# emerge -pqv '=sci-libs/vtk-9.3.1::gentoo' [ebuild R ] sci-libs/vtk-9.3.1 USE="all-modules boost cgns doc examples ffmpeg gdal imaging java las logging mpi mysql netcdf odbc opencascade openmp openvdb pdal postgres python qt6 rendering sdl tbb threads tk truetype views vtkm web -cuda (-debug) -gles2-only -minimal -test" PYTHON_SINGLE_TARGET="python3_12 -python3_10 -python3_11" VIDEO_CARDS="nvidia" # emerge --info '=sci-libs/vtk-9.3.1::gentoo' Portage 3.0.68 (python 3.13.3-final-0, default/linux/amd64/23.0/desktop/gnome/systemd, gcc-14, glibc-2.41-r1, 6.14.3-gentoo-amd64 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-6.14.3-gentoo-amd64-x86_64-13th_Gen_Intel-R-_Core-TM-_i7-1370P-with-glibc2.41 KiB Mem: 65392340 total, 1230872 free KiB Swap: 8388604 total, 7466912 free Timestamp of repository gentoo: Thu, 24 Apr 2025 03:30:01 +0000 Head commit of repository gentoo: e71a15a5b2550714c11d02d31bff72ea6f3a0eae Timestamp of repository HomeAssistantRepository: Mon, 19 Aug 2024 18:34:04 +0000 Head commit of repository HomeAssistantRepository: b3ac1445b4b7810c19215de5a8f5f32a4f70e45d Head commit of repository SarahMiaOverlay: 8f9408f4c6521b226c08bcdaf774b075cc2ff4cd Head commit of repository brave-overlay: 1e6c0bacfd42780050b455bb4a604035bcafb71f Head commit of repository elementary: 99270b6bafdebff2e946d0dc4da8908d86d0f905 Timestamp of repository guru: Wed, 23 Apr 2025 15:38:23 +0000 Head commit of repository guru: c44c7c24eb846309e5a55e54111eb5c58753ebab Head commit of repository inode64-overlay: 8675513800397ec4737e8256da3fce16180aa0c0 Head commit of repository kde: ad864099d9b2844e12bd9cf7e20e08106c98610b Head commit of repository kodi-overlay: c66560a34803e3322c945c6c391e465c7b9a273d Head commit of repository pentoo: c3e707608e98fd688a8ed17cba5c8f6bde2c0ed4 Head commit of repository torbrowser: d90d188b1daaa78f03511d4b886794c9c1ae682a sh bash 5.2_p37 ld GNU ld (Gentoo 2.44 p1) 2.44.0 ccache version 4.11.2 [enabled] app-misc/pax-utils: 1.3.8::gentoo app-shells/bash: 5.2_p37::gentoo dev-build/autoconf: 2.13-r8::gentoo, 2.72-r1::gentoo dev-build/automake: 1.17-r2::gentoo dev-build/cmake: 3.31.7::gentoo dev-build/libtool: 2.5.4::gentoo dev-build/make: 4.4.1-r100::gentoo dev-build/meson: 1.7.2::gentoo dev-java/java-config: 2.3.4::gentoo dev-lang/perl: 5.40.2::gentoo dev-lang/python: 3.10.17::gentoo, 3.11.12::gentoo, 3.12.10::gentoo, 3.13.3::gentoo, 3.13.3-r100::gentoo dev-lang/rust: 1.85.1::gentoo, 1.86.0-r1::gentoo dev-lang/rust-bin: 1.81.0-r103::gentoo, 1.84.1-r2::gentoo, 1.85.1::gentoo, 1.86.0-r1::gentoo dev-util/ccache: 4.11.2::gentoo llvm-core/clang: 15.0.7-r3::gentoo, 16.0.6::gentoo, 17.0.6::gentoo, 18.1.8-r6::gentoo, 19.1.7::gentoo, 20.1.3::gentoo llvm-core/lld: 15.0.7::gentoo, 19.1.7::gentoo llvm-core/llvm: 15.0.7-r7::gentoo, 16.0.6-r5::gentoo, 17.0.6-r3::gentoo, 18.1.8-r6::gentoo, 19.1.7::gentoo, 20.1.3::gentoo sys-apps/baselayout: 2.17::gentoo sys-apps/sandbox: 2.46::gentoo sys-apps/systemd: 257.5::gentoo sys-devel/binutils: 2.44::gentoo sys-devel/binutils-config: 5.5.2::gentoo sys-devel/gcc: 13.3.1_p20250301::gentoo, 14.2.1_p20250301::gentoo sys-devel/gcc-config: 2.12.1::gentoo sys-kernel/linux-headers: 6.14::gentoo (virtual/os-headers) sys-libs/glibc: 2.41-r1::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: rsync sync-uri: rsync://gentoo.kopylovs.net/gentoo-portage priority: -1000 volatile: False sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: yes sync-rsync-verify-max-age: 3 sync-rsync-extra-opts: HomeAssistantRepository location: /var/db/repos/HomeAssistantRepository sync-type: git sync-uri: https://git.edevau.net/onkelbeh/HomeAssistantRepository.git masters: gentoo volatile: False SarahMiaOverlay location: /var/db/repos/SarahMiaOverlay sync-type: git sync-uri: https://gitlab.com/SarahMia/sarahmiaoverlay.git masters: gentoo volatile: False brave-overlay location: /var/db/repos/brave-overlay sync-type: git sync-uri: https://gitlab.com/jason.oliveira/brave-overlay.git masters: gentoo volatile: False elementary location: /var/db/repos/elementary sync-type: git sync-uri: https://github.com/pimvullers/elementary.git masters: gentoo volatile: False guru location: /var/db/repos/guru sync-type: git sync-uri: https://github.com/gentoo-mirror/guru.git masters: gentoo volatile: False inode64-overlay location: /var/db/repos/inode64-overlay sync-type: git sync-uri: https://github.com/inode64/inode64-overlay.git masters: gentoo volatile: False kde location: /var/db/repos/kde sync-type: git sync-uri: https://anongit.gentoo.org/git/proj/kde.git masters: gentoo volatile: False kodi-overlay location: /var/db/repos/kodi-overlay sync-type: git sync-uri: https://github.com/kodi-overlay/kodi-overlay.git masters: gentoo volatile: False pentoo location: /var/db/repos/pentoo sync-type: git sync-uri: https://github.com/pentoo/pentoo-overlay.git masters: gentoo volatile: False torbrowser location: /var/db/repos/torbrowser sync-type: git sync-uri: https://github.com/MeisterP/torbrowser-overlay.git masters: gentoo volatile: False Binary Repositories: gentoobinhost priority: 1 sync-uri: https://distfiles.gentoo.org/releases/amd64/binpackages/23.0/x86-64 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA android AnyDesk-TOS geekbench google-chrome Intel-SDP microsoft-edge Microsoft-vscode NVIDIA-CUDA NVIDIA-SDK OPERA-2018 PUEL-12 RAR TeamViewer Vivaldi" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe -fomit-frame-pointer" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /opt/sonar/conf /opt/zookeeper-bin/conf /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/php/apache2-php8.2/ext-active/ /etc/php/apache2-php8.3/ext-active/ /etc/php/apache2-php8.4/ext-active/ /etc/php/cgi-php8.2/ext-active/ /etc/php/cgi-php8.3/ext-active/ /etc/php/cgi-php8.4/ext-active/ /etc/php/cli-php8.2/ext-active/ /etc/php/cli-php8.3/ext-active/ /etc/php/cli-php8.4/ext-active/ /etc/php/fpm-php8.2/ext-active/ /etc/php/fpm-php8.3/ext-active/ /etc/php/fpm-php8.4/ext-active/ /etc/php/phpdbg-php8.2/ext-active/ /etc/php/phpdbg-php8.3/ext-active/ /etc/php/phpdbg-php8.4/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=native -O2 -pipe -fomit-frame-pointer" DISTDIR="/var/cache/distfiles" 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="-march=native -O2 -pipe -fomit-frame-pointer" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live ccache config-protect-if-modified distlocks ebuild-locks export-pms-vars 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 strict strict-keepdir unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync warn-on-large-env xattr" FFLAGS="-march=native -O2 -pipe -fomit-frame-pointer" GENTOO_MIRRORS="http://mirror.isoc.org.il/pub/gentoo/ https://mirror.eu.oneandone.net/linux/distributions/gentoo/gentoo/" LANG="en_US.utf8" LC_ALL="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs" LEX="flex" MAKEOPTS="-j10" PKGDIR="/var/cache/binpkgs" 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" RUSTFLAGS=" -C target-cpu=native" SHELL="/bin/bash" USE="X a52 aac accessibility acl acpi activities alsa amd64 apparmor audit bash-completion berkdb bidi bluetooth branding brotli btrfs bzip2 cairo cdda cdr cet cli colord crypt cryptsetup cuda cups