Install phase of the package fails. Reproducible: Always emerge --info pymol Portage 3.0.18 (python 3.8.10-final-0, default/linux/amd64/17.1/no-multilib, gcc-11.1.0, glibc-2.33, 5.12.4-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-5.12.4-gentoo-x86_64-AMD_Ryzen_7_3800X_8-Core_Processor-with-glibc2.2.5 KiB Mem: 65844368 total, 33188016 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Mon, 17 May 2021 05:30:01 +0000 Head commit of repository gentoo: 1dc9ddc63ed66854bd981378c9d2f0b523694837 sh bash 5.1_p8 ld GNU ld (Gentoo 2.36.1 p3) 2.36.1 app-shells/bash: 5.1_p8::gentoo dev-java/java-config: 2.3.1::gentoo dev-lang/perl: 5.32.1::gentoo dev-lang/python: 2.7.18_p10::gentoo, 3.8.10_p1::gentoo, 3.9.5_p1::gentoo dev-lang/rust-bin: 1.52.1::gentoo dev-util/cmake: 3.20.2::gentoo sys-apps/baselayout: 2.7-r2::gentoo sys-apps/openrc: 0.43.3::gentoo sys-apps/sandbox: 2.24::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo sys-devel/automake: 1.16.3-r1::gentoo sys-devel/binutils: 2.36.1-r1::gentoo sys-devel/gcc: 11.1.0::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: 5.12::gentoo (virtual/os-headers) sys-libs/glibc: 2.33::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: no sync-rsync-verify-max-age: 24 sync-rsync-extra-opts: sync-rsync-verify-jobs: 1 x-portage location: /usr/local/portage masters: gentoo priority: 0 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=znver2" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /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/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=znver2" DISTDIR="/var/cache/distfiles" 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=znver2" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance 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 strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=znver2" GENTOO_MIRRORS="http://ftp.fi.muni.cz/pub/linux/gentoo/ http://mirror.dkm.cz/gentoo/" LANG="cs_CZ.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="cs en" MAKEOPTS="-j16" PKGDIR="/var/cache/binpkgs" PORTAGE_COMPRESS="" 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 alsa amd64 berkdb blas bluetooth branding bzip2 cairo caps cdda cddb cdparanoia cdr cli colord crypt cups dbus declarative djvu dri dts dv dvb dvd dvdr elogind encode exif ffmpeg fftw flac fontconfig fortran gdbm geoip gif gmp gnuplot graphviz gsl gsm gstreamer hdf5 heif iconv idn ieee1394 imagemagick imlib ipv6 ithreads jbig jpeg jpeg2k kde ladspa lame lapack latex lcms libass libglvnd libsamplerate libtirpc lzma lzo mad matroska mms mng modplug mp3 mp4 mpeg mtp musepack musicbrainz ncurses nls nptl ogg opencl openexr opengl openmp pam pcre pdf plotutils png postscript pulseaudio qt5 quicktime rdp readline seccomp semantic-desktop slang smp sndfile sox speex spell split-usr ssl svg szip taglib tcpd theora threads tiff truetype udev unicode usb v4l vaapi vdpau vorbis wavpack webp x264 xattr xcb xft xinerama xml xosd xpm xscreensaver xv xvid xvmc zlib" ABI_X86="64" ADA_TARGET="gnat_2018" 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="karbon sheets words stage" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt sha sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3" ELIBC="glibc" FFTOOLS="aviocat cws2fws ffescape ffeval ffhash fourcc2pixfmt graph2dot ismindex pktdumper qt-faststart sidxindex trasher" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis 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="evdev libinput" KERNEL="linux" L10N="cs en" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="scripting-beanshell scripting-javascript nlpsolver" LLVM_TARGETS="AMDGPU BPF X86" LUA_SINGLE_TARGET="lua5-3" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-3 php7-4" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_8" PYTHON_TARGETS="python3_8" RUBY_TARGETS="ruby27" SANE_BACKENDS="lexmark net" USERLAND="GNU" VIDEO_CARDS="amdgpu r600 radeonsi" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto 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_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RUSTFLAGS ================================================================= Package Settings ================================================================= sci-chemistry/pymol-2.4.0-r1::gentoo was built with the following: USE="netcdf -web" PYTHON_TARGETS="python3_8 -python3_7 -python3_9" CXXFLAGS="-O2 -pipe -march=znver2 -std=c++0x"
Created attachment 709242 [details] build.log
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=319a93dd7c1b57253d978f4491df7dfb6e9d3108 commit 319a93dd7c1b57253d978f4491df7dfb6e9d3108 Author: Pacho Ramos <pacho@gentoo.org> AuthorDate: 2021-05-20 15:07:07 +0000 Commit: Pacho Ramos <pacho@gentoo.org> CommitDate: 2021-05-20 15:07:21 +0000 sci-chemistry/pymol: apbs_tools.py is not created as apbs package was dropped from the tree Closes: https://bugs.gentoo.org/790629 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org> sci-chemistry/pymol/pymol-2.5.0.ebuild | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-)
