Created attachment 765707 [details] build.log sci-libs/netcdf-4.8.1-r1 mentions -lhdf5_hl-shared and -lhdf5-shared in `Libs.private` in its pkgconfig file: ``` ❯ cat /usr/lib64/pkgconfig/netcdf.pc prefix=/usr exec_prefix=/usr libdir=/usr/lib64 includedir=/usr/include ccompiler=/usr/sbin/x86_64-pc-linux-gnu-gcc Name: netCDF Description: NetCDF Client Library for C URL: http://www.unidata.ucar.edu/netcdf Version: 4.8.1 Libs: -L${libdir} -lnetcdf Libs.private: -lhdf5_hl-shared -lhdf5-shared -lm -lsz -lcurl -lzip Cflags: -I${includedir} ``` These libraries do not exist: ``` # q list sci-libs/hdf5 | rg '\.so$' /usr/lib64/libhdf5.so /usr/lib64/libhdf5_f90cstub.so /usr/lib64/libhdf5_fortran.so /usr/lib64/libhdf5_hl.so /usr/lib64/libhdf5_hl_f90cstub.so /usr/lib64/libhdf5_hl_fortran.so /usr/lib64/libhdf5_tools.so ``` Portage 3.0.30 (python 3.9.10-final-0, default/linux/amd64/17.1/desktop/plasma/systemd, gcc-11.2.1, glibc-2.34-r9, 5.16.10-gentoo-dist x86_64) ================================================================= System Settings ================================================================= System uname: Linux-5.16.10-gentoo-dist-x86_64-AMD_Ryzen_5_2400G_with_Radeon_Vega_Graphics-with-glibc2.34 KiB Mem: 14186512 total, 1425584 free KiB Swap: 4194300 total, 4194300 free Timestamp of repository gentoo: Wed, 23 Feb 2022 06:45:01 +0000 Head commit of repository gentoo: 5c61726c82552751f458b0abcfda412d3888eace Timestamp of repository haskell: Wed, 23 Feb 2022 06:36:45 +0000 Head commit of repository haskell: 5bc1c6cef109538ecfac261ec6b01888366ab013 Head commit of repository local: bcfadff1cc09af836647ac57ae1205efde0e7ba5 sh bash 5.1_p16 ld GNU ld (Gentoo 2.37_p1 p2) 2.37 ccache version 4.5.1 [disabled] app-misc/pax-utils: 1.3.3::gentoo app-shells/bash: 5.1_p16::gentoo dev-java/java-config: 2.3.1::gentoo dev-lang/perl: 5.34.0-r7::gentoo dev-lang/python: 2.7.18_p13::gentoo, 3.9.10-r1::gentoo, 3.10.2-r1::gentoo dev-lang/rust: 1.58.1::gentoo dev-util/ccache: 4.5.1::gentoo dev-util/cmake: 3.22.2::gentoo dev-util/meson: 0.60.3::gentoo sys-apps/baselayout: 2.8::gentoo sys-apps/sandbox: 2.29::gentoo sys-apps/systemd: 250.3::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.71-r1::gentoo sys-devel/automake: 1.16.5::gentoo sys-devel/binutils: 2.37_p1-r2::gentoo sys-devel/binutils-config: 5.4.1::gentoo sys-devel/clang: 13.0.1::gentoo sys-devel/gcc: 11.2.1_p20220115::gentoo sys-devel/gcc-config: 2.5-r1::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/lld: 13.0.1::gentoo sys-devel/llvm: 13.0.1::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.16::gentoo (virtual/os-headers) sys-libs/glibc: 2.34-r9::gentoo Repositories: gentoo location: /var/cache/portage/gentoo sync-type: rsync sync-uri: rsync://rsync.de.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-max-age: 24 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: --new-compress sync-rsync-verify-jobs: 1 haskell location: /var/db/repos/haskell sync-type: git sync-uri: https://github.com/gentoo-mirror/haskell.git masters: gentoo crossdev location: /var/cache/portage/crossdev masters: gentoo priority: 100 local location: /var/cache/portage/local sync-type: git sync-uri: https://github.com/devurandom/gentoo-overlay.git masters: gentoo priority: 1000 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="@FREE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-pipe -O2 -march=znver1" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.8/conf" 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="-pipe -O2 -march=znver1" DISTDIR="/var/cache/portage/distfiles" EMERGE_DEFAULT_OPTS="--nospinner" 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" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live buildsyspkg cgroup compressdebug