’: align.cxx:999:37: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size 7 [-Wformat-truncation=] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~ align.cxx:999:23: note: directive argument in the range [-2147483647, 2147483647] 999 | snprintf(resname, 20, "msa_opt_args_%d", algonum + 1); | ^~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* get_opt_resname(int)’ at align.cxx:999:9: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 15 and 25 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" viewasprots.cxx align.cxx: In function ‘int save_fasta_file_no_gaponly(char*, char**, int, int*, int*)’: align.cxx:1353:47: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 8 [-Wformat-truncation=] 1353 | snprintf(seqname[num], 10, "S_%d", num); | ^~ align.cxx:1353:44: note: directive argument in the range [0, 2147483646] 1353 | snprintf(seqname[num], 10, "S_%d", num); | ^~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘int save_fasta_file_no_gaponly(char*, char**, int, int*, int*)’ at align.cxx:1353:11: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 4 and 13 bytes into a destination of size 10 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ use_mase_files.cxx: In function ‘int read_mase_seqs_header(const char*, char***, char***, char***, char**, char**)’: use_mase_files.cxx:167:32: warning: ‘lpre’ may be used uninitialized [-Wmaybe-uninitialized] 167 | if(lpre+lseq > curr_max_header) { | ~~~~^~~~~ use_mase_files.cxx:137:18: note: ‘lpre’ was declared here 137 | int l, lenseqs, lpre, lseq, l2, totseqs = -1, want_header, curr_max_header; | ^~~~ align.cxx: In function ‘void unalign(SEA_VIEW*)’: align.cxx:1423:91: warning: ‘calc_color_function’ may be used uninitialized [-Wmaybe-uninitialized] 1423 | view->col_rank[num][i] = (char)calc_color_function( res ); | ~~~~~~~~~~~~~~~~~~~^~~~~~~ align.cxx:1395:15: note: ‘calc_color_function’ was declared here 1395 | int (*calc_color_function)(int); | ^~~~~~~~~~~~~~~~~~~ seaview.cxx: In function ‘void help_callback(Fl_Widget*, void*)’: seaview.cxx:3627:53: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 3627 | "Help file %s\nnot found in PATH directories nor in current directory", help_file | ^~ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" racnuc_fetch.cxx seaview.cxx: In function ‘void _Z11draw_headerP9Fl_WidgetP9_SEA_VIEW.part.0(Fl_Widget*, SEA_VIEW*)’: seaview.cxx:1130:28: warning: ‘%7d’ directive output may be truncated writing between 7 and 11 bytes into a region of size 10 [-Wformat-truncation=] 1130 | snprintf(site_line, 10, "%7d", view->first_site + view->tot_sites - 1); | ^~~ seaview.cxx:1130:27: note: directive argument in the range [-2147483648, 2147483646] 1130 | snprintf(site_line, 10, "%7d", view->first_site + view->tot_sites - 1); | ^~~~~ In file included from /usr/include/stdio.h:974, from seaview.h:3, from seaview.cxx:67: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void _Z11draw_headerP9Fl_WidgetP9_SEA_VIEW.part.0(Fl_Widget*, SEA_VIEW*)’ at seaview.cxx:1130:11: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 8 and 12 bytes into a destination of size 10 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ align.cxx: In function ‘int replace_align_part(SEA_VIEW*, int, int, char*, int, int, int*, align_choice, const char**)’: align.cxx:456:83: warning: ‘calc_color_function’ may be used uninitialized [-Wmaybe-uninitialized] 456 | view->col_rank[num][i] = (char)calc_color_function( res ); | ~~~~~~~~~~~~~~~~~~~^~~~~~~ align.cxx:300:7: note: ‘calc_color_function’ was declared here 300 | int (*calc_color_function)(int); | ^~~~~~~~~~~~~~~~~~~ use_mase_files.cxx: In function ‘int read_phylip_align(const char*, char***, char***, char***, char**, char**)’: use_mase_files.cxx:521:7: warning: ‘q’ may be used uninitialized [-Wmaybe-uninitialized] 521 | l = q - seq[totseqs - 1]; | ~~^~~~~~~~~~~~~~~~~~ use_mase_files.cxx:466:11: note: ‘q’ was declared here 466 | char *p, *q; | ^ use_mase_files.cxx: In function ‘int read_clustal_align(const char*, char***, char***, char***, char**, char**)’: use_mase_files.cxx:617:61: warning: ‘wid_name’ may be used uninitialized [-Wmaybe-uninitialized] 617 | seqname[curr_spec] = (char *)malloc(wid_name+1); | ~~~~~~~~^~ use_mase_files.cxx:564:16: note: ‘wid_name’ was declared here 564 | carac, wid_name; | ^~~~~~~~ use_mase_files.cxx:650:15: warning: ‘l’ may be used uninitialized [-Wmaybe-uninitialized] 650 | memcpy(seq[curr_spec]+curr_len, line + wid_name, l); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ use_mase_files.cxx:563:8: note: ‘l’ was declared here 563 | int i, l, curr_spec, first=TRUE, curr_len, next_len, tot_spec, curr_max_len, | ^ align.cxx: In function ‘void profile_align(SEA_VIEW*)’: align.cxx:1289:90: warning: ‘calc_color_function’ may be used uninitialized [-Wmaybe-uninitialized] 1289 | view->col_rank[table[num]][i] = (char)calc_color_function( res ); | ~~~~~~~~~~~~~~~~~~~^~~~~~~ align.cxx:1116:15: note: ‘calc_color_function’ was declared here 1116 | int (*calc_color_function)(int); | ^~~~~~~~~~~~~~~~~~~ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" concatenate.cxx align.cxx: In function ‘int command_line_align(int, char**)’: align.cxx:1515:56: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size 7 [-Wformat-truncation=] 1515 | snprintf(opt_name, sizeof(opt_name), "msa_opt_args_%d", | ^~ align.cxx:1515:42: note: directive argument in the range [-2147483647, 2147483647] 1515 | snprintf(opt_name, sizeof(opt_name), "msa_opt_args_%d", | ^~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘int