| Summary: | sci-libs/cgnslib-4.3.0 fails to configure with >=sci-libs/hdf5-14 | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Leonid Kopylov <leonchik1976> |
| Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | nowa, sam, uleysky |
| Priority: | Normal | Keywords: | PATCH |
| Version: | unspecified | ||
| Hardware: | AMD64 | ||
| OS: | Linux | ||
| See Also: |
https://github.com/HDFGroup/hdf5/issues/2422 https://github.com/HDFGroup/hdf5/issues/2621 https://github.com/HDFGroup/hdf5/pull/2667 https://bugs.gentoo.org/show_bug.cgi?id=904691 |
||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: |
build.log
Fix hdf5 configuration parameters |
||
Created attachment 860325 [details]
build.log
-- Configuring done (2.0s)
CMake Error in src/CMakeLists.txt:
Imported target "hdf5::hdf5-shared" includes non-existent path
"/var/tmp/portage/sci-libs/hdf5-1.14.0/work/hdf5-1.14.0/src/H5FDsubfiling"
in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:
* The path was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and references files it does not
provide.
CMake Error in src/CMakeLists.txt:
Imported target "hdf5::hdf5-shared" includes non-existent path
"/var/tmp/portage/sci-libs/hdf5-1.14.0/work/hdf5-1.14.0/src/H5FDsubfiling"
in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:
* The path was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and references files it does not
provide.
-- Generating done (0.0s)
CMake Generate step failed. Build files cannot be regenerated correctly.
* ERROR: sci-libs/cgnslib-4.3.0::gentoo failed (configure phase):
* cmake failed
---
so hdf5 update's fault, I assume..
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=311e3fd6822338b4313af27521bc57451b8cecc0 commit 311e3fd6822338b4313af27521bc57451b8cecc0 Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org> AuthorDate: 2023-04-18 15:49:28 +0000 Commit: Andrew Ammerlaan <andrewammerlaan@gentoo.org> CommitDate: 2023-04-18 15:49:28 +0000 sci-libs/cgnslib: restrict to hdf5<14 Bug: https://bugs.gentoo.org/904515 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org> sci-libs/cgnslib/{cgnslib-4.3.0.ebuild => cgnslib-4.3.0-r1.ebuild} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) Created attachment 860432 [details, diff]
Fix hdf5 configuration parameters
The problem is in hdf5. I have attached a patch that fixes it.
(In reply to Larry the Git Cow from comment #3) > The bug has been referenced in the following commit(s): > > https://gitweb.gentoo.org/repo/gentoo.git/commit/ > ?id=311e3fd6822338b4313af27521bc57451b8cecc0 > > commit 311e3fd6822338b4313af27521bc57451b8cecc0 > Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org> > AuthorDate: 2023-04-18 15:49:28 +0000 > Commit: Andrew Ammerlaan <andrewammerlaan@gentoo.org> > CommitDate: 2023-04-18 15:49:28 +0000 > > sci-libs/cgnslib: restrict to hdf5<14 > I don't think the problem is specific to cgnslib at all and I think hdf5 is broken, so it would've been better to just mask it. (In reply to Michael Uleysky from comment #4) > Created attachment 860432 [details, diff] [details, diff] > Fix hdf5 configuration parameters > > The problem is in hdf5. I have attached a patch that fixes it. Thanks. It's not yet clear to me why this works but I'll look more. The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=995c8aefa871da5ad197b29b782ff9e2d1e46e83 commit 995c8aefa871da5ad197b29b782ff9e2d1e46e83 Author: Sam James <sam@gentoo.org> AuthorDate: 2023-04-20 19:34:45 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2023-04-20 19:36:51 +0000 sci-libs/hdf5: fix installed CMake files (exclude temporary include dir for build) Closes: https://bugs.gentoo.org/904515 Closes: https://bugs.gentoo.org/904691 Signed-off-by: Sam James <sam@gentoo.org> .../hdf5/files/hdf5-1.14.0-fix-include-path.patch | 34 ++++++++++++++++++++++ .../{hdf5-1.14.0.ebuild => hdf5-1.14.0-r1.ebuild} | 1 + 2 files changed, 35 insertions(+) Additionally, it has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=20a01868e67f513af7a45c44ec9ceb53877863d2 commit 20a01868e67f513af7a45c44ec9ceb53877863d2 Author: Sam James <sam@gentoo.org> AuthorDate: 2023-04-20 19:35:07 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2023-04-20 19:36:52 +0000 Revert "sci-libs/cgnslib: restrict to hdf5<14" This reverts commit 311e3fd6822338b4313af27521bc57451b8cecc0. Not needed anymore and a better solution would've been to mask newer hdf5 given it was broken, not cgnslib. Bug: https://bugs.gentoo.org/904515 Signed-off-by: Sam James <sam@gentoo.org> sci-libs/cgnslib/{cgnslib-4.3.0-r1.ebuild => cgnslib-4.3.0-r2.ebuild} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) |
# emerge -pqv '=sci-libs/cgnslib-4.3.0::gentoo' [ebuild R ] sci-libs/cgnslib-4.3.0 USE="base-scope examples fortran hdf5 scoping szip tools -debug -legacy -mpi -test" # emerge --info '=sci-libs/cgnslib-4.3.0::gentoo' Portage 3.0.46 (python 3.11.3-final-0, default/linux/amd64/17.1/desktop/gnome/systemd/merged-usr, gcc-12, glibc-2.37-r2, 6.2.11-gentoo-amd64 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-6.2.11-gentoo-amd64-x86_64-12th_Gen_Intel-R-_Core-TM-_i7-1260P-with-glibc2.37 KiB Mem: 65423536 total, 62120908 free KiB Swap: 8388604 total, 8388604 free Timestamp of repository gentoo: Tue, 18 Apr 2023 14:30:01 +0000 Head commit of repository gentoo: 93eca38ef76c1a9c568155659b891db542f22939 sh bash 5.2_p15-r2 ld GNU ld (Gentoo 2.40 p4) 2.40.0 ccache version 4.8 [enabled] app-misc/pax-utils: 1.3.7::gentoo app-shells/bash: 5.2_p15-r2::gentoo dev-java/java-config: 2.3.1::gentoo dev-lang/perl: 5.36.0-r2::gentoo dev-lang/python: 3.10.11::gentoo, 3.11.3::gentoo dev-lang/rust: 1.68.2::gentoo dev-util/ccache: 4.8::gentoo dev-util/cmake: 3.26.3::gentoo dev-util/meson: 1.1.0::gentoo sys-apps/baselayout: 2.13-r1::gentoo sys-apps/sandbox: 2.30-r1::gentoo sys-apps/systemd: 253.3::gentoo sys-devel/autoconf: 2.71-r6::gentoo sys-devel/automake: 1.16.5-r1::gentoo sys-devel/binutils: 2.40-r4::gentoo sys-devel/binutils-config: 5.5::gentoo sys-devel/clang: 16.0.1::gentoo sys-devel/gcc: 12.2.1_p20230304::gentoo sys-devel/gcc-config: 2.10::gentoo sys-devel/libtool: 2.4.7-r1::gentoo sys-devel/llvm: 14.0.6-r2::gentoo, 16.0.1::gentoo sys-devel/make: 4.4.1::gentoo sys-kernel/linux-headers: 6.2::gentoo (virtual/os-headers) sys-libs/glibc: 2.37-r2::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 volatile: False sync-rsync-verify-max-age: 24 sync-rsync-extra-opts: sync-rsync-verify-metamanifest: yes sync-rsync-verify-jobs: 1 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA android AnyDesk-TOS geekbench google-chrome Intel-SDP microsoft-edge Microsoft-vscode OPERA-2018 PUEL-11 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 /usr/share/config /usr/share/gnupg/qualified.txt" 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/cgi-php8.2/ext-active/ /etc/php/cli-php8.2/ext-active/ /etc/php/fpm-php8.2/ext-active/ /etc/php/phpdbg-php8.2/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 fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms 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="https://mirror.isoc.org.il/pub/gentoo/" LANG="en_US.utf8" LC_ALL="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" 