hoegger
n00b
Joined: 06 Apr 2008
Posts: 52
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 Posted: Tue Jan 07, 2025 6:25 pm Post subject: sci-libs/vtk-9.3.1 failing to build - configure phase |
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Hello there!
I have tried to emerge sci-libs/vtk-9.3.1 but it fails due to it not finding hdf5.
Any suggestions will be much appreciated.
| Code: |
[ebuild U ] sci-libs/vtk-9.3.1:0/9.3::gentoo [9.3.0-r3:0/9.3::gentoo] USE="boost cgns%* cuda ffmpeg imaging logging mysql netcdf%* openmp python qt6 rendering sdl threads truetype%* views vtkm -all-modules (-debug) -doc -examples -gdal -gles2-only -java -las -minimal% -mpi -odbc -opencascade -openvdb -pdal -postgres -tbb -test -tk -web (-freetype%*) (-qt5%)" PYTHON_SINGLE_TARGET="python3_12 -python3_10 -python3_11" VIDEO_CARDS="nvidia" 97.622 KiB
Total: 1 package (1 upgrade), Size of downloads: 97.622 KiB
...
...
Make Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:233 (message):
Could NOT find HDF5 (missing: HDF5_INCLUDE_DIRS) (found version "")
Call Stack (most recent call first):
/usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:603 (_FPHSA_FAILURE_MESSAGE)
CMake/patches/99/FindHDF5.cmake:1006 (find_package_handle_standard_args)
ThirdParty/vtkm/vtkvtkm/vtk-m/CMakeLists.txt:128 (find_package)
-- Configuring incomplete, errors occurred!
* ERROR: sci-libs/vtk-9.3.1::gentoo failed (configure phase):
* cmake failed
*
* Call stack:
* ebuild.sh, line 136: Called src_configure
* environment, line 5261: Called cmake_src_configure
* environment, line 1808: Called die
* The specific snippet of code:
* "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}" || die "cmake failed";
*
* If you need support, post the output of `emerge --info '=sci-libs/vtk-9.3.1::gentoo'`,
* the complete build log and the output of `emerge -pqv '=sci-libs/vtk-9.3.1::gentoo'`.
!!! When you file a bug report, please include the following information:
GENTOO_VM= CLASSPATH="" JAVA_HOME="/home/ws/.gentoo/java-config-2/current-user-vm"
JAVACFLAGS="" COMPILER=""
and of course, the output of emerge --info =sci-libs/vtk-9.3.1
* The complete build log is located at '/var/tmp/portage/sci-libs/vtk-9.3.1/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/sci-libs/vtk-9.3.1/temp/environment'.
* Working directory: '/var/tmp/portage/sci-libs/vtk-9.3.1/work/VTK-9.3.1_build'
* S: '/var/tmp/portage/sci-libs/vtk-9.3.1/work/VTK-9.3.1'
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| Code: |
emerge --ask --verbose --oneshot hdf5
These are the packages that would be merged, in order:
Calculating dependencies... done!
Dependency resolution took 4.56 s (backtrack: 0/20).
[ebuild R ] sci-libs/hdf5-1.14.4_p3-r1:0/311::gentoo USE="fortran hl szip zlib -cxx -debug -examples -mpi -test -threads -unsupported" 0 KiB
Total: 1 package (1 reinstall), Size of downloads: 0 KiB
Would you like to merge these packages? [Yes/No]
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| Code: |
uname -a
Linux forest 6.12.6-gentoo #1 SMP PREEMPT_DYNAMIC Fri Dec 20 16:29:10 CET 2024 x86_64 Intel(R) Xeon(R) CPU E5-2696 v4 @ 2.20GHz GenuineIntel GNU/Linux
gcc --version
gcc (Gentoo 13.3.1_p20241220 p2) 13.3.1 20241220
Copyright (C) 2023 Free Software Foundation, Inc.
Dies ist freie Software; die Kopierbedingungen stehen in den Quellen. Es
gibt KEINE Garantie; auch nicht für MARKTGÄNGIGKEIT oder FÜR SPEZIELLE ZWECKE.
