After upgrading sci-libs/hdf5 to 1.12.1, building media-libs/vigra errors out with: /var/tmp/portage/media-libs/vigra-1.11.1-r3/work/vigra-1.11.1/src/impex/hdf5impex.cxx: In function ‘H5O_type_t vigra::HDF5_get_type(hid_t, const char*)’: /var/tmp/portage/media-libs/vigra-1.11.1-r3/work/vigra-1.11.1/src/impex/hdf5impex.cxx:193:24: error: too few arguments to function ‘herr_t H5Oget_info_by_name3(hid_t, const char*, H5O_info2_t*, unsigned int, hid_t)’ 193 | H5Oget_info_by_name(loc_id, name, &infobuf, H5P_DEFAULT); | ^ Vigra upstream has a (still unsolved) bug saying this is an API break in HDF5 1.12: https://github.com/ukoethe/vigra/issues/476 Bug 808703 is another build failure with HDF5 1.12.1. Reproducible: Always Portage 3.0.20 (python 3.9.6-final-0, default/linux/amd64/17.1/hardened, gcc-11.2.0, glibc-2.33-r6, 5.12.19-gentoo-x86_64 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-5.12.19-gentoo-x86_64-x86_64-AMD_Ryzen_7_PRO_3700U_w-_Radeon_Vega_Mobile_Gfx-with-glibc2.33 KiB Mem: 14292996 total, 1639972 free KiB Swap: 15729660 total, 15729660 free Timestamp of repository gentoo: Mon, 16 Aug 2021 22:00:02 +0000 Head commit of repository gentoo: 542fd9d9be3c8859def836cf2c26335a84de5500 Head commit of repository creideiki: 650c95cbe66a35b7746c66254bfa6eb65e184f75 sh bash 5.1_p8 ld GNU ld (Gentoo 2.36.1 p4) 2.36.1 app-shells/bash: 5.1_p8::gentoo dev-lang/perl: 5.34.0-r2::gentoo dev-lang/python: 2.7.18_p11::gentoo, 3.9.6_p1::gentoo, 3.10.0_rc1_p1::gentoo dev-lang/rust: 1.54.0::gentoo dev-util/cmake: 3.21.1::gentoo sys-apps/baselayout: 2.7-r3::gentoo sys-apps/openrc: 0.43.4::gentoo sys-apps/sandbox: 2.24::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.71-r1::gentoo sys-devel/automake: 1.13.4-r2::gentoo, 1.16.4::gentoo sys-devel/binutils: 2.36.1-r2::gentoo sys-devel/gcc: 11.2.0::gentoo sys-devel/gcc-config: 2.4::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.13::gentoo (virtual/os-headers) sys-libs/glibc: 2.33-r6::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: yes sync-rsync-verify-max-age: 24 sync-rsync-verify-jobs: 1 sync-rsync-extra-opts: --ipv4 creideiki location: /var/db/repos/creideiki sync-type: git sync-uri: https://github.com/creideiki/portage masters: gentoo steam-overlay location: /var/lib/layman/steam-overlay sync-type: laymansync sync-uri: https://github.com/anyc/steam-overlay.git masters: gentoo priority: 50 torbrowser location: /var/lib/layman/torbrowser sync-type: laymansync sync-uri: https://github.com/MeisterP/torbrowser-overlay.git masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="@FREE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native" 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/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="-O2 -pipe -march=native" DISTDIR="/var/cache/distfiles" EMERGE_DEFAULT_OPTS="--alphabetical --keep-going --quiet-build=n --backtrack=30 --verbose-conflicts" 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 -march=native" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg compressdebug 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 splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=native" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j6" PKGDIR="/var/cache/binpkgs" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_EXTRA_OPTS="--ipv4" 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" USE="X acl alsa amd64 bzip2 crypt dbus elogind eselect-ldso ffmpeg flac gif gles2 hackrf hardened harfbuzz iconv icu ipv6 jpeg libglvnd libtirpc mp3 multilib ncurses nls nptl ogg opencl opengl openmp orc pam pcre pie plasma png qml qt5 rav1e readline screencast seccomp split-usr ssl ssp udev unicode vaapi vorbis vulkan wayland x264 xattr xtpax zlib" ABI_X86="64" ADA_TARGET="gnat_2018" 