config-protect-if-modified distlocks ebuild-locks fakeroot fixlafiles ipc-sandbox merge-sync mount-sandbox multilib-strict network-sandbox news parallel-fetch parallel-install 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" GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://ftp.fau.de/gentoo http://ftp.halifax.rwth-aachen.de/gentoo/ http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j6 -l4" PKGDIR="/var/cache/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_EXTRA_OPTS="--new-compress" 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" SHELL="/bin/bash" USE="7z 7zip X a52 aac aacplus aacs acl acpi activities aio alsa amd64 amr appindicator appstream aptx archive audit avahi avif ayatana bdplus blake2 blas bluetooth bluray bpf branding brotli bs2b btrfs bzip2 cairo caps cdda cddb cdio cdr celt chromaprint cjk cli clipboard color-management colord conntrack crypt cups curl d3d9 dav1d dbus declarative device-mapper dirac djvu dmabuf dri drm dts dvb dvd dvdr ed25519 editorconfig egl elf emoji encode epub evdev exif faudio fax fdk ffmpeg fftw filecaps firefox firewalld fish-completion fits flac fontconfig fontforge fortran fribidi gamepad gbm gdal gdbm geoclue geolocation gif git gles2 gles3 gmp gnome-online-accounts gnupg google googledrive gpg gps graphicsmagick graphite gstreamer gtk gtk3 gui gzip harfbuzz hdf5 heif http2 hugepages ibus iconv icu id3tag idn imlib inotify introspection ipv6 iwd jemalloc jpeg jpeg2k json kde kms kwallet lapack latex lcms ldac libatomic libglvnd libidn2 libinput libnotify libproxy libsecret libsoxr libtirpc libvirt lm-sensors lrz lto lv2 lvm lz4 lzma lzo mad magic man mariadb markdown mbim mercurial mjpeg mng mobi modemmanager modplug mp3 mp4 mpeg mplayer mpris mtp multilib mysql ncurses netlink networkmanager nftables nls nptl numa office ofx ogg openal opencl opencv openexr opengl openh264 openmax openmp opus otf pam pango pcap pcre pcre2 pdf pgo pipewire pixman pkcs11 pkcs7 plasma pm-utils png policykit postscript ppds prison pulseaudio python qml qrcode qt5 rav1e raw rdp readline rtmp rubberband samba sasl scanner schroedinger screencast sctp sdl sdl2 seatd seccomp semantic-desktop share smartcard snappy sparse speech speex spell spice srt ssl startup-notification steamruntime stemmer svg systemd tbb teamd telemetry telepathy tga theora threads thunderbolt tiff timezone tmux tpm truetype udev udisks uinput unicode unwind upnp upnp-av upower usb utempter v4l v4l2 vaapi vamp vdpau vkd3d vorbis vpx vtk vulkan wasm wavpack wayland webchannel webengine webp widgets wireguard wmf woff2 wps x264 x265 xattr xcb xinerama xkb xml xmp xrandr xscreensaver xv xvid xwayland xxhash xz yaml zeroconf zeromq zimg zlib zstd" ABI_X86="64" ADA_TARGET="gnat_2020" ALSA_CARDS="hda-intel" 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" CAMERAS="ptp2" 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 sse4a ssse3" ELIBC="glibc" 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="efi-64" INPUT_DEVICES="joystick libinput" KERNEL="linux" L10N="de de-DE en en-GB ar fa tr ja ko zh zh-CN zh-TW" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver scripting-javascript wiki-publisher" LLVM_TARGETS="AMDGPU BPF RISCV WebAssembly" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1 lua5-4 luajit" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-4 php8-0" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python3_9 pypy3" QEMU_SOFTMMU_TARGETS="riscv32 riscv64 x86_64" QEMU_USER_TARGETS="riscv32 riscv64" RUBY_TARGETS="ruby26 ruby27" USERLAND="GNU" VIDEO_CARDS="amdgpu virgl" 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: 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, LEX, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS ================================================================= Package Settings ================================================================= sci-libs/netcdf-4.8.1-r1::gentoo was built with the following: USE="dap hdf5 szip -doc -examples -hdf -mpi -test -tools" ABI_X86="(64)" CFLAGS="-pipe -O2 -march=znver1 -fno-strict-aliasing" CXXFLAGS="-pipe -O2 -march=znver1 -fno-strict-aliasing" FEATURES="compressdebug binpkg-docompress binpkg-multi-instance buildsyspkg distlocks cgroup fakeroot pid-sandbox ebuild-locks usersandbox binpkg-logs assume-digests multilib-strict userfetch fixlafiles sandbox strict merge-sync config-protect-if-modified buildpkg-live unknown-features-warn unmerge-orphans protect-owned preserve-libs parallel-fetch network-sandbox mount-sandbox keeptemp qa-unresolved-soname-deps news xattr ipc-sandbox userpriv unmerge-logs parallel-install binpkg-dostrip sfperms usersync" sci-libs/hdf5-1.12.1-r1::gentoo was built with the following: USE="fortran hl szip zlib -cxx -debug -doc -examples (-mpi) -ros3 -test -threads -unsupported" ABI_X86="(64)" FEATURES="ebuild-locks preserve-libs binpkg-docompress userfetch assume-digests cgroup fixlafiles xattr unmerge-logs merge-sync sfperms ipc-sandbox sandbox strict news network-sandbox usersandbox parallel-install multilib-strict compressdebug protect-owned pid-sandbox fakeroot unknown-features-warn unmerge-orphans binpkg-multi-instance parallel-fetch binpkg-dostrip binpkg-logs userpriv buildsyspkg qa-unresolved-soname-deps distlocks config-protect-if-modified mount-sandbox usersync"
This also affects /usr/lib64/cmake/netCDF/netCDFTargets.cmake (also owned by sci-libs/netcdf): ``` set_target_properties(netCDF::netcdf PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${_IMPORT_PREFIX}/include;${_IMPORT_PREFIX}/include" INTERFACE_LINK_LIBRARIES "hdf5_hl-shared;hdf5-shared;/usr/lib64/libm.so;/usr/lib64/libsz.so;/usr/lib64/libcurl.so;/usr/lib64/libzip.so" ) ```
(In reply to Dennis Schridde from comment #1) > This also affects /usr/lib64/cmake/netCDF/netCDFTargets.cmake (also owned by > sci-libs/netcdf): > ``` > set_target_properties(netCDF::netcdf PROPERTIES > INTERFACE_INCLUDE_DIRECTORIES > "${_IMPORT_PREFIX}/include;${_IMPORT_PREFIX}/include" > INTERFACE_LINK_LIBRARIES > "hdf5_hl-shared;hdf5-shared;/usr/lib64/libm.so;/usr/lib64/libsz.so;/usr/ > lib64/libcurl.so;/usr/lib64/libzip.so" > ) > ``` Replacing hdf5_hl-shared and hdf5-shared with /usr/lib64/libhdf5_hl.so and /usr/lib64/libhdf5.so, respectively, in /usr/lib64/cmake/netCDF/netCDFTargets.cmake appears to make sci-libs/vtk-9.1.0 build. Sadly I repeatedly run into out-of-memory situations, before the build completes, so I cannot absolutely confirm this. But each time the build progressed well beyond the point where it previously tried to link against the non-existent libraries and failed.
With hdf5-1.12.2-r1 this is fixed. I'm 90% sure this is the commit that fixed it: https://gitweb.gentoo.org/repo/gentoo.git/commit/sci-libs/hdf5?id=78267a0516b2712775242cfa3da73c9b31d77584
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7fa499da25bf08098ba57a7421129c9288443de4 commit 7fa499da25bf08098ba57a7421129c9288443de4 Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org> AuthorDate: 2022-05-18 16:56:56 +0000 Commit: Andrew Ammerlaan <andrewammerlaan@gentoo.org> CommitDate: 2022-05-18 16:58:47 +0000 sci-libs/vtk: unrestrict hdf5 The issue was never in vtk, it was in netcdf which has been fixed. Compiles without problems now. Bug: https://bugs.gentoo.org/833943 Closes: https://bugs.gentoo.org/834087 Closes: https://bugs.gentoo.org/809209 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org> sci-libs/vtk/{vtk-9.1.0-r1.ebuild => vtk-9.1.0-r2.ebuild} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-)
