Bug 729368 – dev-python/h5py-2.10.0-r1 should DEPEND on sci-libs/hdf5 - src_configure(): Loading library to get version: libhdf5.so // error: libhdf5.so: cannot open shared object file: No such file or directory

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description William Throwe 2020-06-24 00:28:38 UTC]

Looks like h5py is missing a build dependency on sci-libs/hdf5.

Full build output:
 * h5py-2.10.0.tar.gz BLAKE2B SHA512 size ;-) ...                        [ ok ]
>>> Unpacking source...
>>> Unpacking h5py-2.10.0.tar.gz to /var/tmp/portage/dev-python/h5py-2.10.0-r1/work
>>> Source unpacked in /var/tmp/portage/dev-python/h5py-2.10.0-r1/work
>>> Preparing source in /var/tmp/portage/dev-python/h5py-2.10.0-r1/work/h5py-2.10.0 ...
 * Applying h5py-2.10.0-tests.patch ...                                  [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/dev-python/h5py-2.10.0-r1/work/h5py-2.10.0 ...
 * python3_7: running distutils-r1_run_phase python_configure
python3.7 setup.py configure
running configure
Loading library to get version: libhdf5.so
error: libhdf5.so: cannot open shared object file: No such file or directory
 * ERROR: dev-python/h5py-2.10.0-r1::gentoo failed (configure phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line  125:  Called src_configure
 *   environment, line 3353:  Called distutils-r1_src_configure
 *   environment, line 1347:  Called _distutils-r1_run_foreach_impl 'python_configure'
 *   environment, line  440:  Called python_foreach_impl 'distutils-r1_run_phase' 'python_configure'
 *   environment, line 2869:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_configure'
 *   environment, line 2313:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_configure'
 *   environment, line 2311:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_configure'
 *   environment, line  892:  Called distutils-r1_run_phase 'python_configure'
 *   environment, line 1327:  Called python_configure
 *   environment, line 2614:  Called esetup.py 'configure'
 *   environment, line 1744:  Called die
 * The specific snippet of code:
 *       "${@}" || die "${die_args[@]}";
 * 
 * If you need support, post the output of `emerge --info '=dev-python/h5py-2.10.0-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=dev-python/h5py-2.10.0-r1::gentoo'`.
 * The complete build log is located at '/var/log/portage/build/dev-python/h5py-2.10.0-r1:20200623-215519.log.gz'.
 * The ebuild environment file is located at '/var/tmp/portage/dev-python/h5py-2.10.0-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/dev-python/h5py-2.10.0-r1/work/h5py-2.10.0'
 * S: '/var/tmp/portage/dev-python/h5py-2.10.0-r1/work/h5py-2.10.0'

$ emerge --info
Portage 2.3.99 (python 3.7.7-final-0, default/linux/amd64/17.1, gcc-9.3.0, glibc-2.30-r8, 5.4.28-gentoo x86_64)
=================================================================
System uname: Linux-5.4.28-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5-2620_v4_@_2.10GHz-with-gentoo-2.6
KiB Mem:    32880272 total,  25745728 free
KiB Swap:   67108856 total,  65015288 free
Timestamp of repository gentoo: Tue, 23 Jun 2020 18:30:01 +0000
Head commit of repository gentoo: 8d21e3aa4366432d35475172b5d10a008918b575
sh bash 5.0_p17
ld GNU ld (Gentoo 2.33.1 p2) 2.33.1
app-shells/bash:          5.0_p17::gentoo
dev-java/java-config:     2.2.0-r4::gentoo
dev-lang/perl:            5.30.3::gentoo
dev-lang/python:          2.7.18::gentoo, 3.7.7-r2::gentoo
sys-apps/baselayout:      2.6-r1::gentoo
sys-apps/openrc:          0.42.1::gentoo
sys-apps/sandbox:         2.18::gentoo
sys-devel/binutils:       2.33.1-r1::gentoo
sys-devel/gcc:            9.3.0::gentoo
sys-devel/gcc-config:     2.2.1::gentoo
sys-devel/make:           4.2.1-r4::gentoo
sys-kernel/linux-headers: 5.4-r1::gentoo (virtual/os-headers)
sys-libs/glibc:           2.30-r8::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-verify-max-age: 24
    sync-rsync-extra-opts: 
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-metamanifest: yes

wthrowe-misc
    location: /usr/local/shared/feanor/overlays/wthrowe-misc
    masters: gentoo
    priority: 0

wthrowe-multilib
    location: /usr/local/shared/feanor/overlays/wthrowe-multilib
    masters: gentoo
    priority: 1

crossdev
    location: /usr/local/shared/feanor/overlays/portage-crossdev
    masters: gentoo
    priority: 10

barnowl
    location: /var/lib/layman/barnowl
    masters: gentoo
    priority: 50

steam-overlay
    location: /var/lib/layman/steam-overlay
    masters: gentoo
    priority: 50

sxs-spectre
    location: /var/lib/layman/sxs-spectre
    masters: gentoo
    priority: 50

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="@FREE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe -ggdb"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe -ggdb"
DISTDIR="/var/cache/distfiles"
EMERGE_DEFAULT_OPTS="--ask --quiet-build=n --autounmask-write=n --usepkg --with-bdeps=n --backtrack=100 --autounmask-backtrack=y --binpkg-respect-use=y --binpkg-changed-deps=n"
ENV_UNSET="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 binpkg-multi-instance buildpkg clean-logs compress-build-logs 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 split-log splitdebug strict unknown-features-warn unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="POSIX"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu"
MAKEOPTS="-j24"
PKGDIR="/var/cache/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"
USE="acl amd64 bzip2 cli crypt dri fortran iconv ipv6 libtirpc multilib ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" 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 fma3 mmx mmxext popcnt 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" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby25" USERLAND="GNU" VIDEO_CARDS="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, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 Jeroen Roovers (RETIRED) 2020-06-26 08:38:33 UTC]

sci-libs/hdf5 is only mentioned in RDEPEND

[Comment 2 Larry the Git Cow 2020-08-17 18:55:08 UTC]

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=525eb57a74300894904c3f0ef358f45e3a4f6182

commit 525eb57a74300894904c3f0ef358f45e3a4f6182
Author:     David Seifert <[e-mail]>
AuthorDate: 2020-08-17 18:54:43 +0000
Commit:     David Seifert <[e-mail]>
CommitDate: 2020-08-17 18:54:43 +0000

    dev-python/h5py: Add python 3.9
    
    * Add 'sci-libs/hdf5' to DEPEND
    
    Closes: https://bugs.gentoo.org/729368
    Package-Manager: Portage-3.0.3, Repoman-3.0.0
    Signed-off-by: David Seifert <[e-mail]>

 dev-python/h5py/h5py-2.10.0-r1.ebuild | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)