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| Code: |
* dev-util/nvidia-cuda-toolkit
Latest version available: 12.4.1
Latest version installed: 12.4.1
Size of files: 4.350.323 KiB
Homepage: https://developer.nvidia.com/cuda-zone
Description: NVIDIA CUDA Toolkit (compiler and friends)
License: NVIDIA-CUDA
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| Code: |
emerge --info '=sci-libs/vtk-9.3.1::gentoo'
Portage 3.0.66.1 (python 3.13.1-final-0, default/linux/amd64/23.0/desktop/plasma/systemd, gcc-13, glibc-2.40-r7, 6.12.6-gentoo x86_64)
=================================================================
System Settings
=================================================================
System uname: Linux-6.12.6-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5-2696_v4_@_2.20GHz-with-glibc2.40
KiB Mem: 131793880 total, 116523108 free
KiB Swap: 3710972 total, 3710972 free
Timestamp of repository gentoo: Tue, 07 Jan 2025 16:30:00 +0000
Head commit of repository gentoo: 764addedbd5fccd3ff9dc7f49a7eae7827b67095
Timestamp of repository gentoo-zh: Tue, 07 Jan 2025 15:03:19 +0000
Head commit of repository gentoo-zh: b7ff8fe5efe3e90d91e9376e30e520702271dbef
Timestamp of repository steam-overlay: Sun, 22 Dec 2024 19:48:21 +0000
Head commit of repository steam-overlay: fc25c23144765c2fcc4726aa19448b0ed507fc3e
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: 2.71-r7::gentoo, 2.72-r1::gentoo
dev-build/automake: 1.16.5-r2::gentoo, 1.17-r1::gentoo
dev-build/cmake: 3.31.3::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: 3.11.11_p1::gentoo, 3.12.8_p1::gentoo, 3.13.1_p1::gentoo
dev-lang/rust: 1.83.0-r1::gentoo
llvm-core/clang: 18.1.8-r6::gentoo, 19.1.6::gentoo
llvm-core/lld: 18.1.8::gentoo, 19.1.6::gentoo
llvm-core/llvm: 17.0.6-r3::gentoo, 18.1.8-r6::gentoo, 19.1.6::gentoo
sys-apps/baselayout: 2.17::gentoo
sys-apps/openrc: 0.56::gentoo
sys-apps/sandbox: 2.42::gentoo
sys-apps/systemd: 257.1::gentoo
sys-devel/binutils: 2.43-r2::gentoo
sys-devel/binutils-config: 5.5.2::gentoo
sys-devel/gcc: 12.4.1_p20241219::gentoo, 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-r7::gentoo
Repositories:
gentoo
location: /usr/portage
sync-type: rsync
sync-uri: rsync://rsync.gentoo.org/gentoo-portage
priority: -1000
volatile: True
sync-rsync-verify-max-age: 3
sync-rsync-verify-metamanifest: yes
sync-rsync-extra-opts:
sync-rsync-verify-jobs: 1
Lokal
location: /usr/local/portage
masters: gentoo
volatile: True
gentoo-zh
location: /var/db/repos/gentoo-zh
sync-type: git
sync-uri: https://github.com/gentoo-mirror/gentoo-zh.git
masters: gentoo
volatile: False
local
location: /var/db/repos/local
masters: gentoo
volatile: False
steam-overlay
location: /var/db/repos/steam-overlay
sync-type: git
sync-uri: https://github.com/gentoo-mirror/steam-overlay.git
masters: gentoo
volatile: False
crossdev
location: /var/db/repos/portage-crossdev
masters: gentoo
priority: 10
volatile: False
Binary Repositories:
binhost
priority: 9999
sync-uri: https://ftp.tu-ilmenau.de/mirror/gentoo/releases/amd64/binpackages/23.0/x86-64
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
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/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-php8.3/ext-active/ /etc/php/cgi-php8.3/ext-active/ /etc/php/cli-php8.3/ext-active/ /etc/php/fpm-php8.3/ext-active/ /etc/php/phpdbg-php8.