* Package: sci-chemistry/pdbmat-3.89 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox @@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix; This ebuild was merged at the following commit: https://github.com/gentoo-mirror/gentoo/commit/1ae8a92316ea0ff34b4e65f83a62d62d347ad77d (Mon Aug 23 05:51:33 UTC 2021) @@@@@ END @@@@@ ################## # emerge --info: # ################## Portage 3.0.22 (python 3.9.6-final-0, default/linux/amd64/17.1, gcc-11.2.0, glibc-2.33-r7, 4.19.174-gentoo x86_64) ================================================================= System uname: Linux-4.19.174-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5-2650_v4_@_2.20GHz-with-glibc2.33 KiB Mem: 264046488 total, 96923812 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Mon, 23 Aug 2021 05:51:31 +0000 sh bash 5.1_p8 ld GNU ld (Gentoo 2.37_p1 p0) 2.37 app-shells/bash: 5.1_p8::gentoo dev-lang/perl: 5.34.0-r2::gentoo dev-lang/python: 3.8.11::gentoo, 3.9.6_p1::gentoo, 3.10.0_rc1_p1::gentoo dev-lang/rust: 1.54.0::gentoo dev-util/cmake: 3.21.1::gentoo sys-apps/baselayout: 2.7-r3::gentoo sys-apps/openrc: 0.43.5::gentoo sys-apps/sandbox: 2.24::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.71-r1::gentoo sys-devel/automake: 1.16.4::gentoo sys-devel/binutils: 2.37_p1::gentoo sys-devel/gcc: 11.2.0::gentoo sys-devel/gcc-config: 2.4::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.13::gentoo (virtual/os-headers) sys-libs/glibc: 2.33-r7::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-extra-opts: sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: yes sync-rsync-verify-max-age: 24 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* CeCILL-2" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color" DISTDIR="/var/tmp/portage/sci-chemistry/pdbmat-3.89/distdir" EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -k -b" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" FCFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="C.UTF8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" MAKEOPTS="-j16" PKGDIR="/root/.packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="acl amd64 bzip2 cli crypt dri elogind fortran gdbm iconv ipv6 jumbo-build libglvnd libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" USERLAND="GNU" Unset: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RUSTFLAGS ############################## # emerge history (qlop -mv): # ############################## 2021-08-23T08:41:49 >>> virtual/fortran-0 ####################################### # installed packages (qlist -ICvUSS): # ####################################### acct-group/input-0-r1:0 acct-group/kvm-0-r1:0 acct-group/man-0-r1:0 acct-group/messagebus-0-r1:0 acct-group/polkitd-0-r1:0 acct-group/portage-0:0 acct-group/render-0-r1:0 acct-group/sshd-0-r1:0 acct-user/man-1-r1:0 acct-user/messagebus-0-r1:0 acct-user/polkitd-0-r1:0 acct-user/portage-0:0 acct-user/sshd-0-r1:0 app-admin/eselect-1.4.17:0 -doc -emacs -vim-syntax app-admin/perl-cleaner-2.30:0 app-arch/bzip2-1.0.8-r1:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 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virtual/perl-Getopt-Long-2.520.0:0 virtual/perl-IO-1.460.0:0 virtual/perl-IO-Compress-2.102.0:0 virtual/perl-IO-Socket-IP-0.410.0:0 virtual/perl-JSON-PP-4.60.0:0 virtual/perl-libnet-3.130.0:0 ssl virtual/perl-MIME-Base64-3.160.0:0 virtual/perl-Module-Metadata-1.0.37-r1:0 virtual/perl-parent-0.238.0-r1:0 virtual/perl-Parse-CPAN-Meta-2.150.10-r5:0 virtual/perl-Perl-OSType-1.10.0-r5:0 virtual/perl-podlators-4.140.0-r2:0 virtual/perl-Scalar-List-Utils-1.560.0:0 virtual/perl-Test-Harness-3.430.0:0 virtual/perl-Text-ParseWords-3.300.0-r8:0 virtual/perl-Time-Local-1.300.0:0 virtual/perl-version-0.992.800:0 virtual/perl-XSLoader-0.300.0-r4:0 virtual/pkgconfig-2:0 virtual/rust-1.54.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -rustfmt virtual/service-manager-1:0 virtual/ssh-0:0 -minimal virtual/tmpfiles-0-r1:0 virtual/ttf-fonts-1-r1:0 virtual/udev-217-r3:0 virtual/yacc-0:0 www-client/pybugz-0.13-r1:0 python_targets_python3_8 python_targets_python3_9 x11-libs/cairo-1.16.0-r4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -aqua -debug -gles2-only glib -opengl -static-libs svg -utils -valgrind -X x11-libs/pixman-0.40.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cpu_flags_arm_iwmmxt -cpu_flags_arm_iwmmxt2 -cpu_flags_arm_neon -cpu_flags_ppc_altivec cpu_flags_x86_mmxext cpu_flags_x86_sse2 -cpu_flags_x86_ssse3 -loongson2f -static-libs x11-misc/shared-mime-info-2.1:0 ####################### # build.log # ####################### * Using following Fortran compiler: * F77: x86_64-pc-linux-gnu-gfortran * FC: x86_64-pc-linux-gnu-gfortran >>> Unpacking source... >>> Unpacking pdbmat-3.89.tar.gz to /var/tmp/portage/sci-chemistry/pdbmat-3.89/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/pdbmat-3.89/work >>> Preparing source in /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/Source_ENM2011 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/Source_ENM2011 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build" cmake -C /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DEXAMPLES=no -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/Source_ENM2011 loading initial cache file /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/gentoo_common_config.cmake CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The Fortran compiler identification is GNU 11.2.0 