curl dbus designer device-mapper doc dri drm dts dvd dvdr eds emacs encode evdev evo examples exif experimental ffmpeg flac fortran fuse gamepad gdbm gdk-pixbuf gif git gmp gnome gnome-keyring gnome-online-accounts gnome-shell gnutls go gpg gpm gstreamer gtk gtk-doc gui hscolour html http iconv icu idn introspection iodbc ios ipv6 jack java javascript jemalloc joystick jpeg json kde kerberos keyring kf6compat lcms ldap libnotify libtirpc lm-sensors lua lvm lz4 lzma lzo mad man mbedtls mng mongodb mp3 mp4 mpeg mpi multilib multimedia mysql nas nautilus ncurses netlink network networkmanager nfs nls nss nvenc odbc offensive ogg opencl opengl openmp openssl pam pango pcap pcre pdf perl pkcs11 plasma plugins png policykit postgres ppds pulseaudio python qml qt5 qt6 readline redis samba sasl screencast sdl seccomp semantic-desktop snmp sound source speech spell sqlite ssl startup-notification svg symlink sysprof systemd tcl telemetry test-rust threads tiff tk tools tpm tracker truetype udev udisks unicode upower usb utils v4l vaapi vala vdpau vim-syntax vnc vorbis vulkan wayland webengine webkit webp wifi wxwidgets x264 xattr xcb xft xinerama xml xv xvid yaml zeroconf zip zlib zsh-completion zstd" ABI_X86="64 32" ADA_TARGET="gcc_14" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_core authn_dbd authn_dbm authn_file authn_socache authz_core authz_dbd authz_dbm authz_groupfile authz_host authz_owner authz_user autoindex brotli cache cgi cgid charset_lite dav dav_fs dav_lock dbd deflate dir env expires ext_filter file_cache filter headers http2 ident imagemap include info log_config logio mime mime_magic negotiation ratelimit reqtimeout rewrite session session_cookie session_crypto session_dbd setenvif socache_shmcb speling status substitute unique_id unixd userdir usertrack version vhost_alias watchdog xml2enc" APACHE2_MPMS="worker" 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 rdrand sha sse sse2 sse3 sse4_1 sse4_2 ssse3 vpclmulqdq" 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="evdev joystick libinput" KERNEL="linux" L10N="en en-US he ru" LCD_DEVICES="bayrad cfontz glk hd44780 lb216 lcdm001 mtxorb text" LIBREOFFICE_EXTENSIONS="nlpsolver scripting-beanshell scripting-javascript wiki-publisher" LUA_SINGLE_TARGET="lua5-4" LUA_TARGETS="lua5-1 lua5-4" NGINX_MODULES_HTTP="access addition auth_basic auth_ldap auth_pam auth_request autoindex brotli browser charset dav dav_ext echo empty_gif fancyindex fastcgi flv geo geoip geoip2 grpc gunzip gzip image_filter javascript limit_conn limit_req map memc memcached metrics mirror mp4 perl proxy push_stream referer rewrite scgi split_clients ssi stub_status upload_progress upstream_check upstream_hash upstream_ip_hash upstream_keepalive upstream_least_conn upstream_zone userid uwsgi vhost_traffic_status vod xslt" NGINX_MODULES_MAIL="imap pop3 smtp" NGINX_MODULES_STREAM="access geo geoip geoip2" OFFICE_IMPLEMENTATION="libreoffice" PERL_FEATURES="ithreads quadmath" PHP_TARGETS="php8-2 php8-3" POSTGRES_TARGETS="postgres16 postgres17" PYTHON_SINGLE_TARGET="python3_13" PYTHON_TARGETS="python3_12 python3_10 python3_11 python3_13 python3_13t" RUBY_TARGETS="ruby32 ruby33 ruby34" UWSGI_PLUGINS="alarm_curl cache carbon cheaper_busyness clock_monotonic clock_realtime corerouter curl_cron dumbloop echo emperor_amqp emperor_pg emperor_zeromq fastrouter forkptyrouter geoip graylog2 http ldap legion_cache_fetch logcrypto logfile logpipe logsocket mongodblog nagios notfound pam ping rados rawrouter redislog router_access router_basicauth router_cache router_expires router_hash router_http