I have sci-libs/openfoam-2.4.0-r1 installed on my system, and it depends on sci-libs/parmetis: # equery depends parmetis * These packages depend on parmetis: sci-libs/cholmod-2.1.2 (metis ? <sci-libs/parmetis-4) sci-libs/openfoam-2.4.0-r1 (sci-libs/parmetis) However, the only parmetis package in the tree is 4.0.3: # ls /usr/portage/sci-libs/parmetis Manifest metadata.xml parmetis-4.0.3.ebuild This is clearly related to https://bugs.gentoo.org/310663 , however, it used to work fine until the parmetis-3.2.0 ebuild was removed from the tree. Was that perhaps premature? # emerge --info fatal: not a git repository (or any parent up to mount point /usr) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). Portage 2.3.62 (python 2.7.15-final-0, default/linux/amd64/17.1/desktop/plasma, gcc-8.2.0, glibc-2.28-r5, 4.19.27-gentoo-r1 x86_64) ================================================================= System uname: Linux-4.19.27-gentoo-r1-x86_64-Intel-R-_Core-TM-_i5-3570_CPU_@_3.40GHz-with-gentoo-2.6 KiB Mem: 32928704 total, 6840596 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Sun, 07 Apr 2019 15:45:01 +0000 Head commit of repository gentoo: d8b1b2460347c29ec01fb6f6b8dd35a6cef8ece2 sh bash 4.4_p23-r1 ld GNU ld (Gentoo 2.31.1 p5) 2.31.1 app-shells/bash: 4.4_p23-r1::gentoo dev-java/java-config: 2.2.0-r4::gentoo dev-lang/perl: 5.26.2::gentoo dev-lang/python: 2.7.15::gentoo, 3.6.5::gentoo dev-util/cmake: 3.9.6::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.6-r1::gentoo sys-apps/openrc: 0.38.3-r1::gentoo sys-apps/sandbox: 2.13::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.11.6-r3::gentoo, 1.15.1-r2::gentoo, 1.16.1-r1::gentoo sys-devel/binutils: 2.31.1-r4::gentoo sys-devel/gcc: 8.2.0-r6::gentoo sys-devel/gcc-config: 2.0::gentoo sys-devel/libtool: 2.4.6-r3::gentoo sys-devel/make: 4.2.1-r4::gentoo sys-kernel/linux-headers: 4.20::gentoo (virtual/os-headers) sys-libs/glibc: 2.28-r5::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.namerica.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: sync-rsync-verify-max-age: 24 local location: /usr/local/portage sync-type: git sync-uri: git://localhost/my/repo.git masters: gentoo printer-drivers location: /var/lib/layman/printer-drivers masters: gentoo priority: 50 science location: /var/lib/layman/science sync-type: laymansync sync-uri: https://anongit.gentoo.org/git/proj/sci.git masters: gentoo priority: 50 stefantalpalaru location: /var/lib/layman/stefantalpalaru sync-type: laymansync sync-uri: https://github.com/stefantalpalaru/gentoo-overlay.git masters: gentoo science priority: 50 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA vmware" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0" 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 /etc/vmware-installer" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN 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="-march=native -O2 -pipe" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs 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 sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-march=native -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en en_US" MAKEOPTS="-j5" 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 acl acpi activities alsa amd64 apache2 berkdb bluetooth branding bzip2 cairo cdda cdr cli colord consolekit crypt cups curl cxx dbus declarative doc dri dts dvd dvdr emboss encode examples exif fam flac fontconfig fortran gcj gd gdbm gif glamor gtk handbook iconv icu ipv6 jack java jbig jpeg jpeg2k kde kipi kpathsea kwallet lcms ldap libnotify libtirpc lzma mad mbox mng mp3 mp4 mpeg multilib ncurses nls nptl odbc ogg openexr opengl openmp pam pango pcre pdf phonon plasma png policykit postgres ppds qml qt5 readline sdl seccomp semantic-desktop source spell ssl startup-notification svg t1lib tcpd threads tiff truetype udev udisks unicode upower usb vim-syntax vorbis webp widgets wxwidgets x264 xattr xcb xcomposite xinerama xml xpm xv xvid zlib" ABI_X86="64 32" 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="actions alias auth_basic auth_digest authn_anon authn_core authn_dbd authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers http2 ident imagemap include info lbmethod_byrequests log_config log_forensic logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" APACHE2_MPMS="worker" CALLIGRA_FEATURES="karbon sheets words" CAMERAS="canon" 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="pc" INPUT_DEVICES="keyboard mouse evdev vmmouse wacom joystick" KERNEL="linux" L10N="en en-US" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver presenter-minimizer wiki-publisher" NETBEANS_MODULES="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres9_5 postgres10" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby24" SANE_BACKENDS="epson2" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel r600 radeon radeonsi vesa vmware" XFCE_PLUGINS="clock trash" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
cholmod ebuild has > || ( <sci-libs/metis-5 <sci-libs/parmetis-4 ) ) so the dependency is satisfied with sci-libs/metis
Oops. I should clarify that it is sci-libs/cholmod-2.1.2 (the only version in the tree) that has the dependency on the non-existent parmetis, but I cannot move cholmod to sci-libs/metis instead due to the requirement for parmetis from openfoam.
I am experimenting with a newer version of suitesparse in the sage-on-gentoo overlay. cholmod-3.0.13 from suitesparse-5.4.0 shouldn't have that problem.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b9c6382f0a37c4ad45f754e897999559a24403aa commit b9c6382f0a37c4ad45f754e897999559a24403aa Author: Michael Orlitzky <mjo@gentoo.org> AuthorDate: 2020-03-02 00:37:22 +0000 Commit: Michael Orlitzky <mjo@gentoo.org> CommitDate: 2020-03-02 17:20:45 +0000 sci-libs/cholmod: new version 3.0.13. Update to EAPI=7 and fix the HOMEPAGE, SRC_URI, and LICENSE. This is part of a larger SuiteSparse v5.4.0 upgrade thanks to François Bissey whose sage-on-gentoo ebuilds I'm using. There's a newer release (v5.7.1) of SuiteSparse, but v5.4.0 has seen more testing. This new version also refactors the package's USE flags, because USE=minimal was being used to control the installation of several different modules that all do different things. It's much better for users to have three individual flags that control those options. Moreover, with USE=minimal, there was a conflict between the "minimal" and "metis" flags; both would try to control the --with-partition option. Finally, the "metis" USE flag was dropped in favor of the name "partition". Closes: https://bugs.gentoo.org/526910 Closes: https://bugs.gentoo.org/682838 Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Michael Orlitzky <mjo@gentoo.org> sci-libs/cholmod/Manifest | 1 + sci-libs/cholmod/cholmod-3.0.13.ebuild | 57 ++++++++++++++++++++++++++++++++++ sci-libs/cholmod/metadata.xml | 16 +++++++++- 3 files changed, 73 insertions(+), 1 deletion(-)
This issue is still present for the cholmod-2.1.2 ebuild
