Created attachment 529690 [details, diff] cmake fix for gcc-8.1.0 sci-chemistry/openbabel-2.4.1 fails to build with because gcc-8 is not expected in CMakeLists.txt - attached a patch This is the emerge --info openbabel Portage 2.3.33 (python 3.6.5-final-0, default/linux/amd64/17.1/systemd, gcc-8.1.0, glibc-2.27-r2, 4.16.7-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.16.7-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E31245_@_3.30GHz-with-gentoo-2.4.1 KiB Mem: 16316836 total, 6484760 free KiB Swap: 62545212 total, 62509372 free Timestamp of repository gentoo: Thu, 03 May 2018 05:00:01 +0000 Head commit of repository gentoo: 487fa7aefbcb55972eccd81c15c6394b5be17464 sh bash 4.4_p19 ld GNU ld (Gentoo 2.30 p2) 2.30.0 distcc 3.2rc1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.4_p19::gentoo dev-java/java-config: 2.2.0-r4::gentoo dev-lang/perl: 5.26.2::gentoo dev-lang/python: 2.7.14-r2::gentoo, 3.5.5-r1::gentoo, 3.6.5-r1::gentoo dev-util/cmake: 3.11.1::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.4.1-r2::gentoo sys-apps/openrc: 0.35.5::gentoo sys-apps/sandbox: 2.13::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.11.6-r3::gentoo, 1.13.4-r2::gentoo, 1.15.1-r2::gentoo, 1.16.1-r1::gentoo sys-devel/binutils: 2.30-r2::gentoo sys-devel/gcc: 6.4.0-r1::gentoo, 7.3.0-r2::gentoo, 8.1.0::gentoo sys-devel/gcc-config: 1.9.1::gentoo sys-devel/libtool: 2.4.6-r5::gentoo sys-devel/make: 4.2.1-r3::gentoo sys-kernel/linux-headers: 4.16-r1::gentoo (virtual/os-headers) sys-libs/glibc: 2.27-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://s6/portage priority: -1000 sync-rsync-verify-max-age: 24 sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: no sync-rsync-extra-opts: local location: /usr/local/portage masters: gentoo priority: 0 flatpak-overlay location: /var/lib/layman/flatpak-overlay masters: gentoo priority: 50 kde location: /var/lib/layman/kde masters: gentoo priority: 50 matrix location: /var/lib/layman/matrix masters: gentoo priority: 50 rion location: /var/lib/layman/rion masters: gentoo priority: 50 science location: /var/lib/layman/science masters: gentoo priority: 50 Installed sets: @kde-apps-next, @kde-frameworks-live, @kde-plasma-live, @mykde ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=corei7" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.2/ext-active/ /etc/php/cgi-php7.2/ext-active/ /etc/php/cli-php7.2/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -pipe -march=corei7" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--quiet-build=n --with-bdeps=y" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs candy config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=corei7" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.utf8" LC_ALL="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="us" MAKEOPTS="-j 8" PKGDIR="/usr/portage/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="X a52 aac aacplus aalib acl alac alsa amd64 amr ansi apache2 apng applet assistant audiofile autoipd avahi berkdb bitmapfonts bittorrent boost branding btrfs bzip2 cairo canna cdda cdio cdr cjk clang cli clozurecl clucene crossdev crypt css curl cxx daap dbus dconf dcraw declarative demosaic device-mapper dga dirac dri dv dvd dvdr dvdread eds emacs emovix encode eps exif extensions extra extras f77 faac faad fastcgi fdk ffmpeg flac fltk fontconfig foomaticdb fortran fortran2003 fortran95 frei0r g3dvl gcj gd gdbm gdu gif gimp gimpprint gkrellm glib gnuplot gphoto2 gsf gstreamer gtk gtk3 gudev gzip hdri hwdb hwinfo iconv icu imagemagick introspection ipv6 java javascript jbig jpeg jpeg2k kde kdenlive kdepim kdrive lapack latex lcms ldap legacy-systray libinput libkms libxml2 lxc mad matplotlib matroska mbox mdnsresponder-compat melt minizip mjpeg mng modemmanager modules mozilla mp3 mp4 mpm-itk multilib multiuser musepack musicbrainz mysql native-exceptions ncurses network networkmanager nftables nls nptl nsplugin nss numpy objc offensive ogg oggvorbis openbabel openexr opengl openmp opus pam pcntl pcre pcre16 pdf perl plasma plotutils png pnm policykit posix postscript preview-latex printsupport private-headers pstricks pulseaudio python python3 qml qt5 rar readline rendering rle romio rtc sasl schroedinger scipy script scripttools sdl seccomp smp smpeg sna sndfile sockets socks5 sox speex spell sql sqlite ssl staging static-libs svc svg systemd tagwriting tbb tcl tcltk tcpd tetex tga theora threads tiff tk tracker truetype udev udisks unicode upcall usb user-session uvm vaapi vala vcd vdr vhosts vim vim-pager vorbis vpx wav wavpack webm webp widgets winbind wmf wxgtk1 x264 xattr xcb xetex xft xinerama xkb xml xmp xorg xvfb xvid xvmc yv12 zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="krita stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="efi-64 pc" INPUT_DEVICES="libinput" KERNEL="linux" L10N="us" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="intel i965" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CC, CPPFLAGS, CTARGET, CXX, ENV_UNSET, INSTALL_MASK, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= sci-chemistry/openbabel-2.4.1::gentoo was built with the following: USE="openmp -doc -test -wxwidgets" ABI_X86="(64)"
The package fails to build without patch on my system with gcc-8.1.0-r1 too. I build it with USE="openmp wxwidgets -doc {-test} Proposed patch works just fine. (I think it's unnecessary to provide my emerge --info, but if I'm wrong, let me know please)
Looks good. And also upstream (and was reworked since as well).
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4ec881ef10b4bcbffd3b56bc78a680b29cd59853 commit 4ec881ef10b4bcbffd3b56bc78a680b29cd59853 Author: Sergei Trofimovich <slyfox@gentoo.org> AuthorDate: 2018-05-06 22:13:04 +0000 Commit: Sergei Trofimovich <slyfox@gentoo.org> CommitDate: 2018-05-06 22:13:32 +0000 sci-chemistry/openbabel: allow gcc-8, bug #654800 openbabel explicitly whitelists list of major GCC versions. The change by Milan allow gcc-8. Newer upstream versions fixed the code to handle in in a more generic way: https://github.com/openbabel/openbabel/commit/00120f89cf62b121c30d0b2a891b159e19b53624 Fixed-by: milan hodoscek Closes: https://bugs.gentoo.org/654800 Package-Manager: Portage-2.3.36, Repoman-2.3.9 sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8.patch | 15 +++++++++++++++ sci-chemistry/openbabel/openbabel-2.4.1.ebuild | 3 ++- 2 files changed, 17 insertions(+), 1 deletion(-)