command_line_align(int, char**)’ at align.cxx:1515:13: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 15 and 25 bytes into a destination of size 20 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from seaview.h:13: In member function ‘void Fl_Menu_Item::clear()’, inlined from ‘int command_line_align(int, char**)’ at align.cxx:1512:14: /usr/include/FL/Fl_Menu_Item.H:326:17: warning: ‘((Fl_Menu_Item*))[16].Fl_Menu_Item::flags’ is used uninitialized [-Wuninitialized] 326 | void clear() {flags &= ~FL_MENU_VALUE;} | ^~~~~ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" statistics.cxx use_mase_files.cxx: In function ‘int printout(SEA_VIEW*, const char*, int, int, Fl_Paged_Device::Page_Format, int, int, int, Fl_Paged_Device::Page_Layout, int)’: use_mase_files.cxx:1833:35: warning: ‘lines_per_page’ may be used uninitialized [-Wmaybe-uninitialized] 1833 | if( use_pdf && (!firstpage) && (curr_lines + view->tot_seqs + nl > lines_per_page)) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ use_mase_files.cxx:1678:32: note: ‘lines_per_page’ was declared here 1678 | res_per_line, nl, firstpage, lines_per_page, use_pdf, use_svg, top_margin; | ^~~~~~~~~~~~~~ use_mase_files.cxx:1769:14: warning: ‘top_margin’ may be used uninitialized [-Wmaybe-uninitialized] 1769 | fl_draw(oneline, margin, top_margin); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ use_mase_files.cxx:1678:66: note: ‘top_margin’ was declared here 1678 | res_per_line, nl, firstpage, lines_per_page, use_pdf, use_svg, top_margin; | ^~~~~~~~~~ In function ‘void color_pdf_display(SEA_VIEW*, int (*)(int), char*, int, double, double, int, double, double, int, int)’, inlined from ‘int printout(SEA_VIEW*, const char*, int, int, Fl_Paged_Device::Page_Format, int, int, int, Fl_Paged_Device::Page_Layout, int)’ at use_mase_files.cxx:1920:34: use_mase_files.cxx:1984:33: warning: ‘descender’ may be used uninitialized [-Wmaybe-uninitialized] 1984 | fl_rectf(xx, y - fontsize + descender, char_width+1, fontsize); | ~~~~~~~~~~~~~^~~~~~~~~~~ use_mase_files.cxx: In function ‘int printout(SEA_VIEW*, const char*, int, int, Fl_Paged_Device::Page_Format, int, int, int, Fl_Paged_Device::Page_Layout, int)’: use_mase_files.cxx:1689:42: note: ‘descender’ was declared here 1689 | double char_width = fontsize/2, descender, margin = 25; | ^~~~~~~~~ use_mase_files.cxx:1767:48: warning: ‘surface’ may be used uninitialized [-Wmaybe-uninitialized] 1767 | ((PDF_or_PS_File_Device*)surface)->origin(0, fontsize); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ use_mase_files.cxx:1679:22: note: ‘surface’ was declared here 1679 | Fl_Surface_Device *surface; | ^~~~~~~ In file included from /usr/include/string.h:580, from seaview.h:5, from use_mase_files.cxx:1: In function ‘void* memset(void*, int, size_t)’, inlined from ‘int printout(SEA_VIEW*, const char*, int, int, Fl_Paged_Device::Page_Format, int, int, int, Fl_Paged_Device::Page_Layout, int)’ at use_mase_files.cxx:1822:8: /usr/include/bits/string_fortified.h:59:33: warning: ‘vary_pos’ may be used uninitialized [-Wmaybe-uninitialized] 59 | return __builtin___memset_chk (__dest, __ch, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 60 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ use_mase_files.cxx: In function ‘int printout(SEA_VIEW*, const char*, int, int, Fl_Paged_Device::Page_Format, int, int, int, Fl_Paged_Device::Page_Layout, int)’: use_mase_files.cxx:1686:8: note: ‘vary_pos’ was declared here 1686 | int *vary_pos; /* rang ds alignement de la colonne imprimée */ | ^~~~~~~~ concatenate.cxx: In function ‘void concatenate(SEA_VIEW*, SEA_VIEW*, bool, bool, bool)’: concatenate.cxx:123:32: warning: ‘found’ may be used uninitialized [-Wmaybe-uninitialized] 123 | if (want_addgaps) found[j] = TRUE; | ^ concatenate.cxx:99:17: note: ‘found’ was declared here 99 | int i, j, l, *found, target_length = target->seq_length; | ^~~~~ concatenate.cxx:113:25: warning: ‘gaps’ may be used uninitialized [-Wmaybe-uninitialized] 113 | add_seq_to_align(target, source->seqname[i], gaps, target_length, no_gui); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ concatenate.cxx:100:9: note: ‘gaps’ was declared here 100 | char *gaps; | ^~~~ xfmatpt.cxx: In function ‘int really_close(FD_matpt*)’: xfmatpt.cxx:889:5: warning: ‘void free(void*)’ called on pointer ‘*matpt.FD_matpt::seq1’ with nonzero offset 1 [-Wfree-nonheap-object] 889 | free(matpt->seq1 + 1); | ~~~~^~~~~~~~~~~~~~~~~ xfmatpt.cxx:890:5: warning: ‘void free(void*)’ called on pointer ‘*matpt.FD_matpt::seq2’ with nonzero offset 1 [-Wfree-nonheap-object] 890 | free(matpt->seq2 + 1); | ~~~~^~~~~~~~~~~~~~~~~ xfmatpt.cxx: In function ‘void show_dot_plot(char*, char*, char*, char*, int, int, int, void*)’: xfmatpt.cxx:124:21: warning: ‘void free(void*)’ called on pointer ‘*matpt.FD_matpt::seq1’ with nonzero offset 1 [-Wfree-nonheap-object] 124 | free(matpt->seq1+1); | ~~~~^~~~~~~~~~~~~~~ xfmatpt.cxx:125:21: warning: ‘void free(void*)’ called on pointer ‘*matpt.FD_matpt::seq2’ with nonzero offset 1 [-Wfree-nonheap-object] 125 | free(matpt->seq2+1); | ~~~~^~~~~~~~~~~~~~~ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" trees.cxx c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" treedraw.cxx c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" addbootstrap.cxx statistics.cxx: In function ‘void geni_act(SEA_VIEW*)’: statistics.cxx:365:24: warning: variable ‘nbcp’ set but not used [-Wunused-but-set-variable=] 365 | int *selected, nbaa, nbcp; | ^~~~ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" least_squares_brl.cxx