Compiling gromacs-2025_rc[-doc] fails on the documentation jobs, requesting additional sphinx packages: sphinx-copybutton, shpinx-inline-tabs, sphinx-argpars, sphinxcontrib-autoprogram After emerging these additional packages, gromacs emerges. Though these packages are conditionally mentioned in the ebuild, this seems to not have worked for me. [ebuild UD] sci-chemistry/gromacs-2025_rc [2025.0_beta] USE="cuda custom-cflags fftw gmxapi gmxapi-legacy openmp single-precision threads tng -blas -build-manual -clang -clang-cuda -doc -double-precision -hwloc -lapack -mkl -mpi -nnpot -offensive -opencl (-python) -test (-hdf5%)" CPU_FLAGS_X86="avx avx2 sse2 sse4_1 -avx512f -fma4" PYTHON_SINGLE_TARGET="python3_12 -python3_10 -python3_11" (N.B. Portage believes 2025_rc is a downgrade from 2025.0_beta) Reproducible: Always Portage 3.0.66.1 (python 3.12.8-final-0, default/linux/amd64/23.0/split-usr/desktop, gcc-13, glibc-2.40-r8, 6.13.1-gentoo-x86_64 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-6.13.1-gentoo-x86_64-x86_64-AMD_Ryzen_9_3950X_16-Core_Processor-with-glibc2.40 KiB Mem: 131819772 total, 86747152 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Tue, 04 Feb 2025 01:00:01 +0000 Head commit of repository gentoo: c43ae53bc1dabee1a745634f0f9a888c2d0fc0cc Timestamp of repository guru: Tue, 04 Feb 2025 13:48:19 +0000 Head commit of repository guru: 19083886e96a0ccb7d42fd55fb47733455421613 Head commit of repository supertux88: 7011077e2370c82b48a6916183d6f43167978300 Head commit of repository oubliette: fc0860d42b6a2f3985839aab66414200252e5dae Head commit of repository palemoon: 2ad4eecd3d42ba12f0f70e6b5a99a4bb30fe0a91 Head commit of repository pentoo: c6aff06c03d0061f2f52c8d4710c2de23c5908ea Head commit of repository pf4public: 241e08a849a0d9b7d8cd9a5f3afde432f0d7c056 Head commit of repository pg_overlay: db21ef2e9b5bd5015da25b411829ca735734546b Head commit of repository science: 1e2e5e5c5128af6c57924c4785746b90b77882f4 Head commit of repository stuff: bae532189afa2d047b062ef793d5ed53e91ec722 sh bash 5.2_p37 ld GNU ld (Gentoo 2.43 p3) 2.43.1 app-misc/pax-utils: 1.3.8::gentoo app-shells/bash: 5.2_p37::gentoo dev-build/autoconf: 2.13-r8::gentoo, 2.71-r7::gentoo, 2.72-r1::gentoo dev-build/automake: 1.16.5-r2::gentoo dev-build/cmake: 3.30.6::gentoo dev-build/libtool: 2.5.4::gentoo dev-build/make: 4.4.1-r100::gentoo dev-build/meson: 1.6.1::gentoo dev-java/java-config: 2.3.4::gentoo dev-lang/perl: 5.40.0-r1::gentoo dev-lang/python: 2.7.18_p16-r2::gentoo, 3.10.16_p1::gentoo, 3.11.11_p1::gentoo, 3.12.8_p1::gentoo, 3.13.1_p1::gentoo dev-lang/rust: 1.81.0-r100::gentoo, 1.82.0-r101::gentoo, 1.83.0-r1::gentoo llvm-core/clang: 18.1.8-r6::gentoo, 19.1.7::gentoo llvm-core/lld: 19.1.7::gentoo llvm-core/llvm: 18.1.8-r6::gentoo, 19.1.7::gentoo sys-apps/baselayout: 2.17::gentoo sys-apps/openrc: 0.55.1::gentoo sys-apps/sandbox: 2.39::gentoo sys-devel/binutils: 2.43-r2::gentoo sys-devel/binutils-config: 5.5.2::gentoo sys-devel/gcc: 13.3.1_p20241220::gentoo, 14.2.1_p20241221::gentoo sys-devel/gcc-config: 2.12.1::gentoo sys-kernel/linux-headers: 6.12::gentoo (virtual/os-headers) sys-libs/glibc: 2.40-r8::gentoo Repositories: gentoo location: /tmp/repos/gentoo sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 volatile: True sync-rsync-verify-max-age: 24 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: --quiet --times --omit-dir-times --omit-link-times sync-rsync-verify-jobs: 1 guru location: /var/db/repos/guru sync-type: git sync-uri: https://github.com/gentoo-mirror/guru.git masters: gentoo volatile: False localrepo location: /var/db/repos/localrepo masters: gentoo volatile: False supertux88 location: /var/db/repos/supertux88 sync-type: git sync-uri: https://github.com/SuperTux88/gentoo-overlay.git masters: gentoo volatile: False x-portage location: /usr/local/portage masters: gentoo priority: 0 volatile: True oubliette location: /var/lib/layman/oubliette sync-type: git sync-uri: https://github.com/nabbi/oubliette-overlay.git masters: gentoo priority: 50 volatile: True palemoon location: /var/lib/layman/palemoon sync-type: git sync-uri: https://github.com/deu/palemoon-overlay.git masters: gentoo priority: 50 volatile: True pentoo location: /var/lib/layman/pentoo sync-type: git sync-uri: https://github.com/pentoo/pentoo-overlay.git masters: gentoo priority: 50 volatile: True pf4public location: /var/lib/layman/pf4public sync-type: git sync-uri: https://github.com/PF4Public/gentoo-overlay.git masters: gentoo priority: 50 volatile: True pg_overlay location: /var/lib/layman/pg_overlay sync-type: git sync-uri: https://gitlab.com/Perfect_Gentleman/PG_Overlay.git masters: gentoo priority: 50 volatile: True science location: /var/lib/layman/science sync-type: git sync-uri: https://anongit.gentoo.org/git/proj/sci.git masters: gentoo priority: 50 volatile: True stuff location: /var/lib/layman/stuff sync-type: git sync-uri: https://github.com/istitov/stuff.git masters: gentoo priority: 50 volatile: True Binary Repositories: binhost priority: 9999 sync-uri: https://ftp.rnl.tecnico.ulisboa.pt/pub/gentoo/gentoo-distfiles/releases/amd64/binpackages/23.0/x86-64-v3 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="@FREE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -flto -march=native " CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /var/bind" 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 -flto -march=native " DISTDIR="/tmp/var/cache/distfiles" EMERGE_DEFAULT_OPTS="--with-bdeps=y --keep-going --jobs 4" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE 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 XDG_STATE_HOME" FCFLAGS="-O2 -pipe -flto -march=native " FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg-live config-protect-if-modified distlocks downgrade-backup ebuild-locks fixlafiles ipc-sandbox merge-sync merge-wait multilib-strict network-sandbox news parallel-fetch pid-sandbox pkgdir-index-trusted 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 -flto -march=native " GENTOO_MIRRORS="ftp://ftp.halifax.rwth-aachen.de/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo" LANG="fr_FR.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -fuse-ld=mold" LEX="flex" MAKEOPTS="-j32" PKGDIR="/var/cache/binpkgs" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_EXTRA_OPTS="--quiet --times --omit-dir-times --omit-link-times" 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="/tmp/var/tmp" RUSTFLAGS=" -Clinker-plugin-lto" SHELL="/bin/bash" USE="X a52 aac acl acpi alsa amd64 avif bluetooth branding bzip2 cairo cdda cdr cdrom cet crypt cuda cups dbus dri dropbox dts dvd dvdr elogind encode exif ffmpeg flac gdbm gif gmic gmp gpm gtk gui iconv icu ipv6 jpeg jpeg2k jpegxl jumbo-build kde kf6compat lcms libnotify libtirpc lto lzma mad mp3 mp4 mpeg multilib ncurses nls nvenc ogg openexr opengl openmp opus pam pango pcre pdf png policykit ppds qml qt5 qt6 readline replaygain sdl seccomp sound spell split-usr ssl startup-notification svg test-rust tiff truetype udev udisks unicode upower usb v4l vaapi vdpau vim-syntax vorbis vpx vulkan webp wxwidgets x264 xattr xcb xft xml xv xvid zlib zstd" ABI_X86="64" ADA_TARGET="gcc_13" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_anon authn_dbm authn_file authz_dbm authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir env expires ext_filter file_cache filter headers include info log_config logio mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets stage words" 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" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax navcom oceanserver oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 tsip tripmate tnt ublox" GRUB_PLATFORMS="efi-64" GUILE_SINGLE_TARGET="3-0" GUILE_TARGETS="3-0" INPUT_DEVICES="libinput" KERNEL="linux" L10N="fr fr-FR" LCD_DEVICES="bayrad cfontz glk hd44780 lb216 lcdm001 mtxorb text" LLVM_TARGETS="NVPTX" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PERL_FEATURES="ithreads" PHP_TARGETS="php8-2" POSTGRES_TARGETS="postgres16" PYTHON_SINGLE_TARGET="python3_12" PYTHON_TARGETS="python3_12" RUBY_TARGETS="ruby25" SANE_BACKENDS="pixma net" VIDEO_CARDS="fbdev vesa dummy nvidia" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipp2p iface geoip fuzzy condition tarpit sysrq proto logmark ipmark dhcpmac delude chaos account" Unset: ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PYTHONPATH, RANLIB, READELF, SIZE, STRINGS, STRIP, YACC, YFLAGS
Created attachment 918192 [details] build log failure 1
Created attachment 918193 [details] build log 2 failure 2
Created attachment 918194 [details] build log 3 failure 3
Created attachment 918195 [details] build log 4 failure 4
Can you check with 2025.0?
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cbfb93682e2c96c8189bee787f46012edf5ca8dc commit cbfb93682e2c96c8189bee787f46012edf5ca8dc Author: Alexey Shvetsov <alexxy@gentoo.org> AuthorDate: 2025-02-24 10:43:33 +0000 Commit: Alexey Shvetsov <alexxy@gentoo.org> CommitDate: 2025-02-24 10:44:05 +0000 sci-chemistry/gromacs: sphinx and Co now needed for building man pages Closes: https://bugs.gentoo.org/949320 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org> sci-chemistry/gromacs/gromacs-2025.0.ebuild | 4 +--- sci-chemistry/gromacs/gromacs-2025.9999.ebuild | 4 +--- sci-chemistry/gromacs/gromacs-9999.ebuild | 4 +--- 3 files changed, 3 insertions(+), 9 deletions(-)
