Created attachment 769232 [details] Emerge log Emerge build log attached. Error message shown during configuration phase. Looking at this, it appears a pat configuration is at fault: ian2 ~ # equery files sys-libs/glibc | grep libdl /lib/libdl.so.2 /lib64/libdl.so.2 /usr/lib/libdl.a /usr/lib64/libdl.a ian2 ~ # -------------------------------------------------------------- ian2 ~ # emerge --info =sci-libs/vtk-9.0.3-r4::gentoo Portage 3.0.30 (python 3.9.9-final-0, default/linux/amd64/17.1, gcc-11.2.1, glibc-2.34-r10, 5.17.1-gentoo-r1 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-5.17.1-gentoo-r1-x86_64-AMD_Ryzen_7_2700_Eight-Core_Processor-with-glibc2.34 KiB Mem: 65825880 total, 1161364 free KiB Swap: 16777212 total, 16777212 free Timestamp of repository gentoo: Wed, 06 Apr 2022 23:15:01 +0000 Head commit of repository gentoo: 556db192c5062e0df2b536be15c2ffbaaf574d4e Head commit of repository dsiggis-gentoo-overlay: c1dac01243a339bb9e2e5ff63a911a43a88bb3f3 Timestamp of repository src_prepare-overlay: Tue, 05 Apr 2022 14:04:35 +0000 Head commit of repository src_prepare-overlay: fb774c7db634f3f05a7f5cadc5f6329a4ff0377b Timestamp of repository steam-overlay: Sat, 02 Apr 2022 16:36:17 +0000 Head commit of repository steam-overlay: a66630753214c6962b012dc5c7d4dc89cccc278c sh bash 5.1_p16 ld GNU ld (Gentoo 2.37_p1 p2) 2.37 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-r6::gentoo dev-lang/python: 3.9.9-r1::gentoo, 3.10.2_p1::gentoo dev-lang/rust: 1.58.1::gentoo dev-util/cmake: 3.22.2::gentoo dev-util/meson: 0.60.3::gentoo sys-apps/baselayout: 2.7-r3::gentoo sys-apps/openrc: 0.44.10::gentoo sys-apps/sandbox: 2.29::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.71-r1::gentoo sys-devel/automake: 1.16.4::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/llvm: 13.0.1::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.15-r3::gentoo (virtual/os-headers) sys-libs/glibc: 2.34-r10::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.uk.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-max-age: 24 sync-rsync-verify-jobs: 0 sync-rsync-extra-opts: sync-rsync-verify-metamanifest: yes dsiggis-gentoo-overlay location: /var/db/repos/dsiggis-gentoo-overlay sync-type: git sync-uri: https://github.com/dsiggi/dsiggis-gentoo-overlay.git masters: gentoo irp-overlay location: /var/lib/irp-overlay masters: gentoo src_prepare-overlay location: /var/db/repos/src_prepare-overlay sync-type: git sync-uri: https://github.com/gentoo-mirror/src_prepare-overlay.git masters: gentoo steam-overlay location: /var/db/repos/steam-overlay sync-type: git sync-uri: https://github.com/gentoo-mirror/steam-overlay.git masters: gentoo ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="@FREE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.8/conf /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" CXXFLAGS="-O2 -pipe" DISTDIR="/usr/portage/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" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg-live clean-logs 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 split-elog strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_GB.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j16" 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 alsa amd64 bluetooth branding bzip2 cairo cdda cli crypt cups dbus dri drm dts dvb dvb_cards_dibusb-usb1 dvb_cards_dibusb-usb2 elogind encode exif fbcondecor flac fortran gdbm gif gpm gtk iconv icu ipv6 jpeg lcms ldap libglvnd libnotify libtirpc mad mmx mng mp3 mpeg multilib ncurses netirfc nls nptl ogg opengl openmp pam pango pcre pdf png policykit pulseaudio readline sdl seccomp split-usr sse sse2 ssl svg text tiff truetype udev udisks unicode upower usb v4l vaapi vdpau vorbis vulkan vulkan-overlay x264 xattr xfce_plugins_brightness xfce_plugins_clock xfce_plugins_multiload-nandhp xfce_plugins_power xfce_plugins_trash xfce_plugins_xmonad xml xvid zlib" ABI_X86="64" ADA_TARGET="gnat_2020" 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" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" 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="coreboot efi-32 efi-64 pc" INPUT_DEVICES="libinput joystick" KERNEL="linux" L10N="en en-GB" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-4 php8-0" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python3_9" QEMU_SOFTMMU_TARGETS="aarch64 arm i386 x86_64" QEMU_USER_TARGETS="x86_64" RUBY_TARGETS="ruby26 ruby27" USERLAND="GNU" VIDEO_CARDS="amdgpu radeon radeonsi v4l" 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, EMERGE_DEFAULT_OPTS, 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, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS ================================================================= Package Settings ================================================================= sci-libs/vtk-9.0.3-r4::gentoo was built with the following: USE="X boost json openmp python qt5 rendering -all-modules -cuda -doc -examples -ffmpeg -gdal -imaging -java -kits -mpi -mysql -odbc -offscreen -pegtl -postgres -tbb -test -theora -tk -views -web" ABI_X86="(64)" PYTHON_SINGLE_TARGET="python3_9 -python3_8" VIDEO_CARDS="-nvidia" FEATURES="split-elog usersync network-sandbox parallel-fetch fixlafiles binpkg-logs unmerge-orphans xattr unknown-features-warn usersandbox multilib-strict buildpkg-live userpriv qa-unresolved-soname-deps merge-sync preserve-libs protect-owned sfperms strict sandbox news ebuild-locks clean-logs binpkg-docompress pid-sandbox userfetch unmerge-logs binpkg-dostrip distlocks config-protect-if-modified assume-digests ipc-sandbox" ian2 ~ #
Please try rebuilding netcdf.
*** This bug has been marked as a duplicate of bug 827188 ***
(In reply to Sam James from comment #1) > Please try rebuilding netcdf. I re-emerged sci-libs/netcdf-4.8.1-r1::gentoo Following that, sci-libs/vtk-9.0.3-r4::gentoo emerge clean and OK. Thanks
(In reply to Ian Pickworth from comment #3) > (In reply to Sam James from comment #1) > > Please try rebuilding netcdf. > > I re-emerged sci-libs/netcdf-4.8.1-r1::gentoo > Following that, sci-libs/vtk-9.0.3-r4::gentoo emerge clean and OK. > > Thanks I had the same issue, and resolved it successfully using the same method.
Thanks, had the same problem and rebuilding netcdf fixed it.