nexus.cxx: In function ‘char** process_taxa_taxlabels(FILE*, int)’: nexus.cxx:357:1: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 357 | if(p != NULL && *p != ';') skip_command(in); | ^~ nexus.cxx:343:7: note: ‘p’ was declared here 343 | char *p, **names; | ^ least_squares_brl.cxx: In function ‘int tree_ctob(char*, char**, int, int**)’: least_squares_brl.cxx:190:23: warning: variable ‘k’ set but not used [-Wunused-but-set-variable=] 190 | int i=0, j, k, fin=0, nbpo=0, | ^ nexus.cxx: In function ‘char** process_block_characters(FILE*, int*, char***, int*, int*)’: nexus.cxx:685:52: warning: ‘gap’ may be used uninitialized [-Wmaybe-uninitialized] 685 | seqs = process_chars_matrix(in, *nsites, gap, | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 686 | *pntaxa, *taxnames, FALSE, matchchar, missing, *protein); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nexus.cxx:667:19: note: ‘gap’ was declared here 667 | int interleave=0, gap, matchchar = 0, missing = 0; | ^~~ use_mase_files.cxx: In function ‘void format_conversion(int, char**)’: use_mase_files.cxx:2373:3: warning: ‘err_message’ may be used uninitialized [-Wmaybe-uninitialized] 2373 | if (err_message) { | ^~ use_mase_files.cxx:2175:9: note: ‘err_message’ was declared here 2175 | char *err_message, *p; | ^~~~~~~~~~~ use_mase_files.cxx:2274:27: warning: ‘current_seg’ may be used uninitialized [-Wmaybe-uninitialized] 2274 | current_seg->next = seg; | ~~~~~~~~~~~~~~~~~~^~~~~ use_mase_files.cxx:2239:20: note: ‘current_seg’ was declared here 2239 | list_segments *current_seg; | ^~~~~~~~~~~ least_squares_brl.cxx: In function ‘int tree_btos(int**, int, double*, double*, double*, char**, noeud2**)’: least_squares_brl.cxx:373:41: warning: ‘tax1’ may be used uninitialized [-Wmaybe-uninitialized] 373 | p1 = bottomnode(arbre_s[tax1]); | ^~~~ least_squares_brl.cxx:310:48: note: ‘tax1’ was declared here 310 | int notuv, i, j, k, sommebi, tax1, tax2, n1=0, n2=0, n3=0, cpt1=-1; | ^~~~ least_squares_brl.cxx:374:41: warning: ‘tax2’ may be used uninitialized [-Wmaybe-uninitialized] 374 | p2 = bottomnode(arbre_s[tax2]); | ^~~~ least_squares_brl.cxx:310:54: note: ‘tax2’ was declared here 310 | int notuv, i, j, k, sommebi, tax1, tax2, n1=0, n2=0, n3=0, cpt1=-1; | ^~~~ least_squares_brl.cxx:349:17: warning: ‘sommebi’ may be used uninitialized [-Wmaybe-uninitialized] 349 | if (sommebi == 2) { | ^~ least_squares_brl.cxx:310:39: note: ‘sommebi’ was declared here 310 | int notuv, i, j, k, sommebi, tax1, tax2, n1=0, n2=0, n3=0, cpt1=-1; | ^~~~~~~ seaview.cxx: In function ‘void goto_callback(Fl_Widget*, void*)’: seaview.cxx:2737:16: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2737 | strncpy(target, p, l); target[l] = 0; majuscules(target); | ^ seaview.cxx:2735:19: note: length computed here 2735 | l = strlen(p); | ~~~~~~^~~ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" pseudoterminal.cxx c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" unrooted.cxx statistics.cxx:366:43: warning: ‘compgroup’ may be used uninitialized [-Wmaybe-uninitialized] 366 | double **comp, *compall, compcomp[4], **compgroup, *compgroupall, min[4], max[4]; | ^~~~~~~~~ statistics.cxx:366:55: warning: ‘compgroupall’ may be used uninitialized [-Wmaybe-uninitialized] 366 | double **comp, *compall, compcomp[4], **compgroup, *compgroupall, min[4], max[4]; | ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:974, from seaview.h:3, from statistics.cxx:1: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void geni_act(SEA_VIEW*)’ at statistics.cxx:653:15: /usr/include/bits/stdio2.h:68:35: warning: ‘titvmin’ may be used uninitialized [-Wmaybe-uninitialized] 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ statistics.cxx: In function ‘void geni_act(SEA_VIEW*)’: statistics.cxx:367:77: note: ‘titvmin’ was declared here 367 | double P, Psum=0., Q, Qsum=0., Pmin=0, Pmax=0, Qmin=0, Qmax=0, titvratio, titvmin, titvmax, freq[16], mat_obs[16], *ti, *tv; | ^~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void geni_act(SEA_VIEW*)’ at statistics.cxx:655:15: /usr/include/bits/stdio2.h:68:35: warning: ‘titvmax’ may be used uninitialized [-Wmaybe-uninitialized] 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ statistics.cxx: In function ‘void geni_act(SEA_VIEW*)’: statistics.cxx:367:86: note: ‘titvmax’ was declared here 367 | double P, Psum=0., Q, Qsum=0., Pmin=0, Pmax=0, Qmin=0, Qmax=0, titvratio, titvmin, titvmax, freq[16], mat_obs[16], *ti, *tv; | ^~~~~~~ In file included from /usr/include/string.h:580, from seaview.h:5: In function ‘void* memset(void*, int, size_t)’, inlined from ‘int insert_gaps_at(SEA_VIEW*, int, int, int)’ at seaview.cxx:3685:8: /usr/include/bits/string_fortified.h:59:33: warning: ‘gapcolor’ may be used uninitialized [-Wmaybe-uninitialized] 59 | return __builtin___memset_chk (__dest, __ch, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 60 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ seaview.cxx: In function ‘int insert_gaps_at(SEA_VIEW*, int, int, int)’: seaview.cxx:3665:8: note: ‘gapcolor’ was declared here 3665 | int l, gapcolor, *plength; | ^~~~~~~~ trees.cxx: In function ‘matrix* Obs_Dist(allseq*, model*)’: trees.cxx:1599:16: warning: variable ‘unc_len’ set but not used [-Wunused-but-set-variable=] 1599 | phydbl unc_len; | ^~~~~~~ trees.cxx: In function ‘matrix* K80_dist_nogamma(allseq*)’: trees.cxx:1741:16: warning: variable ‘unc_len’ set but not used [-Wunused-but-set-variable=] 1741 | phydbl unc_len; | ^~~~~~~ treedraw.cxx: