Created attachment 453142 [details] build.log =sci-libs/netcdf-4.3.2-r1 [dap hdf5] does not build with =sci-libs/hdf5-1.8.17 [-hl] with the following error: "configure: error: Can't find or link to the hdf5 high-level. Use --disable-netcdf-4, or see config.log for errors." Reemerging sci-libs/hdf5 with hl use flag enabled resolves the issue. $ emerge --info '=sci-libs/netcdf-4.3.2-r1::gentoo' Portage 2.3.0 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/plasma, gcc-5.4.0, glibc-2.22-r4, 4.4.6-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.4.6-gentoo-x86_64-AMD_Athlon-tm-_64_X2_Dual_Core_Processor_6400+-with-gentoo-2.2 KiB Mem: 6102276 total, 2101616 free KiB Swap: 4194300 total, 3797260 free Timestamp of repository gentoo: Fri, 11 Nov 2016 20:30:01 +0000 Timestamp of repository overnight: 1477127858 sh bash 4.3_p48 ld GNU gold (Gentoo 2.25.1 p1.1 2.25.1) 1.11 distcc 3.2rc1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.3_p48::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.0-r2::gentoo dev-lang/python: 2.7.10-r1::gentoo, 3.4.3-r1::gentoo, 3.5.2::gentoo dev-util/cmake: 3.5.2-r1::gentoo dev-util/pkgconfig: 0.28-r2::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.21.7::gentoo sys-apps/sandbox: 2.10-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.11.6-r1::gentoo, 1.12.6::gentoo, 1.14.1::gentoo, 1.15::gentoo sys-devel/binutils: 2.25.1-r1::gentoo sys-devel/gcc: 5.4.0::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers) sys-libs/glibc: 2.22-r4::gentoo Repositories: gentoo location: /home/portage/tree/portage sync-type: rsync sync-uri: rsync://192.168.1.1/gentoo-portage priority: -1000 haskell location: /home/portage/tree/layman/haskell sync-type: laymansync sync-uri: git://github.com/gentoo-haskell/gentoo-haskell.git masters: gentoo priority: 50 kde location: /home/portage/tree/layman/kde sync-type: laymansync sync-uri: git://anongit.gentoo.org/proj/kde.git masters: gentoo priority: 50 sage-on-gentoo location: /home/portage/tree/layman/sage-on-gentoo sync-type: laymansync sync-uri: git://github.com/cschwan/sage-on-gentoo.git masters: gentoo science priority: 50 science location: /home/portage/tree/layman/science sync-type: laymansync sync-uri: git://anongit.gentoo.org/proj/sci.git masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-w -O2 -pipe -fno-stack-protector -march=k8-sse3 -mmmx -m3dnow -msse -msse2 -msse3 -mcx16 -msahf -mfxsr --param l1-cache-size=64 --param l1-cache-line-size=64 --param l2-cache-size=1024 -mtune=k8 -ftracer -fpredictive-commoning -fgcse-after-reload -ftree-partial-pre -ftree-loop-distribution -ftree-loop-distribute-patterns -ftree-loop-ivcanon -ftree-vectorize -fvect-cost-model=cheap -funsafe-math-optimizations -flto=2" 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="-w -O2 -pipe -fno-stack-protector -march=k8-sse3 -mmmx -m3dnow -msse -msse2 -msse3 -mcx16 -msahf -mfxsr --param l1-cache-size=64 --param l1-cache-line-size=64 --param l2-cache-size=1024 -mtune=k8 -ftracer -fpredictive-commoning -fgcse-after-reload -ftree-partial-pre -ftree-loop-distribution -ftree-loop-distribute-patterns -ftree-loop-ivcanon -ftree-vectorize -fvect-cost-model=cheap -funsafe-math-optimizations -flto=2" DISTDIR="/home/portage/distfiles" EMERGE_DEFAULT_OPTS="--jobs=2 --load-average=1.6" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs candy cgroup