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/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="-O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance binpkg-request-signature buildpkg-live 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 sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="https://mirror.eu.oneandone.net/linux/distributions/gentoo/gentoo/ http://mirror.eu.oneandone.net/linux/distributions/gentoo/gentoo/ rsync://mirror.eu.oneandone.net/gentoo/ https://mirror.dogado.de/gentoo http://ftp.agdsn.de/gentoo https://ftp.agdsn.de/gentoo rsync://ftp.agdsn.de/gentoo https://ftp.spline.inf.fu-berlin.de/mirrors/gentoo/ http://ftp.spline.inf.fu-berlin.de/mirrors/gentoo/ rsync://ftp.spline.inf.fu-berlin.de/gentoo-distfiles/ https://ftp.gwdg.de/pub/linux/gentoo/ http://ftp.gwdg.de/pub/linux/gentoo/ ftp://ftp.gwdg.de/pub/linux/gentoo/ rsync://ftp.gwdg.de/gentoo/ https://ftp.uni-hannover.de/gentoo/ http://ftp.uni-hannover.de/gentoo/ ftp://ftp.uni-hannover.de/gentoo/ ftp://mirror.netcologne.de/gentoo/ https://mirror.netcologne.de/gentoo/ http://mirror.netcologne.de/gentoo/ rsync://mirror.netcologne.de/gentoo/ https://mirror.netzwerge.de/gentoo/ http://mirror.netzwerge.de/gentoo/ rsync://mirror.netzwerge.de/gentoo https://packages.hs-regensburg.de/gentoo-distfiles/ https://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ ftp://linux.rz.ruhr-uni-bochum.de/gentoo-mirror/ rsync://linux.rz.ruhr-uni-bochum.de/gentoo https://ftp.halifax.rwth-aachen.de/gentoo/ http://ftp.halifax.rwth-aachen.de/gentoo/ ftp://ftp.halifax.rwth-aachen.de/gentoo/ rsync://ftp.halifax.rwth-aachen.de/gentoo/ https://ftp.tu-ilmenau.de/mirror/gentoo/ http://ftp.tu-ilmenau.de/mirror/gentoo/ rsync://ftp.tu-ilmenau.de/gentoo/ https://ftp.fau.de/gentoo http://ftp.fau.de/gentoo ftp://ftp.fau.de/gentoo rsync://ftp.fau.de/gentoo https://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ rsync://ftp-stud.hs-esslingen.de/gentoo/ https://ftp.uni-stuttgart.de/gentoo-distfiles/ http://ftp.uni-stuttgart.de/gentoo-distfiles/ ftp://ftp.uni-stuttgart.de/gentoo-distfiles/"
LANG="de_DE.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs"
LEX="flex"
LINGUAS="de_DE de en"
MAKEOPTS="-j44 -l44"
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"
SHELL="/bin/bash"
USE="X a52 aac acl acpi activities aes alsa amd64 apache2 avx avx2 bcmath bluetooth branding bzip2 cairo cdda cdr cet colord crypt cuda cups curl dbus declarative dmx dri dts dvd dvdr encode exif ffmpeg flac fma3 gd gdbm gentoo-vm gif gimp gpm gtk gui iconv icu imagemagick intl ipv6 jpeg kde kf6compat kwallet lcms libnotify libtirpc lm-sensors mad mmx mmxext mng mp3 mp4 mpeg multilib mysql mysqli ncurses networkmanager nls nvenc nvidia ogg opcache opengl openmp pam pango pcre pdf pdo pipewire plasma png policykit popcnt postscript ppds pulseaudio qml qt5 qt6 rdp readline samba screencast sdl seccomp semantic-desktop soap sound spell sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 startup-notification svg systemd test-rust tiff truetype udev udisks unicode upower usb v4l vaapi vdpau vnc vorbis vulkan wayland widgets wxwidgets x264 xattr xcb xft xinerama xml xslt xv xvid xvmc zip zlib" 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 words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sse sse2 sse3 sse4_1 sse4_2 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" GUILE_SINGLE_TARGET="3-0" GUILE_TARGETS="3-0" INPUT_DEVICES="evdev libinput" KERNEL="linux" L10N="de" 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" PHP_TARGETS="php8_0" POSTGRES_TARGETS="postgres16" PYTHON_SINGLE_TARGET="python3_12" PYTHON_TARGETS="python3_12 python3_11 python3_13" QEMU_SOFTMMU_TARGETS="x86_64 i386" QEMU_USER_TARGETS="x86_64 i386" RUBY_TARGETS="ruby32 ruby33 ruby34" VIDEO_CARDS="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, LC_ALL, LD, LFLAGS, LIBTOOL, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS
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Portage & Programming
