Building against hdf5-1.12.2-r1 fails with an error -- Unable to determine HDF5 C flags from HDF5 wrapper. -- Unable to determine HDF5 C version_var from HDF5 wrapper. -- Could NOT find HDF5 (missing: HDF5_INCLUDE_DIRS) (found version "1.12.2") CMake Error at cmake/helpers/CheckDependentLibraries.cmake:178 (message): Configured to use HDF5, but not found Call Stack (most recent call first): cmake/helpers/CheckDependentLibraries.cmake:502 (gdal_check_package) gdal.cmake:223 (include) CMakeLists.txt:218 (include) -- Configuring incomplete, errors occurred! See also "/var/tmp/portage/sci-libs/gdal-3.5.0-r3/work/gdal-3.5.0_build/CMakeFiles/CMakeOutput.log". See also "/var/tmp/portage/sci-libs/gdal-3.5.0-r3/work/gdal-3.5.0_build/CMakeFiles/CMakeError.log". Reproducible: Always Steps to Reproduce: 1. emerge =hdf5-1.12.2-r1 2. USE=hdf5 emerge =gdal-3.5.0-r3 3. Actual Results: Failure in src_configure # emerge --info gdal Portage 3.0.30 (python 3.9.13-final-0, default/linux/amd64/17.1/systemd, gcc-11.3.0, glibc-2.35-r5, 5.17.9-gentoo-0 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-5.17.9-gentoo-0-x86_64-AMD_Ryzen_7_3800X_8-Core_Processor-with-glibc2.35 KiB Mem: 32888644 total, 20525036 free KiB Swap: 33554428 total, 33554428 free Head commit of repository guru: 7501806d964157702edeb41043a642689a492ec9 Timestamp of repository steam-overlay: Tue, 17 May 2022 03:23:15 +0000 Head commit of repository steam-overlay: d9dd07b19a17994512155d551807a1e0fdf3e9b7 Head commit of repository qt: a9800a9311231f163d736bc0f81e2a143c187424 Head commit of repository science: e59efb1f834bd94c49c3ef6afbfd91a932c23b89 Head commit of repository gentoo-git: 2c7677455aed2bc2b236e8eaf77e704b29b705f7 Head commit of repository waebbl: bb55f99b04ef6f6f1e0eff28b702f922496eda1e Timestamp of repository gentoo: Thu, 19 May 2022 17:03:04 +0000 Head commit of repository gentoo: 5f01617c26414b5c449b05b94e49bcbc3d1ea327 sh bash 5.1_p16 ld GNU ld (Gentoo 2.38 p4) 2.38 app-misc/pax-utils: 1.3.4::gentoo app-shells/bash: 5.1_p16::gentoo dev-java/java-config: 2.3.1::gentoo dev-lang/perl: 5.34.1-r3::gentoo dev-lang/python: 3.9.13::gentoo, 3.10.4_p1::gentoo dev-lang/rust: 1.60.0::gentoo dev-util/cmake: 3.23.1::gentoo dev-util/meson: 0.62.1::gentoo sys-apps/baselayout: 2.8::gentoo sys-apps/sandbox: 2.29::gentoo sys-apps/systemd: 250.5-r1::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.71-r1::gentoo sys-devel/automake: 1.16.5::gentoo sys-devel/binutils: 2.38-r2::gentoo sys-devel/binutils-config: 5.4.1::gentoo sys-devel/clang: 13.0.1::gentoo, 14.0.3::gentoo sys-devel/gcc: 11.3.0::gentoo sys-devel/gcc-config: 2.5-r1::gentoo sys-devel/libtool: 2.4.7::gentoo sys-devel/lld: 14.0.3::gentoo sys-devel/llvm: 13.0.1::gentoo, 14.0.3::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.17-r1::gentoo (virtual/os-headers) sys-libs/glibc: 2.35-r5::gentoo sys-libs/libselinux: 3.4_rc1::gentoo Repositories: guru location: /mnt/data/code/github/portage-overlays/guru sync-type: git sync-uri: git@git.gentoo.org:repo/proj/guru.git masters: gentoo priority: -1000 steam-overlay location: /var/db/repos/steam-overlay sync-type: git sync-uri: https://github.com/gentoo-mirror/steam-overlay.git masters: gentoo qt location: /mnt/data/code/github/portage-overlays/qt sync-type: git sync-uri: https://github.com/gentoo-mirror/qt.git masters: gentoo priority: 60 science location: /mnt/data/code/github/portage-overlays/sci sync-type: git sync-uri: git://github.com/waebbl/sci.git masters: gentoo priority: 60 gentoo-git location: /mnt/data/code/github/portage-overlays/gentoo-git sync-type: git sync-uri: https://github.com/waebbl/gentoo.git masters: gentoo priority: 99 waebbl location: /mnt/data/code/github/portage-overlays/waebbl sync-type: git sync-uri: https://github.com/waebbl/waebbl-gentoo.git masters: gentoo priority: 99 gentoo location: /var/db/repos/gentoo sync-type: git sync-uri: https://github.com/gentoo-mirror/gentoo.git priority: 100 Installed sets: @3D, @Qt6, @admin-tools, @desktop, @dev-tools, @docs, @esteam, @games, @net-tools, @science ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="@FREE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=znver2 -frecord-gcc-switches -fstack-protector-strong -fstack-check" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /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=znver2 -frecord-gcc-switches -fstack-protector-strong -fstack-check" DISTDIR="/var/cache/distfiles" EMERGE_DEFAULT_OPTS="--complete-graph --keep-going --fail-clean --usepkg --buildpkg --buildpkg-exclude='x11-drivers/nvidia-drivers virtual/* acct-user/* acct-group/* app-eselect/* dev-util/nvidia-cuda-toolkit' --autounmask=n --binpkg-respect-use=y --binpkg-changed-deps=y" 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=znver2 -frecord-gcc-switches -fstack-protector-strong -fstack-check" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg buildpkg-live buildsyspkg cgroup clean-logs config-protect-if-modified distlocks downgrade-backup ebuild-locks fail-clean fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-elog split-log strict strict-keepdir unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=znver2 -frecord-gcc-switches -fstack-protector-strong -fstack-check" GENTOO_MIRRORS="https://ftp.fau.de/gentoo/ https://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ https://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ https://ftp.halifax.rwth-aachen.de/gentoo/" INSTALL_MASK="/usr/share/locale -/usr/share/locale/de* -/usr/share/locale/en*" LANG="C.UTF8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" MAKEOPTS="-j8" 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 acl alsa amd64 branding bzip2 cli crypt dbus dri egl emacs fortran gdbm gif gnome gtk-doc iconv ipv6 jpeg jpeg2k kde lcms libglvnd libinput libtirpc man multilib ncurses networkmanager nls nptl offensive ogg opengl openmp pam pcre pic png policykit pulseaudio python qml qt5 readline seccomp sound split-usr ssl svg systemd tga theora threads tiff udev unicode vorbis webp wifi x264 x265 xattr xpm zlib zstd" 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="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="pc multiboot qemu" INPUT_DEVICES="libinput wacom" KERNEL="linux" L10N="de de-DE en en-GB en-US" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver" LLVM_TARGETS="NVPTX WebAssembly" 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" RUBY_TARGETS="ruby31" STEAMGAMES="witcher2" USERLAND="GNU" VIDEO_CARDS="dummy fbdev nvidia 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, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, 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/gdal-3.4.3-r1::gentoo was built with the following: USE="aux-xml curl fits geos gif gml hdf5 heif jpeg jpeg2k lzma netcdf pdf png python sqlite threads webp xls zstd -armadillo -debug (-doc) -java -mdb -mysql -odbc -ogdi -opencl -oracle -perl -postgres -spatialite" ABI_X86="(64)" CPU_FLAGS_X86="avx sse ssse3" PYTHON_TARGETS="python3_9 -python3_10 -python3_8"
Created attachment 779591 [details] gdal-3.5.0-r3:20220520-055725.log build log
Without USE=hdf5 (and using gdal-3.5.0-r4 to avoid https://bugs.gentoo.org/845369) the package builds.
I can confirm the issue... It looks like sci-libs/gdal strictly requires `USE=cxx` for sci-libs/hdf5 now...
Thanks Fat-Zer, enabling USE=cxx for hdf5 indeed solves this.
Given much of gdal is written in C++, that seems reasonable enough.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=032d9fc2b5dfaa6d45ae78d346aa7795f497a1a5 commit 032d9fc2b5dfaa6d45ae78d346aa7795f497a1a5 Author: Sam James <sam@gentoo.org> AuthorDate: 2022-05-23 21:51:19 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2022-05-23 21:51:19 +0000 sci-libs/gdal: needs hdf5[cxx] Closes: https://bugs.gentoo.org/846530 Signed-off-by: Sam James <sam@gentoo.org> sci-libs/gdal/gdal-3.5.0-r4.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-)