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="canon" 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="libinput wacom" KERNEL="linux" L10N="en en-US en-GB sv" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LLVM_TARGETS="BPF AMDGPU X86" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-3 php7-4" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python3_9" QEMU_SOFTMMU_TARGETS="i386 x86_64" RUBY_TARGETS="ruby27 ruby30" SANE_BACKENDS="hp" USERLAND="GNU" VIDEO_CARDS="amdgpu radeonsi" 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: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, RUSTFLAGS ================================================================= Package Settings ================================================================= sci-libs/hdf5-1.12.1::gentoo was built with the following: USE="-cxx -debug -doc -examples -fortran hl (-mpi) -szip -test -threads -unsupported zlib" ABI_X86="(64)" FEATURES="ipc-sandbox sandbox unmerge-logs binpkg-docompress ebuild-locks assume-digests pid-sandbox strict binpkg-logs unknown-features-warn usersandbox binpkg-multi-instance usersync distlocks multilib-strict merge-sync userfetch preserve-libs compressdebug binpkg-dostrip config-protect-if-modified sfperms userpriv network-sandbox unmerge-orphans xattr buildpkg splitdebug protect-owned qa-unresolved-soname-deps parallel-fetch news fixlafiles" media-libs/vigra-1.11.1-r3::gentoo was built with the following: USE="-doc fftw hdf5 jpeg -mpi openexr png python -test tiff -valgrind zlib" ABI_X86="(64)" PYTHON_TARGETS="-python3_8 python3_9" FEATURES="news binpkg-multi-instance unmerge-logs protect-owned fixlafiles merge-sync multilib-strict userfetch binpkg-logs parallel-fetch splitdebug xattr buildpkg ipc-sandbox strict assume-digests unmerge-orphans sfperms pid-sandbox qa-unresolved-soname-deps distlocks binpkg-dostrip ebuild-locks compressdebug unknown-features-warn usersync preserve-libs binpkg-docompress userpriv usersandbox config-protect-if-modified network-sandbox sandbox"
Created attachment 733525 [details] build.log for media-libs/vigra-1.11.1-r3 with sci-libs/hdf5-1.12.1
HDF5 upstream describes the API break at https://portal.hdfgroup.org/display/HDF5/H5O_GET_INFO_BY_NAME .
Created attachment 733607 [details, diff] Patch for vigra ebuild to use older API It was mentioned in the upstream bug report that setting the hdf5 API compatibility macros allows vigra to build using hdf5 1.12. The attached patch does this and makes vigra compile with hdf-1.12.1.
A working vigra-1.11.1-r4 is available in my overlay: https://github.com/stefantalpalaru/gentoo-overlay I used 'append-cppflags "-DH5_USE_110_API"' because defining CMAKE_C_FLAGS and CMAKE_CXX_FLAGS on the CMake command line overwrites the environment's CFLAGS and CXXFLAGS, respectively.
(In reply to Ștefan Talpalaru from comment #4) > A working vigra-1.11.1-r4 is available in my overlay: > https://github.com/stefantalpalaru/gentoo-overlay > > I used 'append-cppflags "-DH5_USE_110_API"' because defining CMAKE_C_FLAGS > and CMAKE_CXX_FLAGS on the CMake command line overwrites the environment's > CFLAGS and CXXFLAGS, respectively. I confirm that this ebuild works. When will it be in the tree??
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b0ca3df14e110dba28d75a7023b423c79346b58b commit b0ca3df14e110dba28d75a7023b423c79346b58b Author: Sam James <sam@gentoo.org> AuthorDate: 2021-09-10 05:22:31 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2021-09-10 05:23:26 +0000 media-libs/vigra: add -DH5_USE_110_API workaround Bug: https://bugs.gentoo.org/808731 Signed-off-by: Sam James <sam@gentoo.org> media-libs/vigra/vigra-1.11.1-r3.ebuild | 6 +++++- media-libs/vigra/vigra-9999.ebuild | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-)
