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Bug 473306 - sci-physics/geant-4.9.6_p02-r1 - fatal error: Inventor/Xt/SoXtCursor.h: No such file or directory
Summary: sci-physics/geant-4.9.6_p02-r1 - fatal error: Inventor/Xt/SoXtCursor.h: No su...
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: AMD64 Linux
: Normal normal (vote)
Assignee: Gentoo Science Physics related packages
Depends on:
Reported: 2013-06-14 19:51 UTC by Robert Penny
Modified: 2013-06-17 21:48 UTC (History)
0 users

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

build.log.bz2 (build.log.bz2,134.00 KB, application/x-bzip)
2013-06-15 18:25 UTC, Robert Penny

Note You need to log in before you can comment on or make changes to this bug.
Description Robert Penny 2013-06-14 19:51:22 UTC
Geant is trying to link to an include file that should be a part of the media-libs/coin installation but isn't. My understanding is that the standard SGI OpenInventor package contains:


.. but Inventor/Xt/SoXtCursor.h is a part of coin.

In fact, media-libs/coin is not generating any of the SoXt or SoQt bindings.. and I can't figure out how to convince it to do so. So, I can't figure if this counts as a media-libs/coin bug or a sci-physics/geant bug. However, I would expect the Geant ebuild to specify any depdenencies on Coin necessary to build.

I had a brief discussion with the Geant maintainers last month, because I thought they were phasing out dependence on coin and just relying on SGI OpenInventor. Turns out they gave up on that and really do want coin to be installed.

The error in the Geant build log appears here:

[ 92%] Building CXX object source/visualization/OpenInventor/CMakeFiles/G4OpenInventor.dir/src/
cd /var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant-4.9.6_p02_build/source/visualization/OpenInventor && /usr/bin/x86_64-pc-linux-gnu-g++  -DG4INTY_BUILD_XT -DG4OpenInventor_EXPORTS -DG4VERBOSE -DG4VIS_BUILD_OIX_DRIVER -DG4VI
S_BUILD_OI_DRIVER -DG4_STORE_TRAJECTORY  -DNDEBUG -march=corei7 -O2 -pipe -W -Wall -pedantic -Wno-non-virtual-dtor -Wno-long-long -Wwrite-strings -Wpointer-arith -Woverloaded-virtual -pipe -std=c++98 -fPIC -I/var/tmp/portage/sci-physic
s/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/digits_hits/hits/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/geometry/management/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/ge
ant4.9.6.p02/source/geometry/solids/CSG/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/geometry/solids/specific/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/
global/HEPGeometry/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/global/HEPRandom/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/global/management/include -I/
var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/graphics_reps/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/intercoms/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p
02-r1/work/geant4.9.6.p02/source/interfaces/common/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/materials/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/trac
king/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/visualization/externals/gl2ps/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/visualization/management/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/visualization/modeling/include -I/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/visualization/OpenInventor/include    -o CMakeF
iles/G4OpenInventor.dir/src/ -c /var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/visualization/OpenInventor/src/
/usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant-4.9.6_p02_build/CMakeFiles 

 92%] Building CXX object source/visualization/OpenInventor/CMakeFiles/G4OpenInventor.dir/src/
/var/tmp/portage/sci-physics/geant-4.9.6_p02-r1/work/geant4.9.6.p02/source/visualization/OpenInventor/src/ fatal error: Inventor/Xt/SoXtCursor.h: No such file or directory
compilation terminated.

Reproducible: Always

Currenat packages installed:

*  media-libs/coin
      Latest version available: 3.1.3-r2
      Latest version installed: 3.1.3-r2
      Size of files: 5,841 kB
      Description:   A high-level 3D graphics toolkit, fully compatible with SGI Open Inventor 2.1.
      License:       || ( GPL-2 PEL )

*  media-libs/openinventor
      Latest version available:
      Latest version installed:
      Size of files: 8,088 kB
      Description:   SGI OpenInventor Toolkit and Utilities
      License:       LGPL-2

$ equery uses coin
[ Legend : U - final flag setting for installation]
[        : I - package is installed with flag     ]
[ Colors : set, unset                             ]
 * Found these USE flags for media-libs/coin-3.1.3-r2:
 U I
 + + bzip2       : Use the bzlib compression library
 - - debug       : Enable extra debug codepaths, like asserts and extra output. If you want to get meaningful backtraces see
 + + doc         : Adds extra documentation (API, Javadoc, etc). It is recommended to enable per package instead of globally
 - - javascript  : Enables javascript support
 - - openal      : Adds support for the Open Audio Library
 - - simage      : Texture loading via media-libs/simage library
 - - static-libs : Build static libraries
 - - threads     : Adds threads support for various packages. Usually pthreads
 + + zlib        : Adds support for zlib (de)compression

$ equery uses geant 
[ Legend : U - final flag setting for installation]
[        : I - package is installed with flag     ]
[ Colors : set, unset                             ]
 * Found these USE flags for sci-physics/geant-4.9.6_p02-r1:
 U I
 + - data         : Add a lot of standard physics data files for geant4
 + - dawn         : Add support for media-gfx/dawn (3D postscript rendering)
 + - examples     : Install examples, usually source code
 + - gdml         : Enable geometry markup language for xml
 - - geant3       : Add compatibility for geant321 to geant4
 + - motif        : Adds support for the Motif toolkit
 + + opengl       : Adds support for OpenGL (3D graphics)
 + - openinventor : Add support for media-libs/openinventor SGI toolkit
 + + qt4          : Adds support for the Qt GUI/Application Toolkit version 4.x
 - - raytracerx   : Enable raytracing for physics events
 - - static-libs  : Build static libraries
 + - vrml         : Enable output of geant4 in vrml formats
 + + zlib         : Adds support for zlib (de)compression

I'll attach emerge --info as a separate attachment.