In function ‘int compare_newick_with_names(const char*, char**, int, char**)’: treedraw.cxx:2936:13: warning: variable ‘found’ set but not used [-Wunused-but-set-variable=] 2936 | int found = 0, i, l, *seen, retval; | ^~~~~ seaview.cxx: In function ‘void del_gap_only_sites(SEA_VIEW*)’: seaview.cxx:1696:23: warning: ‘debut’ may be used uninitialized [-Wmaybe-uninitialized] 1696 | count = position - debut; | ~~~~~~^~~~~~~~~~~~~~~~~~ seaview.cxx:1675:39: note: ‘debut’ was declared here 1675 | int position, numseq, allgaps, inrun, debut, count; | ^~~~~ pseudoterminal.cxx: In function ‘int run_external_prog_in_pseudoterm(char*, const char*, const char*)’: pseudoterminal.cxx:354:24: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 354 | freopen( (dialogfname ? dialogfname : slavename), "r", stdin); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pseudoterminal.cxx:355:24: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | freopen(slavename, "a", stderr); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" pdf_or_ps.cxx seaview.cxx: In function ‘int delete_selected_seqs(SEA_VIEW*)’: seaview.cxx:1730:48: warning: ‘temp_data’ may be used uninitialized [-Wmaybe-uninitialized] 1730 | if( ! view->sel_seqs[i] ) temp_data[j++] = (void *) view->sequence[i]; | ^ seaview.cxx:1718:8: note: ‘temp_data’ was declared here 1718 | void **temp_data; | ^~~~~~~~~ seaview.cxx:1755:47: warning: ‘temp_int’ may be used uninitialized [-Wmaybe-uninitialized] 1755 | if( ! view->sel_seqs[i] ) temp_int[j++]= view->each_length[i]; | ^ seaview.cxx:1720:26: note: ‘temp_int’ was declared here 1720 | int new_tot_seqs, i, j, *temp_int, numset; | ^~~~~~~~ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" svg.cxx trees.cxx: In function ‘char* replace_tree_names_by_rank(const char*, char**, int)’: trees.cxx:2736:13: warning: variable ‘found’ set but not used [-Wunused-but-set-variable=] 2736 | int found = 0, i, l; | ^~~~~ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" threads.cxx seaview.cxx: In function ‘void deplacer_grp_seqs(SEA_VIEW*, int)’: seaview.cxx:3882:57: warning: ‘*’ may be used uninitialized [-Wmaybe-uninitialized] 3882 | view->cursor_seq = new_rank[view->cursor_seq - 1] + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" tbe.cxx unrooted.cxx: In function ‘hit try_angle_draw(float, int*, int*, float*, int, int, int, int)’: unrooted.cxx:636:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 636 | if(x2 > xmax) xmax = x2; if(x3 > xmax) xmax = x3; if(x4 > xmax) xmax = x4; | ^~ unrooted.cxx:636:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 636 | if(x2 > xmax) xmax = x2; if(x3 > xmax) xmax = x3; if(x4 > xmax) xmax = x4; | ^~ unrooted.cxx:637:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 637 | if(x2 < xmin) xmin = x2; if(x3 < xmin) xmin = x3; if(x4 < xmin) xmin = x4; | ^~ unrooted.cxx:637:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 637 | if(x2 < xmin) xmin = x2; if(x3 < xmin) xmin = x3; if(x4 < xmin) xmin = x4; | ^~ unrooted.cxx:638:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 638 | if(y2 > ymax) ymax = y2; if(y3 > ymax) ymax = y3; if(y4 > ymax) ymax = y4; | ^~ unrooted.cxx:638:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 638 | if(y2 > ymax) ymax = y2; if(y3 > ymax) ymax = y3; if(y4 > ymax) ymax = y4; | ^~ unrooted.cxx:639:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 639 | if(y2 < ymin) ymin = y2; if(y3 < ymin) ymin = y3; if(y4 < ymin) ymin = y4; | ^~ unrooted.cxx:639:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 639 | if(y2 < ymin) ymin = y2; if(y3 < ymin) ymin = y3; if(y4 < ymin) ymin = y4; | ^~ unrooted.cxx: In function ‘int set_angles_noeuds(bignoeud*, bignoeud*, double, double*, double)’: unrooted.cxx:1084:20: warning: variable ‘totfeuilles’ set but not used [-Wunused-but-set-variable=] 1084 | static int totfeuilles=0; | ^~~~~~~~~~~ c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" treerecs_draw.cxx c++ -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I. -Icsrc -DDEFAULT_HELPFILE=\"/usr/share/doc/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" FL/Fl_SVG_Image.cxx trees.cxx: In function ‘void run_phyml_callback(Fl_Widget*, void*)’: trees.cxx:1309:16: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1309 | fread(bootstrap_trees, l, 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ seaview.cxx: In function ‘void edit_menu_callback(Fl_Widget*, void*)’: seaview.cxx:2572:17: warning: ‘new_pos’ may be used uninitialized [-Wmaybe-uninitialized] 2572 | new_pos += 2; | ~~~~~~~~^~~~ seaview.cxx:2556:30: note: ‘new_pos’ was declared here 2556 | int old_total, *tmp, new_pos, i, old_first_seq; | ^~~~~~~ trees.cxx: In function ‘void command_line_phylogeny(int, char**)’: trees.cxx:2823:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2823 | fread(utree, s, 1, in); | ~~~~~^~~~~~~~~~~~~~~~~ trees.cxx: In function ‘char* parsimony_with_bootstrap(allseq*, char**, char**, int, int, int, int*, int, int, Fl_Box*, int*, dnapars_S_option, int, float, int*, char**)’: trees.cxx:2434:25: warning: pointer ‘bootstrap_trees’ used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free] 2434 | q = tmpc + (q - bootstrap_trees); | ~~^~~~~~~~~~~~~~~~~ trees.cxx:2433:38: note: call to ‘void* realloc(void*, size_t)’ here 2433 | char *tmpc = (char*)realloc(bootstrap_trees, lbtrees + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ trees.cxx: In function ‘void run_phyml_callback(Fl_Widget*, void*)’: trees.cxx:1290:30: warning: pointer ‘b_tree’ used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free] 