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/x86_64-pc-linux-gnu-gfortran - skipped -- Checking whether /usr/bin/x86_64-pc-linux-gnu-gfortran supports Fortran 90 -- Checking whether /usr/bin/x86_64-pc-linux-gnu-gfortran supports Fortran 90 - yes -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C C++ Linker flags: Executable -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Module -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 Shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/Source_ENM2011 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build" make -j16 VERBOSE=1 /usr/bin/cmake -S/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/Source_ENM2011 -B/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/CMakeFiles /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build' make -f CMakeFiles/pdbmat.dir/build.make CMakeFiles/pdbmat.dir/depend make -f CMakeFiles/diagstd.dir/build.make CMakeFiles/diagstd.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build' cd /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/Source_ENM2011 /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/Source_ENM2011 /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/CMakeFiles/pdbmat.dir/DependInfo.cmake make[2]: Entering directory '/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build' cd /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/Source_ENM2011 /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/Source_ENM2011 /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/CMakeFiles/diagstd.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/CMakeFiles/pdbmat.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/CMakeFiles/pdbmat.dir/depend.internal". Dependee "/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/CMakeFiles/pdbmat.dir/depend.internal". Scanning dependencies of target pdbmat Dependee "/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/CMakeFiles/diagstd.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/CMakeFiles/diagstd.dir/depend.internal". Dependee "/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/CMakeFiles/diagstd.dir/depend.internal". Scanning dependencies of target diagstd make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build' make -f CMakeFiles/diagstd.dir/build.make CMakeFiles/diagstd.dir/build make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build' make -f CMakeFiles/pdbmat.dir/build.make CMakeFiles/pdbmat.dir/build make[2]: Entering directory '/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build' make[2]: Entering directory '/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build' [ 25%] Building Fortran object CMakeFiles/diagstd.dir/diagstd.f.o /usr/bin/x86_64-pc-linux-gnu-gfortran -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -o CMakeFiles/diagstd.dir/diagstd.f.o -c /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/Source_ENM2011/diagstd.f [ 50%] Building Fortran object CMakeFiles/pdbmat.dir/pdbmat.f.o /usr/bin/x86_64-pc-linux-gnu-gfortran -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -o CMakeFiles/pdbmat.dir/pdbmat.f.o -c /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/Source_ENM2011/pdbmat.f /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/Source_ENM2011/diagstd.f:677:72: 677 | IF(ITER.EQ.30)PAUSE 'too many iterations' | 1 Warning: Deleted feature: PAUSE statement at (1) [ 75%] Linking Fortran executable diagstd /usr/bin/cmake -E cmake_link_script CMakeFiles/diagstd.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-gfortran -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color CMakeFiles/diagstd.dir/diagstd.f.o -o diagstd make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build' [ 75%] Built target diagstd [100%] Linking Fortran executable pdbmat /usr/bin/cmake -E cmake_link_script CMakeFiles/pdbmat.dir/link.txt --verbose=1 /usr/bin/x86_64-pc-linux-gnu-gfortran -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color CMakeFiles/pdbmat.dir/pdbmat.f.o -o pdbmat make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build' [100%] Built target pdbmat make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build' /usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build/CMakeFiles 0 >>> Source compiled. >>> Test phase [not enabled]: sci-chemistry/pdbmat-3.89 >>> Install sci-chemistry/pdbmat-3.89 into /var/tmp/portage/sci-chemistry/pdbmat-3.89/image/ >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/pdbmat-3.89/work/pdbmat-3.89_build" make -j16 install [ 50%] Built target pdbmat [100%] Built target diagstd Install the project... -- Install configuration: "Gentoo" -- Installing: /var/tmp/portage/sci-chemistry/pdbmat-3.89/image/usr/bin/diagstd -- Installing: /var/tmp/portage/sci-chemistry/pdbmat-3.89/image/usr/bin/pdbmat -- Installing: /var/tmp/portage/sci-chemistry/pdbmat-3.89/image/usr/share/doc/pdbmat/diagstd.README -- Installing: /var/tmp/portage/sci-chemistry/pdbmat-3.89/image/usr/share/doc/pdbmat/pdbmat.README >>> Completed installing sci-chemistry/pdbmat-3.89 into /var/tmp/portage/sci-chemistry/pdbmat-3.89/image/ * Final size of build directory: 1044 KiB (1.0 MiB) * Final size of installed tree: 152 KiB * QA Notice: The ebuild is installing to one or more unexpected paths: * * /usr/share/doc/pdbmat * * Please fix the ebuild to use correct FHS/Gentoo policy paths. strip: x86_64-pc-linux-gnu-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version /usr/bin/diagstd /usr/bin/pdbmat >>> Done.