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Bug 639784 - sci-libs/hdf5-1.10.1 - In file included from .../work/hdf5-1.10.1/testpar/t_span_tree.c:40:0: .../work/hdf5-1.10.1/src/H5Spkg.h:23:2: error: #error "Do not include this file outside the H5S package!"
Summary: sci-libs/hdf5-1.10.1 - In file included from .../work/hdf5-1.10.1/testpar/t_s...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2017-12-04 16:19 UTC by Eugene Shalygin
Modified: 2017-12-08 00:26 UTC (History)
4 users (show)

See Also:
Package list:
Runtime testing required: ---

Attachments
build.log.xz (build.log.xz,41.95 KB, application/x-xz)
2017-12-04 16:19 UTC, Eugene Shalygin 		Details
View All Add an attachment (proposed patch, testcase, etc.)

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Description Eugene Shalygin 2017-12-04 16:19:00 UTC 
Created attachment 508032 [details]
build.log.xz

In file included from /var/portage/tmp/portage/sci-libs/hdf5-1.10.1/work/hdf5-1.10.1/testpar/t_span_tree.c:40:0:
/var/portage/tmp/portage/sci-libs/hdf5-1.10.1/work/hdf5-1.10.1/src/H5Spkg.h:23:2: error: #error "Do not include this file outside the H5S package!"
 #error "Do not include this file outside the H5S package!"

 emerge --info sci-libs/hdf5
Portage 2.3.16 (python 3.6.3-final-0, default/linux/amd64/17.0/desktop/plasma/systemd, gcc-7.2.0, glibc-2.26-r3, 4.14.3-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.14.3-gentoo-x86_64-Intel-R-_Core-TM-_i7-4810MQ_CPU_@_2.80GHz-with-gentoo-2.4.1
KiB Mem:    32860116 total,    248332 free
KiB Swap:   50331644 total,  50331644 free
Timestamp of repository gentoo: Mon, 04 Dec 2017 15:15:01 +0000
Head commit of repository gentoo: 909df428f723a6dd46dad82b08fa967e7778f0ca
Head commit of repository andy: 5a2ee311471f364b23b9e9e8b9d83f5ea2c99dbb

Head commit of repository bobwya: 8b594f8092fe3f48e86b317f765e6a066ebe7890

Head commit of repository dotnet: 366b8cc77dc32ef44909748af4f00b3d8067992f

Head commit of repository eigenlay: 0c9b7988587be42ecc2906eab6b070ac37ee5d6c

Head commit of repository fkmclane: 2f284cbb2b739a763d408d6be9dfcf84c0bc5198

Head commit of repository gamerlay: 67b1676d8aad29ad695b1bdd90c299458e07b23d

Head commit of repository kde: 5b503f3f555481b3a33148d33a67a8d09f7aef83

Head commit of repository multimedia: 289a9692f686e16d73e7d9f84d4d9c0e8081f19b

Head commit of repository mv: 938a18ff45192c4dff86e2f111c7fc12a0b014ad

Head commit of repository qt: e6695b211ef56dad8692898630a52a6f9eabf4a3

Head commit of repository science: bc5ece9b4c76283a1c5511202f842dba041e8495

Head commit of repository steam-overlay: 699d267a7358ca340ee684e68e5366419f8e0ded

Head commit of repository sunrise: 181ef805dad4d70f58b8bf6a1fdc698a65584146

Head commit of repository x11: c5b5b210f52e4536727c18afb4a0586507d13dac

sh bash 4.4_p12
ld GNU ld (Gentoo 2.29.1 p3) 2.29.1
app-shells/bash:          4.4_p12::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.26.1-r1::gentoo
dev-lang/python:          2.7.14-r1::gentoo, 3.5.4-r1::gentoo, 3.6.3-r1::gentoo
dev-util/cmake:           3.10.0::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.4.1-r2::gentoo
sys-apps/sandbox:         2.12::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15.1-r1::gentoo
sys-devel/binutils:       2.29.1-r1::gentoo
sys-devel/gcc:            7.2.0::gentoo
sys-devel/gcc-config:     1.9.0-r1::gentoo
sys-devel/libtool:        2.4.6-r4::gentoo
sys-devel/make:           4.2.1-r1::gentoo
sys-kernel/linux-headers: 4.13::gentoo (virtual/os-headers)
sys-libs/glibc:           2.26-r3::gentoo
Repositories:

gentoo
    location: /var/portage/gentoo
    sync-type: rsync
    sync-uri: rsync://rsync.de.gentoo.org/gentoo-portage/
    priority: -1000
    sync-rsync-extra-opts: --quiet