1290 | q = tree2 + (q - b_tree); | ~~^~~~~~~~ trees.cxx:1289:38: note: call to ‘void* realloc(void*, size_t)’ here 1289 | tree2 = (char *)realloc(b_tree, l + 1); | ~~~~~~~^~~~~~~~~~~~~~~ tbe.cxx: In function ‘char* TBE_Compute(char*, char*)’: tbe.cxx:85:16: warning: pointer ‘ref_branches’ used after ‘void free(void*)’ [-Wuse-after-free] 85 | TBE_PrintTree(newtree,fd_reftree,ref_branches, nboot); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tbe.cxx:83:7: note: call to ‘void free(void*)’ here 83 | free(ref_branches); | ~~~~^~~~~~~~~~~~~~ addbootstrap.cxx: In function ‘char* compute_consensus_tree(char**, int**, int)’: addbootstrap.cxx:896:7: warning: ‘k’ may be used uninitialized [-Wmaybe-uninitialized] 896 | if (k < height) { // columns were not all identical, try columns on 0-side of branch i | ^~ addbootstrap.cxx:854:13: note: ‘k’ was declared here 854 | int i, j, k, l, w, word, restbranches, j1; | ^ seaview.cxx: In function ‘void handle_keyboard(SEA_VIEW*, unsigned int, int)’: seaview.cxx:4608:9: warning: ‘count_each’ may be used uninitialized [-Wmaybe-uninitialized] 4608 | if(count_each == multipl && | ^~ seaview.cxx:4572:20: note: ‘count_each’ was declared here 4572 | int count, count_each, debut, fin, test; | ^~~~~~~~~~ seaview.cxx:4735:17: warning: ‘count_each’ may be used uninitialized [-Wmaybe-uninitialized] 4735 | if(count_each == multipl && | ^~ seaview.cxx:4670:39: note: ‘count_each’ was declared here 4670 | int newlength = 0, count = 0, count_each, debut, fin, test; | ^~~~~~~~~~ seaview.cxx:4659:9: warning: ‘count_each’ may be used uninitialized [-Wmaybe-uninitialized] 4659 | if(count_each == multipl && view->regions != NULL) | ^~ seaview.cxx:4636:13: note: ‘count_each’ was declared here 4636 | int count_each; | ^~~~~~~~~~ seaview.cxx:4618:17: warning: ‘count’ may be used uninitialized [-Wmaybe-uninitialized] 4618 | new_pos = view->cursor_site - count; | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ seaview.cxx:4572:13: note: ‘count’ was declared here 4572 | int count, count_each, debut, fin, test; | ^~~~~ unrooted.cxx:1123:48: warning: ‘poids1’ may be used uninitialized [-Wmaybe-uninitialized] 1123 | debut->position.angle = (poids1*angle1 + poids2*angle2)/(poids1+poids2); | ~~~~~~^~~~~~~ unrooted.cxx:1082:20: note: ‘poids1’ was declared here 1082 | int poids, poids1, poids2; | ^~~~~~ unrooted.cxx:1123:64: warning: ‘poids2’ may be used uninitialized [-Wmaybe-uninitialized] 1123 | debut->position.angle = (poids1*angle1 + poids2*angle2)/(poids1+poids2); | ~~~~~~^~~~~~~ unrooted.cxx:1082:28: note: ‘poids2’ was declared here 1082 | int poids, poids1, poids2; | ^~~~~~ unrooted.cxx:1130:16: warning: ‘poids’ may be used uninitialized [-Wmaybe-uninitialized] 1130 | return poids; | ^~~~~ unrooted.cxx:1082:13: note: ‘poids’ was declared here 1082 | int poids, poids1, poids2; | ^~~~~ cc -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -Icsrc csrc/raa_acnuc.c FL/Fl_SVG_Image.cxx: In function ‘char* svg_inflate(const char*)’: FL/Fl_SVG_Image.cxx:87:20: warning: pointer ‘out’ used after ‘void* realloc(void*, size_t)’ [-Wuse-after-free] 87 | p = tmp + (p - out); | ~~^~~~~ FL/Fl_SVG_Image.cxx:86:33: note: call to ‘void* realloc(void*, size_t)’ here 86 | char *tmp = (char*)realloc(out, out_size + 1); | ~~~~~~~^~~~~~~~~~~~~~~~~~~ csrc/raa_acnuc.c: In function ‘raa_bit1’: csrc/raa_acnuc.c:1086:7: warning: variable ‘reponse’ set but not used [-Wunused-but-set-variable=] 1086 | char *reponse; | ^~~~~~~ csrc/raa_acnuc.c: In function ‘raa_bit0’: csrc/raa_acnuc.c:1096:7: warning: variable ‘reponse’ set but not used [-Wunused-but-set-variable=] 1096 | char *reponse; | ^~~~~~~ csrc/raa_acnuc.c: In function ‘raa_copylist’: csrc/raa_acnuc.c:1117:7: warning: variable ‘reponse’ set but not used [-Wunused-but-set-variable=] 1117 | char *reponse; | ^~~~~~~ csrc/raa_acnuc.c: In function ‘raa_zerolist’: csrc/raa_acnuc.c:1127:7: warning: variable ‘reponse’ set but not used [-Wunused-but-set-variable=] 1127 | char *reponse; | ^~~~~~~ csrc/raa_acnuc.c: In function ‘raa_setliststate’: csrc/raa_acnuc.c:1137:7: warning: variable ‘reponse’ set but not used [-Wunused-but-set-variable=] 1137 | char *reponse, str_type[3]; | ^~~~~~~ cc -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -Icsrc csrc/parser.c cc -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -Icsrc csrc/md5.c csrc/md5.c:200:34: warning: argument 1 of type ‘uint32[4]’ {aka ‘unsigned int[4]’} with mismatched bound [-Warray-parameter=] 200 | static void MD5_Transform(uint32 buf[4], uint32 const in[16]) | ~~~~~~~^~~~~~ csrc/md5.c:47:35: note: previously declared as ‘uint32 *’ {aka ‘unsigned int *’} 47 | static void MD5_Transform(uint32 *buf, uint32 const *in); | ~~~~~~~~^~~ csrc/md5.c:200:55: warning: argument 2 of type ‘const uint32[16]’ {aka ‘const unsigned int[16]’} with mismatched bound [-Warray-parameter=] 200 | static void MD5_Transform(uint32 buf[4], uint32 const in[16]) | ~~~~~~~~~~~~~^~~~~~ csrc/md5.c:47:54: note: previously declared as ‘const uint32 *’ {aka ‘const unsigned int *’} 47 | static void MD5_Transform(uint32 *buf, uint32 const *in); | ~~~~~~~~~~~~~~^~ cc -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -Icsrc csrc/zsockr.c cc -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -Icsrc csrc/misc_acnuc.c cc -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -Icsrc csrc/dnapars.c cc -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -Icsrc csrc/protpars.c csrc/dnapars.c: In function ‘dnapars’: csrc/dnapars.c:1682:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1682 | fread(tree, L, 1, outtree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ csrc/protpars.c: In function ‘protpars’: csrc/protpars.c:2096:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2096 | fread(tree, L, 1, outtree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -Icsrc csrc/seq.c csrc/seq.c: In function ‘collapsetree’: csrc/seq.c:4015:11: warning: variable ‘j’ set but not used [-Wunused-but-set-variable=] 4015 | long i, j, index, index2, numd; | ^ trees.cxx: In function ‘char* add_equally_best(char*, char*, int)’: trees.cxx:2047:46: warning: ‘]’ directive output may be truncated writing 1 byte into a region of size between 0 and 9 [-Wformat-truncation=] 2047 | snprintf(q, 30, "[equally best tree #%d]", ++rank); | ^ In file included from /usr/include/stdio.h:974, from seaview.h:3, from trees.cxx:6: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* add_equally_best(char*, char*, int)’ at trees.cxx:2047:15: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 23 and 32 bytes into a destination of size 30 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ trees.cxx: In function ‘char* run_parsimony_method(SEA_VIEW*, int, const char*, int, int, int, int, Fl_Box*, dnapars_S_option, const char**, float, int, char**, void (*)(const char*, ...))’: trees.cxx:2408:59: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=] 2408 | snprintf(tmp, 30, "Bootstrap replicate: %d", j + 1); | ^~ In function ‘char* parsimony_with_bootstrap(allseq*, char**, char**, int, int, int, int*, int, int, Fl_Box*, int*, dnapars_S_option, int, float, int*, char**)’, inlined from ‘char* run_parsimony_method(SEA_VIEW*, int, const char*, int, int, int, int, Fl_Box*, dnapars_S_option, const char**, float, int, char**, void (*)(const char*, ...))’ at trees.cxx:2085:36: trees.cxx:2408:37: note: directive argument in the range [1, 2147483647] 2408 | snprintf(tmp, 30, "Bootstrap replicate: %d", j + 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* parsimony_with_bootstrap(allseq*, char**, char**, int, int, int, int*, int, int, Fl_Box*, int*, dnapars_S_option, int, float, int*, char**)’ at trees.cxx:2408:13, inlined from ‘char* run_parsimony_method(SEA_VIEW*, int, const char*, int, int, int, int, Fl_Box*, dnapars_S_option, const char**, float, int, char**, void (*)(const char*, ...))’ at trees.cxx:2085:36: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 23 and 32 bytes into a destination of size 30 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ trees.cxx: In function ‘char* run_parsimony_method(SEA_VIEW*, int, const char*, int, int, int, int, Fl_Box*, dnapars_S_option, const char**, float, int, char**, void (*)(const char*, ...))’: trees.cxx:2091:62: warning: ‘ best trees, ’ directive output may be truncated writing 13 bytes into a region of size between 12 and 21 [-Wformat-truncation=] 2091 | if (count_best > 1) snprintf(best, 35, "consensus of %d best trees, ", count_best); | ^~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* run_parsimony_method(SEA_VIEW*, int, const char*, int, int, int, int, Fl_Box*, dnapars_S_option, const char**, float, int, char**, void (*)(const char*, ...))’ at trees.cxx:2091:35: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 28 and 37 bytes into a destination of size 35 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function ‘char* parsimony_with_bootstrap(allseq*, char**, char**, int, int, int, int*, int, int, Fl_Box*, int*, dnapars_S_option, int, float, int*, char**)’, inlined from ‘char* run_parsimony_method(SEA_VIEW*, int, const char*, int, int, int, int, Fl_Box*, dnapars_S_option, const char**, float, int, char**, void (*)(const char*, ...))’ at trees.cxx:2085:36: trees.cxx:2453:41: warning: ‘all_best’ may be used uninitialized [-Wmaybe-uninitialized] 2453 | if (count > 1) tree = add_equally_best(tree, all_best, count); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ trees.cxx: In function ‘char* run_parsimony_method(SEA_VIEW*, int, const char*, int, int, int, int, Fl_Box*, dnapars_S_option, const char**, float, int, char**, void (*)(const char*, ...))’: trees.cxx:2386:40: note: ‘all_best’ was declared here 2386 | char *tree, *newtree, *p, *q, *all_best, *bootstrap_trees = NULL; | ^~~~~~~~ cc -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -Icsrc csrc/phylip.c In file included from /usr/include/FL/Fl_Return_Button.H:24, from seaview.h:18: In member function ‘char Fl_Button::value() const’, inlined from ‘void parsimony_dialog(SEA_VIEW*)’ at trees.cxx:2288:26: /usr/include/FL/Fl_Button.H:102:30: warning: ‘thorough_b’ may be used uninitialized [-Wmaybe-uninitialized] 102 | char value() const {return value_;} | ^~~~~~ trees.cxx: In function ‘void parsimony_dialog(SEA_VIEW*)’: trees.cxx:2194:20: note: ‘thorough_b’ was declared here 2194 | Fl_Round_Button *thorough_b, *less_thorough_b; | ^~~~~~~~~~ In member function ‘char Fl_Button::value() const’, inlined from ‘void parsimony_dialog(SEA_VIEW*)’ at trees.cxx:2289:36: /usr/include/FL/Fl_Button.H:102:30: warning: ‘less_thorough_b’ may be used uninitialized [-Wmaybe-uninitialized] 102 | char value() const {return value_;} | ^~~~~~ trees.cxx: In function ‘void parsimony_dialog(SEA_VIEW*)’: trees.cxx:2194:33: note: ‘less_thorough_b’ was declared here 2194 | Fl_Round_Button *thorough_b, *less_thorough_b; | ^~~~~~~~~~~~~~~ In file included from /usr/include/FL/Fl_Input.H:25, from seaview.h:16: In member function ‘const char* Fl_Input_::value() const’, inlined from ‘void parsimony_dialog(SEA_VIEW*)’ at trees.cxx:2291:22: /usr/include/FL/Fl_Input_.H:244:37: warning: ‘w_best’ may be used uninitialized [-Wmaybe-uninitialized] 244 | const char* value() const {return value_;} | ^~~~~~ trees.cxx: In function ‘void parsimony_dialog(SEA_VIEW*)’: trees.cxx:2195:17: note: ‘w_best’ was declared here 2195 | Fl_Int_Input *w_best; | ^~~~~~ csrc/phylip.c: In function ‘scan_eoln’: csrc/phylip.c:161:8: warning: variable ‘ch’ set but not used [-Wunused-but-set-variable=] 161 | char ch; | ^~ csrc/phylip.c: In function ‘get_command_name’: csrc/phylip.c:212:14: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 212 | last_slash = strrchr (vektor, DELIMITER); | ^ csrc/phylip.c: In function ‘stringnames_new’: csrc/phylip.c:2980:8: warning: variable ‘len’ set but not used [-Wunused-but-set-variable=] 2980 | long len, i; | ^~~ cc -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -Icsrc csrc/lwl.c csrc/lwl.c: In function ‘prefastlwl’: csrc/lwl.c:412:1: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 412 | else | ^~~~ csrc/lwl.c:414:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 414 | aa[9] = 14;/* agc S */ | ^~ csrc/lwl.c:417:1: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 417 | else | ^~~~ csrc/lwl.c:419:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 419 | aa[11] = 14;/* agt S */ | ^~ csrc/lwl.c:422:1: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 422 | else | ^~~~ csrc/lwl.c:424:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 424 | aa[13] = 7;/* atc I */ | ^~ csrc/lwl.c:469:1: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 469 | else | ^~~~ csrc/lwl.c:471:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 471 | aa[57] = 10;/* tgc */ | ^~ treedraw.cxx: In function ‘char* recur_ecrit_arbre(FD_nj_plot*, noeud*, char*, char*)’: treedraw.cxx:2652:40: warning: ‘%g’ directive output may be truncated writing between 1 and 13 bytes into a region of size 10 [-Wformat-truncation=] 2652 | snprintf(++arbre, 11,":%g",centre->l1); | ^~ treedraw.cxx:2652:38: note: assuming directive output of 12 bytes 2652 | snprintf(++arbre, 11,":%g",centre->l1); | ^~~~~ In file included from /usr/include/stdio.h:974, from /usr/include/FL/Fl_Preferences.H:25, from /usr/include/FL/Fl_Plugin.H:25, from /usr/include/FL/Fl_Device.H:29, from /usr/include/FL/Fl_Paged_Device.H:26, from /usr/include/FL/Fl_Printer.H:27, from treedraw.cxx:16: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* recur_ecrit_arbre(FD_nj_plot*, noeud*, char*, char*)’ at treedraw.cxx:2652:11: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 3 and 15 bytes into a destination of size 11 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ treedraw.cxx: In function ‘char* recur_ecrit_arbre(FD_nj_plot*, noeud*, char*, char*)’: treedraw.cxx:2661:40: warning: ‘%g’ directive output may be truncated writing between 1 and 13 bytes into a region of size 10 [-Wformat-truncation=] 2661 | snprintf(++arbre, 11,":%g",centre->l2); | ^~ treedraw.cxx:2661:38: note: assuming directive output of 12 bytes 2661 | snprintf(++arbre, 11,":%g",centre->l2); | ^~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘char* recur_ecrit_arbre(FD_nj_plot*, noeud*, char*, char*)’ at treedraw.cxx:2661:11: /usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 3 and 15 bytes into a destination of size 11 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ trees.cxx: In function ‘char* run_distance_method(SEA_VIEW*, int, int, int, int, int, Fl_Box*, const char*, int, const char*, const char*, int, void (*)(const char*, ...), int, int)’: trees.cxx:522:24: warning: ‘display_tree’ may be used uninitialized [-Wmaybe-uninitialized] 522 | return display_tree; | ^~~~~~~~~~~~ trees.cxx:461:15: note: ‘display_tree’ was declared here 461 | char *display_tree, *bootstrap_trees = NULL, *err_mess, tree_label[100]=""; | ^~~~~~~~~~~~ cc -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -Icsrc csrc/bionj.c treedraw.cxx: In function ‘int count_node(noeud*, noeud*)’: treedraw.cxx:3306:15: warning: argument 2 null where non-null expected [-Wnonnull] 3306 | if (strcmp(centre->nom, target1) == 0 || strcmp(centre->nom, target2) == 0 || strcmp(centre->nom, target3) == 0) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ In file included from seaview.h:5, from treedraw.h:4, from treedraw.cxx:18: /usr/include/string.h:171:12: note: in a call to function ‘int strcmp(const char*, const char*)’ declared ‘nonnull’ 171 | extern int strcmp (const char *__s1, const char *__s2) | ^~~~~~ treedraw.cxx:3306:52: warning: argument 2 null where non-null expected [-Wnonnull] 3306 | if (strcmp(centre->nom, target1) == 0 || strcmp(centre->nom, target2) == 0 || strcmp(centre->nom, target3) == 0) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:171:12: note: in a call to function ‘int strcmp(const char*, const char*)’ declared ‘nonnull’ 171 | extern int strcmp (const char *__s1, const char *__s2) | ^~~~~~ treedraw.cxx:3306:89: warning: argument 2 null where non-null expected [-Wnonnull] 3306 | if (strcmp(centre->nom, target1) == 0 || strcmp(centre->nom, target2) == 0 || strcmp(centre->nom, target3) == 0) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/string.h:171:12: note: in a call to function ‘int strcmp(const char*, const char*)’ declared ‘nonnull’ 171 | extern int strcmp (const char *__s1, const char *__s2) | ^~~~~~ cc -c -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Dunix -Icsrc csrc/phyml_util.c csrc/phyml_util.c: In function ‘Warn_And_Exit’: csrc/phyml_util.c:47:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 47 | fscanf(stdin,"%c",&c); | ^~~~~~~~~~~~~~~~~~~~~ trees.cxx: In function ‘void command_line_phylogeny(int, char**)’: trees.cxx:2871:3: warning: ‘tree’ may be used uninitialized [-Wmaybe-uninitialized] 2871 | if (tree) { | ^~ trees.cxx:2774:9: note: ‘tree’ was declared here 2774 | char *tree, *p; | ^~~~ c++ -o seaview -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes seaview.