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" SHELL="/bin/bash" USE="X a52 aac aalib accessibility acl acpi activities alsa amd64 ao appindicator archive aspell audit bash-completion berkdb bidi bluetooth bluray boost branding brotli btrfs bzip2 cairo cdda cddb cdio cdr cgi cli colord contrib cron crypt cryptsetup cups curl dbi dbus designer device-mapper djvu doc dri drm dts dv dvb dvd dvdr eds emacs enchant encode evdev evo examples executable exif expat experimental extra extras fam fastcgi fbcon ffmpeg fftw firebird flac fluidsynth fontconfig fontforge fortran freetds ftp fuse gamepad games gcrypt gd gdbm gdk-pixbuf geoip geolocation gif git glade glib glusterfs gme gmp gnome gnome-keyring gnome-online-accounts gnuplot gnutls go gpg gphoto2 gpm graphite graphviz gsm gssapi gstreamer gtk gtk-doc gtk3 gui guile harfbuzz hdf5 heif highlight hscolour html http http2 ibus iconv icu idn imagemagick imap imlib introspection iodbc ios ipv6 jack java javascript jbig jemalloc joystick jpeg jpeg2k jpegxl json kde kerberos ladspa lame latex lcms ldap libass libcaca libevent libglvnd libnotify libsamplerate libsecret libtirpc libxml2 lm-sensors lmdb lua lv2 lvm lz4 lzma lzo mad magic maildir man mbedtls mbox memcached midi mmap mms mng modplug mono mp3 mp4 mpeg mpi mplayer mssql mtp multilib multimedia musepack mysql nas nautilus ncurses netlink nettle network networkmanager nfs nls nptl nss ntlm odbc offensive ogg openal opencl openexr opengl openmp openssl opus pam pango pcap pcre pdf perl phonon pkcs11 plasma plugins png policykit portaudio postgres postscript ppds pulseaudio python qdbm qml qrcode qt5 raw rdma readline redis rss samba sasl screencast sctp sdl seccomp semantic-desktop sftp share skey smp smtp snappy sndfile sndio snmp sound source sox speech speex spell sql sqlite ssh ssl startup-notification svg symlink syslog sysprof systemd taglib tbb tcl tcpd telemetry telepathy test-rust theora threads tiff tk tools tpm tracker tremor truetype twolame udev udisks unicode unwind upnp upower usb utils uuid v4l vaapi vala vcd vim-syntax vnc vorbis vpx vulkan wavpack wayland webengine webkit webp websockets widgets wifi wmf wxwidgets x264 x265 xattr xcb xface xft xinerama xml xmp xpm xscreensaver xv xvid yaml zeroconf zip zlib zsh-completion zstd" ABI_X86="64 32" ADA_TARGET="gnat_2021" 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 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" 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="evdev joystick libinput" KERNEL="linux" L10N="en en-US he ru" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver scripting-beanshell scripting-javascript wiki-publisher" 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_11" PYTHON_TARGETS="python3_10 python3_11" RUBY_TARGETS="ruby30 ruby31 ruby32" USERLAND="GNU" VIDEO_CARDS="intel fbdev vesa" 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, LD, 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/cgnslib-4.3.0::gentoo was built with the following: USE="base-scope examples fortran hdf5 scoping szip tools -debug -legacy -mpi -test" ABI_X86="(64)" FEATURES="unmerge-orphans usersandbox binpkg-dostrip ccache fixlafiles parallel-fetch userfetch pid-sandbox usersync unknown-features-warn binpkg-logs warn-on-large-env network-sandbox distlocks ebuild-locks buildpkg-live ipc-sandbox protect-owned binpkg-docompress sfperms preserve-libs strict merge-sync strict-keepdir binpkg-multi-instance userpriv news config-protect-if-modified xattr unmerge-logs qa-unresolved-soname-deps sandbox multilib-strict assume-digests"