andy
    location: /var/portage/repository/andy
    sync-type: git
    sync-uri: git://anongit.gentoo.org/user/andy.git
    masters: gentoo
    priority: 50

bobwya
    location: /var/portage/repository/bobwya
    sync-type: git
    sync-uri: https://github.com/bobwya/miscellaneous_ebuilds.git
    masters: gentoo
    priority: 50

dotnet
    location: /var/portage/repository/dotnet
    sync-type: git
    sync-uri: git://anongit.gentoo.org/proj/dotnet.git
    masters: gentoo
    priority: 50

eigenlay
    location: /var/portage/repository/eigenlay
    sync-type: git
    sync-uri: https://git.gitorious.org/eigennet/eigenlay.git
    masters: gentoo
    priority: 50

fkmclane
    location: /var/portage/repository/fkmclane
    sync-type: git
    sync-uri: git://github.com/fkmclane/overlay.git
    masters: gentoo
    priority: 50

gamerlay
    location: /var/portage/repository/gamerlay
    sync-type: git
    sync-uri: git://anongit.gentoo.org/proj/gamerlay.git
    masters: gentoo
    priority: 50

kde
    location: /var/portage/repository/kde
    sync-type: git
    sync-uri: git://anongit.gentoo.org/proj/kde.git
    masters: gentoo
    priority: 50

multimedia
    location: /var/portage/repository/multimedia
    sync-type: git
    sync-uri: https://github.com/gentoo/multimedia.git
    masters: gentoo
    priority: 50

mv
    location: /var/portage/repository/mv
    sync-type: git
    sync-uri: git://anongit.gentoo.org/user/mv.git
    masters: gentoo
    priority: 50

qt
    location: /var/portage/repository/qt
    sync-type: git
    sync-uri: git://anongit.gentoo.org/proj/qt.git
    masters: gentoo
    priority: 50

science
    location: /var/portage/repository/science
    sync-type: git
    sync-uri: git://anongit.gentoo.org/proj/sci.git
    masters: gentoo
    priority: 50

steam-overlay
    location: /var/portage/repository/steam-overlay
    sync-type: git
    sync-uri: git://github.com/anyc/steam-overlay.git
    masters: gentoo
    priority: 50

sunrise
    location: /var/portage/repository/sunrise
    sync-type: git
    sync-uri: https://anongit.gentoo.org/git/proj/sunrise-reviewed.git
    masters: gentoo
    priority: 50

x11
    location: /var/portage/repository/x11
    sync-type: git
    sync-uri: git://anongit.gentoo.org/proj/x11
    masters: gentoo
    priority: 50

fontconfig-ultimate
    location: /var/portage/repository/fontconfig-ultimate
    masters: gentoo
    priority: 80

my-gentoo
    location: /var/portage/repository/my-gentoo
    masters: gentoo
    priority: 80

xanf
    location: /home/eugene/develop/xanf/distribution/Gentoo/repository
    masters: gentoo
    priority: 80