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o resource.o nexus.o viewasprots.o racnuc_fetch.o concatenate.o statistics.o trees.o treedraw.o addbootstrap.o least_squares_brl.o pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o tbe.o treerecs_draw.o Fl_SVG_Image.o raa_acnuc.o parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o `fltk-config --use-images --ldflags` -ldl -lpthread -lz -Wl,-z,muldefs + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.4zBzBx + umask 022 + cd /builddir/build/BUILD/seaview-5.1-build + '[' /builddir/build/BUILD/seaview-5.1-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/seaview-5.1-build/BUILDROOT ++ dirname /builddir/build/BUILD/seaview-5.1-build/BUILDROOT + mkdir -p /builddir/build/BUILD/seaview-5.1-build + mkdir /builddir/build/BUILD/seaview-5.1-build/BUILDROOT + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 seaview + rm -rf /builddir/build/BUILD/seaview-5.1-build/BUILDROOT + mkdir -p /builddir/build/BUILD/seaview-5.1-build/BUILDROOT/usr/share/seaview + mkdir -p /builddir/build/BUILD/seaview-5.1-build/BUILDROOT/usr/bin + mkdir -p /builddir/build/BUILD/seaview-5.1-build/BUILDROOT//usr/share/man/man1 + install -m 755 seaview /builddir/build/BUILD/seaview-5.1-build/BUILDROOT//usr/bin + desktop-file-install --dir /builddir/build/BUILD/seaview-5.1-build/BUILDROOT/usr/share/applications /builddir/build/SOURCES/seaview.desktop + mkdir -p /builddir/build/BUILD/seaview-5.1-build/BUILDROOT/usr/share/pixmaps/ + install -m 0644 -p seaview.xpm /builddir/build/BUILD/seaview-5.1-build/BUILDROOT/usr/share/pixmaps/seaview.xpm + install -m 0644 -p seaview.svg /builddir/build/BUILD/seaview-5.1-build/BUILDROOT/usr/share/pixmaps/seaview.svg + mkdir -p /builddir/build/BUILD/seaview-5.1-build/BUILDROOT/usr/share/appdata/ + install -m 0644 -p seaview.appdata.xml /builddir/build/BUILD/seaview-5.1-build/BUILDROOT/usr/share/appdata/seaview.appdata.xml + install -m 644 seaview.1 /builddir/build/BUILD/seaview-5.1-build/BUILDROOT//usr/share/man/man1 + /usr/bin/find-debuginfo -j8 --strict-build-id -m -i --build-id-seed 5.1-5.fc45 --unique-debug-suffix -5.1-5.fc45.riscv64 --unique-debug-src-base seaview-5.1-5.fc45.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/seaview-5.1-build/seaview find-debuginfo: starting Extracting debug info from 1 files DWARF-compressing 1 files sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/seaview-5.1-5.fc45.riscv64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + COMPRESS='gzip -9 -n' + COMPRESS_EXT=.gz + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /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-rpm-in-distinfo + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j8 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-det --brp -j8 /builddir/build/BUILD/seaview-5.1-build/BUILDROOT Scanned 19 directories and 61 files, processed 1 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors + /usr/bin/linkdupes --brp /builddir/build/BUILD/seaview-5.1-build/BUILDROOT/usr Scanned 18 directories and 61 files, considered 61 files, read 2 files, linked 1 files, 0 errors sum of sizes of linked files: 3757 bytes Reading /builddir/build/BUILD/seaview-5.1-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.zSUnqj + umask 022 + cd /builddir/build/BUILD/seaview-5.1-build + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 seaview + RPM_EC=0 ++ jobs -p Processing files: seaview-5.1-5.fc45.riscv64 + exit 0 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.CwSU00 + umask 022 + cd /builddir/build/BUILD/seaview-5.1-build + cd seaview + DOCDIR=/builddir/build/BUILD/seaview-5.1-build/BUILDROOT/usr/share/doc/seaview + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/seaview-5.1-build/BUILDROOT/usr/share/doc/seaview + cp -pr /builddir/build/BUILD/seaview-5.1-build/seaview/seaview.1.xml /builddir/build/BUILD/seaview-5.1-build/BUILDROOT/usr/share/doc/seaview + cp -pr /builddir/build/BUILD/seaview-5.1-build/seaview/seaview.html /builddir/build/BUILD/seaview-5.1-build/BUILDROOT/usr/share/doc/seaview + RPM_EC=0 ++ jobs -p + exit 0 Provides: application() application(seaview.desktop) metainfo() metainfo(seaview.appdata.xml) seaview = 5.1-5.fc45 seaview(riscv-64) = 5.1-5.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libfltk.so.1.3()(64bit) libfltk_images.so.1.3()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: seaview-debugsource-5.1-5.fc45.riscv64 Provides: seaview-debugsource = 5.1-5.fc45 seaview-debugsource(riscv-64) = 5.1-5.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: seaview-debuginfo-5.1-5.fc45.riscv64 Provides: debuginfo(build-id) = 50254cb4eccf3cc10dd2edce4de40adca28645d9 seaview-debuginfo = 5.1-5.fc45 seaview-debuginfo(riscv-64) = 5.1-5.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: seaview-debugsource(riscv-64) = 5.1-5.fc45 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/seaview-5.1-build/BUILDROOT Wrote: /builddir/build/RPMS/seaview-5.1-5.fc45.riscv64.rpm Wrote: /builddir/build/RPMS/seaview-debugsource-5.1-5.fc45.riscv64.rpm Wrote: /builddir/build/RPMS/seaview-debuginfo-5.1-5.fc45.riscv64.rpm Child return code was: 0