Comment 1 Robert Penny 2013-06-14 19:52:41 UTC
emerge --info
Portage (default/linux/amd64/13.0/desktop/gnome, gcc-4.6.3, glibc-2.15-r3, 3.4.34-gentoo x86_64)
System uname: Linux-3.4.34-gentoo-x86_64-Intel-R-_Core-TM-_i7-3930K_CPU_@_3.20GHz-with-gentoo-2.2
KiB Mem:    32845540 total,  25121000 free
KiB Swap:   16383992 total,  16383992 free
Timestamp of tree: Fri, 14 Jun 2013 18:30:01 +0000
ld GNU ld (GNU Binutils) 2.22
ccache version 3.1.9 [disabled]
app-shells/bash:          4.2_p45
dev-java/java-config:     2.1.12-r1
dev-lang/python:          2.7.3-r3, 3.2.3-r2
dev-util/ccache:          3.1.9
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.11.8
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.6, 1.12.6
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.6.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.7 (virtual/os-headers)
sys-libs/glibc:           2.15-r3
Repositories: gentoo seden java-overlay
CFLAGS="-march=corei7 -O2 -pipe"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /var/bind"
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"
CXXFLAGS="-march=corei7 -O2 -pipe"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -pipe"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTDIR_OVERLAY="/var/lib/layman/seden /var/lib/layman/java-overlay"
USE="X a52 aac acl acpi alsa amd64 berkdb bindist bluetooth branding bzip2 cairo cdda cdr cli colord consolekit cracklib crypt cups cxx dbus device-mapper dmraid dri dts dvd dvdr eds emboss encode evo exif fam firefox flac fortran gdbm gif git gnome gnome-keyring gnome-online-accounts gpm gstreamer gtk iconv ipv6 jpeg lcms ldap libnotify libsecret mad mdadm mmx mng modules mp3 mp4 mpeg mudflap multilib nautilus ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds pulseaudio qt3support qt4 readline sdl session socialweb spell sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 startup-notification subversion svg tcpd tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xcb xml xv xvid zlib" 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse wacom synaptics 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="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby19 ruby18" 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"
Comment 2 Jeroen Roovers (RETIRED) gentoo-dev 2013-06-15 14:00:08 UTC
Please attach the entire build log to this bug report.
Comment 3 Robert Penny 2013-06-15 18:25:37 UTC
Created attachment 351032 [details]

Attaching bzipped copy of failed build.log.
Comment 4 Sébastien Fabbro (RETIRED) gentoo-dev 2013-06-17 19:02:39 UTC
+  17 Jun 2013; Sébastien Fabbro <> -geant-4.9.6_p02.ebuild,
+  geant-4.9.6_p02-r1.ebuild, metadata.xml:
+  Switch optional OpenInventor to Coin3D SoXt implementation, fixing bug #473306
+  and bug #473396
Comment 5 Robert Penny 2013-06-17 19:15:34 UTC
Hi Sébastien. I'm not sure I understand your resolution. I do have 

media-libs/coin-3.1.3-r2 installed. When I look at the manifest of files installed by coin there seems to be no installation of SoXt.

Should I file a bug report against coin for not installing SoXt?

Please forgive me if this is misguided in some sense. I just can't see any use flags for coin that cause SoXt to be generated.


Comment 6 Sébastien Fabbro (RETIRED) gentoo-dev 2013-06-17 19:44:45 UTC
you have to re-sync your tree. in order to fix this bug, i had to introduce a new package: media-libs/SoXt
Comment 7 Robert Penny 2013-06-17 19:57:12 UTC
The manifest is failing. I can force the manifest to rebuild locally but thought I should point it out in case more needed to be done to update the portage tree.

$ sudo emerge --deep --pretend geant

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

Calculating dependencies | * Digest verification failed:
 * /usr/portage/sci-physics/geant/geant-4.9.6_p02-r1.ebuild
 * Reason: Filesize does not match recorded size
 * Got: 2758
 * Expected: 2712
... done!
Comment 8 Sébastien Fabbro (RETIRED) gentoo-dev 2013-06-17 20:17:58 UTC
(In reply to Robert Penny from comment #7)

> Calculating dependencies | * Digest verification failed:
>  * /usr/portage/sci-physics/geant/geant-4.9.6_p02-r1.ebuild
>  * Reason: Filesize does not match recorded size

hmm, not getting it here. i suspect something screwed up during the commit, so i committed a new manifest.
re-sync after a while, it takes time to hit the mirrors.
Comment 9 Robert Penny 2013-06-17 20:29:47 UTC
I manually updated my manifest (ebuild geant-4.9.6_p02-r1.ebuild manifest) and got a successful build of..


...on ~amd64. I'm getting a compilation error when compiling some of my existing GEANT code against the installation, but I don't think that's a problem with the installation per se. I'm tracking this down.

Thanks so much for turning this around so quickly! It's very much appreciated.
Comment 10 Robert Penny 2013-06-17 21:48:25 UTC
I found the problem in my test code. It was completely my fault and nothing to do with the GEANT library or the ebuild.

So, I can confirm the bug is resolved on my ~amd64 architecture.

Thanks so much Sébastien. Very much appreciated!!