Installed sets: @system
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA @FSF-APPROVED google-chrome skype-eula dlj-1.1 PUEL Google-TOS googleearth TeamViewer Oracle-BCLA-JavaSE skype-4.0.0.7-copyright AdobeFlash-11.x Intel-SDP"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0"
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="-march=native -O2 -pipe"
DISTDIR="/var/portage/distfiles"
EMERGE_DEFAULT_OPTS="--quiet-build --keep-going"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs cgroup collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://de-mirror.org/gentoo/"
LANG="uk_UA.UTF-8"
LDFLAGS="-Wl,-O1 -march=native -O2 -pipe"
MAKEOPTS="-j4"
PKGDIR="/var/portage/packages"
PORTAGE_COMPRESS="xz"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_EXTRA_OPTS="--quiet"
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/portage/tmp"
USE="X a52 aac acl acpi activities alsa amd64 amr apng attica avahi bash-completion berkdb bluetooth bluray branding bs2b btrfs bzip2 cairo canberra caps cdda cdr cli colord cracklib crypt css cups cxx dbus declarative dirac djvu dovecot dri dts dv dvd dvdnav dvdr efi egl emboss encode exif faac fam ffmpeg firefox flac fontconfig fortran fuse gdbm geoip gif git glamor gmp gnuplot gnutls gold gpm gsm gstreamer gtk gtk3 harfbuzz iconv idn ieee1394 imagemagick inotify iproute2 ipv6 jemalloc jit jpeg jpeg2k kde kerberos kipi kwallet lame lapack latex lcms ldap libass libinput libnotify libsamplerate libsecret live lto luatex lzma mad metalink mng modules mp3 mp4 mpeg mpi mpris mtp multicall multilib ncurses netlink network networkmanager nfs nftables nls nptl ogg openexr opengl openmp openssl pam pango pch pcre pdf phonon pkcs11 plasma png policykit postscript ppds pulseaudio qml qt3support qt5 quicktime quvi radio readline romio rss rtmp samba scanner sctp sdl seccomp semantic-desktop session slp smartcard smp speex spell sqlite ssl startup-notification svg symlink system-icu system-sqlite systemd taglib tcpd theora threads thumbnail tiff truetype udev udisks unicode upnp upower usb v4l v4l2 vaapi vdpau vim-syntax vorbis vpx wayland webp widgets wifi wxwidgets x264 x265 xattr xcb xcomposite xetex xft xinerama xml xmp xrandr xv xvid yv12 zeroconf zlib zsh-completion" ABI_X86="64" 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 proxy" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon ptp2 fuji" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma fma3 mmx mmxext popcnt sse sse2 sse3 sse4 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="garmin garmintxt gpsclock timing" GRUB_PLATFORMS="pc efi-64" INPUT_DEVICES="libinput evdev libinput" KERNEL="linux" L10N="en en-GB eo de ru uk ru uk" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer nlpsolver" LINGUAS="en en_GB eo de ru uk ru_RU uk_UA" LIRC_DEVICES="alsa_usb" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby23 ruby24" SANE_BACKENDS="epson2 net" USERLAND="GNU" VIDEO_CARDS="v4l radeon radeonsi intel i965 amdgpu" 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_COMPRESS_FLAGS

=================================================================
                        Package Settings
=================================================================

sci-libs/hdf5-1.8.18::gentoo was built with the following:
USE="hl mpi szip zlib -cxx -debug -examples -fortran -fortran2003 -static-libs -threads" ABI_X86="(64)"
Comment 1 Benda Xu gentoo-dev 2017-12-07 03:35:29 UTC 
Could you please also paste the output of `emerge -pv sci-libs/hdf5`?
Comment 2 Guilherme Amadio gentoo-dev 2017-12-07 08:49:10 UTC 
(In reply to Benda Xu from comment #1)
> Could you please also paste the output of `emerge -pv sci-libs/hdf5`?

Hi Benda, I can confirm this bug. Here's what I get.

# emerge -pv hdf5

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild  r  U  ] sci-libs/hdf5-1.10.1:0/1.10.1::gentoo [1.8.18:0/1.8.18::gentoo] USE="mpi zlib -cxx -debug -examples -fortran -static-libs -szip -threads (-fortran2003%) (-hl%*)" 0 KiB
[ebuild  rR    ] dev-python/pytables-3.4.2::gentoo  USE="-doc -examples" PYTHON_TARGETS="python2_7 python3_5 python3_6 -python3_4" 0 KiB

Total: 2 packages (1 upgrade, 1 reinstall), Size of downloads: 0 KiB

The following packages are causing rebuilds:

  (sci-libs/hdf5-1.10.1:0/1.10.1::gentoo, ebuild scheduled for merge) causes rebuilds for:
    (dev-python/pytables-3.4.2:0/0::gentoo, ebuild scheduled for merge)
Comment 3 milan hodoscek 2017-12-07 09:29:57 UTC 
hdf5-1.8.15-implicits.patch is maybe not needed any more - this is the one that causes the error message from the title of this bug report. I successfully compiled hdf5-1.10.1 commenting out this patch in the hdf5-1.10.1.ebuild file
Comment 4 Larry the Git Cow gentoo-dev 2017-12-08 00:26:37 UTC 
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bd9658269764306015ce6e48cf4567688498e102

commit bd9658269764306015ce6e48cf4567688498e102
Author:     Benda Xu <heroxbd@gentoo.org>
AuthorDate: 2017-12-08 00:26:10 +0000
Commit:     Benda Xu <heroxbd@gentoo.org>
CommitDate: 2017-12-08 00:26:28 +0000

    sci-libs/hdf5: drop implicits.patch.
    
      The patch is not needed any more and causes compilation error.
    
    Reported-by: Eugene Shalygin <eugene.shalygin@gmail.com>
    Suggested-by: milan hodoscek <milan@cmm.ki.si>
    Closes: https://bugs.gentoo.org/639784
    Package-Manager: Portage-2.3.16, Repoman-2.3.6

 sci-libs/hdf5/hdf5-1.10.1.ebuild | 1 -
 1 file changed, 1 deletion(-)