router_memcached router_metrics router_redirect router_redis router_rewrite router_spnego router_static router_uwsgi router_xmldir rpc rrdtool rsyslog signal spooler sqlite ssi sslrouter stats_pusher_statsd symcall syslog systemd_logger transformation_chunked transformation_gzip transformation_offload transformation_tofile transformation_toupper tuntap ugreen webdav xattr xslt zabbix zergpool" VIDEO_CARDS="intel fbdev vesa 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, EMERGE_DEFAULT_OPTS, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LD, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, RANLIB, READELF, SIZE, STRINGS, STRIP, YACC, YFLAGS ================================================================= Package Settings ================================================================= sci-libs/vtk-9.3.1::gentoo was built with the following: USE="all-modules boost cgns doc examples ffmpeg gdal imaging java las logging mpi mysql netcdf odbc opencascade openmp openvdb pdal postgres python qt6 rendering sdl tbb threads tk truetype views vtkm web -cuda (-debug) -gles2-only -minimal -test" ABI_X86="(64)" PYTHON_SINGLE_TARGET="python3_12 -python3_10 -python3_11" VIDEO_CARDS="nvidia" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live ccache config-protect-if-modified distlocks 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 strict strict-keepdir unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync warn-on-large-env xattr"
Created attachment 925980 [details] build.log
Looks like it needs sci-libs/hdf5[cxx,hl] (now)?
(In reply to Michał Górny from comment #2) > Looks like it needs sci-libs/hdf5[cxx,hl] (now)? that at least seems to be not sufficient. I also have: sci-libs/hdf5-1.14.6-r1[cxx,fortran,hl,szip,zlib,-debug,-mpi,-test,-threads,-unsupported] and vtk fails with the same error.
Created attachment 925984 [details] another failed build.log
Oh, it's USE=vtkm.
I've just set USE=-vtkm and indeed the cmake failure is gone with that and it starts compiling. However, it then later bails out in linking phase: > usr/lib/gcc/x86_64-pc-linux-gnu/14/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lhdf5_hl-shared: No such file or directory > /usr/lib/gcc/x86_64-pc-linux-gnu/14/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lhdf5-shared: No such file or directory > collect2: error: ld returned 1 exit status and sci-libs/hdf5 indeed does not deliver /usr/lib64/libhdf5[_hl]-shared.*
but interestingly enough: neither did =sci-libs/hdf5-1.14.6 … however, /usr/lib64/libhdf5.settings of 1.14.6 and 1.14.6-r1 seem to differ a lot:
Created attachment 925985 [details] /usr/lib64/libhdf5.settings of sci-libs/hdf5-1.14.6
Created attachment 925986 [details] /usr/lib64/libhdf5.settings of sci-libs/hdf5-1.14.6-r1
My guess is that vtk CMake logic makes wrong assumptions here. FWICS it's horrible and has had some major bugs in the past.
*** Bug 954385 has been marked as a duplicate of this bug. ***
(In reply to Christian Bricart from comment #6) > I've just set USE=-vtkm and indeed the cmake failure is gone with that and > it starts compiling. > > However, it then later bails out in linking phase: > > > usr/lib/gcc/x86_64-pc-linux-gnu/14/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lhdf5_hl-shared: No such file or directory > > /usr/lib/gcc/x86_64-pc-linux-gnu/14/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lhdf5-shared: No such file or directory > > collect2: error: ld returned 1 exit status > > and sci-libs/hdf5 indeed does not deliver /usr/lib64/libhdf5[_hl]-shared.* This is also what I am getting [-vtkm].