config-protect-if-modified distlocks fixlafiles merge-sync news parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS=" http://mirror.isoc.org.il/pub/gentoo/ http://ftp.linux.org.tr/gentoo/ http://files.gentoo.gr/ http://ftp.ntua.gr/pub/linux/gentoo/ " LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--sort-common -flto=2" MAKEOPTS="--jobs=2" PKGDIR="/home/portage/packages/night" PORTAGE_COMPRESS="xz" PORTAGE_COMPRESS_FLAGS="--threads=0 -9e" 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/portage/tmpfs" USE="X a52 aac acl acpi alsa amd64 branding bzip2 cairo caps cdda cdr cjk cli consolekit crypt cxx dbus declarative device-mapper djvu dri dts dvd dvdr emboss encode exif fam fftw firefox flac fontconfig fribidi g3dvl gcrypt gdbm gif gmp i18n iconv icu infinality jemalloc jit jpeg jpeg2k kde kipi lcms libnotify lm_sensors luajit lzma mad mmx mmxext mng modules mp3 mp4 mpeg multilib ncurses nls nptl nvidia ogg opencl openexr opengl openmp opus pam pango pcre pdf phonon plasma pm-utils png policykit ppds qml qt3support qt4 qt5 readline rubberband sdl2 seccomp semantic-desktop session smp spell sse sse2 ssl startup-notification svg tcpd theora threads tiff truetype udev udisks unicode upnp upower usb vdpau vim-syntax vorbis vpx wide-unicode widgets x264 x265 xa xattr xcb xcomposite xinerama xml xscreensaver xv xvid zlib zsh-completion" ABI_X86="64" ALSA_CARDS="hda-intel ca0110" CALLIGRA_FEATURES="krita" CAMERAS="ptp2 canon fuji" COLLECTD_PLUGINS="aggregation cpu df disk entropy exec fhcount fscache hddtemp interface irq load lvm match_regex memory netlink network ntpd postgresql rrdtool sensors smart snmp swap syslog tail thermal uptime vmem" CPU_FLAGS_X86="3dnow 3dnowext mmx mmxext sse sse2 sse3" ELIBC="glibc" GRUB_PLATFORMS="pc" INPUT_DEVICES="evdev wacom" KERNEL="linux" L10N="en en-US" LINGUAS="en en_US" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python3_4" PYTHON_TARGETS="python2_7 python3_4" QEMU_SOFTMMU_TARGETS="x86_64 i386 arm" QEMU_USER_TARGETS="x86_64 i386 arm" RUBY_TARGETS="ruby21" SANE_BACKENDS="epson2 canon pixma" USERLAND="GNU" VIDEO_CARDS="vesa nvidia" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON ================================================================= Package Settings ================================================================= sci-libs/netcdf-4.3.2-r1::gentoo was built with the following: USE="dap hdf5 -examples -hdf -mpi -static-libs -szip -test -tools" ABI_X86="64"
emerging USE="hl" sci-libs/hdf5 helps, but this doesn't like "threads" :(
The configure runs fine when i disable netcdf4: --disable-netcdf-4 but i don't know if this makes sense. If i read the ebuild correct "--enable-netcdf-4" comes from sci-libs/netcdf[hdf5] (which is required by sci-libs/netcdf[szip]), so sci-libs/netcdf[-hdf5,-szip] compiles fine. On my system only sci-libs/gdal[netcdf] depends on sci-libs/netcdf, and it can live with sci-libs/netcdf[-hdf5,-szip] (or at least it compiles fine).
=sci-libs/netcdf-4.4.0-r1 is also affected :/
Even 4.4.1.1 (bumped locally) fails :S The error in config.log is: ld: cannot find -lhdf5dll What is providing that with sci-libs/hdf5-1.8.18?
Ah, this needs hdf5[hl], sorry for the noise
[master deadb3b] sci-libs/netcdf: hl support is needed for hdf5 versions that allow it to be disabled (#599600). 2 files changed, 3 insertions(+), 3 deletions(-)
