Bug 497224 – sci-libs/vtk-5.10.1 - In file included from .../work/VTK5.10.1/IO/vtkPostgreSQLDatabase.cxx:21: /usr/include/postgres_ext.h:26:27: fatal error: pg_config_ext.h: No such file or directory

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Bob Johnson 2014-01-06 09:33:59 UTC]

Created attachment 367158 [details]
vtklog.tgz

sci-libs/vtk-5.10.1 fails to compile with the following error message:

In file included from /usr/include/libpq-fe.h:29:0,
                 from /var/tmp/portage/sci-libs/vtk-5.10.1/work/VTK5.10.1/IO/vtkPostgreSQLDatabasePrivate.h:41,
                 from /var/tmp/portage/sci-libs/vtk-5.10.1/work/VTK5.10.1/IO/vtkPostgreSQLDatabase.cxx:21:
/usr/include/postgres_ext.h:26:27: fatal error: pg_config_ext.h: No such file or directory
compilation terminated.
make[2]: *** [IO/CMakeFiles/vtkIO.dir/vtkPostgreSQLDatabase.cxx.o] Error 1
make[2]: Leaving directory `/var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build'
make[1]: *** [IO/CMakeFiles/vtkIO.dir/all] Error 2
make[1]: Leaving directory `/var/tmp/portage/sci-libs/vtk-5.10.1/work/vtk-5.10.1_build'
make: *** [all] Error 2
emake failed
 * ERROR: sci-libs/vtk-5.10.1::gentoo failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line   93:  Called src_compile
 *   environment, line 7566:  Called cmake-utils_src_compile
 *   environment, line 1510:  Called _execute_optionaly 'src_compile'
 *   environment, line  542:  Called enable_cmake-utils_src_compile
 *   environment, line 1951:  Called cmake-utils_src_make
 *   environment, line 1525:  Called emake_src_make
 *   environment, line 1919:  Called die
 * The specific snippet of code:
 *           emake VERBOSE=1 "$@" || die;
 * 
 * If you need support, post the output of `emerge --info '=sci-libs/vtk-5.10.1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-libs/vtk-5.10.1::gentoo'`.
!!! When you file a bug report, please include the following information:
GENTOO_VM=icedtea-bin-6  CLASSPATH="" JAVA_HOME="/opt/icedtea-bin-6.1.12.7"
JAVACFLAGS="-source 1.5 -target 1.5" COMPILER=""
and of course, the output of emerge --info =vtk-5.10.1

# emerge --info '=sci-libs/vtk-5.10.1::gentoo'
Portage 2.2.7 (default/linux/amd64/13.0, gcc-4.7.3, glibc-2.17, 3.10.25-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.10.25-gentoo-x86_64-Intel-R-_Core-TM-_i5-2500_CPU_@_3.30GHz-with-gentoo-2.2
KiB Mem:    32953400 total,  28504100 free
KiB Swap:    2097148 total,   2097148 free
Timestamp of tree: Sun, 05 Jan 2014 16:45:01 +0000
ld GNU ld (GNU Binutils) 2.23.2
app-shells/bash:          4.2_p45
dev-java/java-config:     2.1.12-r1
dev-lang/python:          2.7.5-r3, 3.3.2-r2
dev-util/cmake:           2.8.11.2
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.11.6, 1.12.6, 1.13.4
sys-devel/binutils:       2.23.2
sys-devel/gcc:            4.7.3-r1
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.9 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo vmware printer-drivers local
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA vmware"
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 /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.5/ext-active/ /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="/usr/portage/distfiles"
FCFLAGS="-march=native -O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-march=native -O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
PKGDIR="/usr/portage/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"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/vmware /var/lib/layman/printer-drivers /usr/local/portage"
SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage"
USE="X acl alsa amd64 apache2 berkdb bzip2 cairo cli clucene colord consolekit cracklib crypt cups curl cxx dbus doc dri examples exif fontconfig fortran gcj gd gdbm gif handbook iconv icu ipv6 jack java jbig jpeg jpeg2k kde kipi kpathsea lcms lzma mbox mmx mng modules mudflap multilib ncurses nls nptl nsplugin odbc ogg openexr opengl openmp pam pango pcre pdf plasma png policykit postgres qt3support readline scanner semantic-desktop session source spell sse sse2 sse4_1 ssl ssse3 svg t1lib tcpd threads tiff truetype unicode webp xattr xinerama xml xpm 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="actions alias auth_basic auth_digest authn_anon authn_core authn_dbd authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config log_forensic logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" APACHE2_MPMS="worker" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon" 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 ublox ubx" GRUB_PLATFORMS="pc" INPUT_DEVICES="keyboard mouse evdev vmmouse wacom joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver presenter-minimizer wiki-publisher" LINGUAS="en_US" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19" SANE_BACKENDS="epson2" USERLAND="GNU" VIDEO_CARDS="fbdev intel radeon vesa vmware" 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:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, MAKEOPTS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

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

sci-libs/vtk-5.10.1 was built with the following:
USE="X doc ffmpeg java mpi (multilib) odbc patented postgres qt4 theora threads -R -boost -cg -chemistry -examples -mysql -python -tk" ABI_X86="64" VIDEO_CARDS="-nvidia"


# emerge -pqv '=sci-libs/vtk-5.10.1::gentoo'
[ebuild   R   ] sci-libs/vtk-5.10.1  USE="X doc ffmpeg java mpi odbc patented postgres qt4 theora threads -R -boost -cg -chemistry -examples -mysql -python -tk" VIDEO_CARDS="-nvidia"

[Comment 1 Bob Johnson 2014-01-06 09:50:02 UTC]

Probably caused by this fix:

https://bugs.gentoo.org/show_bug.cgi?id=486674

Almost certainly the result of a broken build system, as in:

https://bugs.gentoo.org/show_bug.cgi?id=477638

Compiles fine with the postgres USE flag disabled.

[Comment 2 Bob Johnson 2014-01-06 10:02:32 UTC]

Oops, meant to say 'issue', not 'fix'. Once eselect-postgresql-1.2.1 hits stable this bug should be resolved (although the real fix is to get the vtk build system to use pg_config properly.)

Sorry. This bug can probably be closed due to the above. I didn't find the eselect-postgresql issue until after I'd filed the bug.

[Comment 3 Jeroen Roovers (RETIRED) 2014-01-07 14:52:32 UTC]

Comment on attachment 367158 [details]
vtklog.tgz

How does stuffing it in a tar archive help compression?

[Comment 4 Justin Lecher (RETIRED) 2014-01-07 17:18:42 UTC]

I am heavily working on a version bump, which should fix all problems.

[Comment 5 Aaron W. Swenson 2014-01-11 04:28:59 UTC]

Which version of app-admin/eselect-postgresql do you have installed?

[Comment 6 Bob Johnson 2014-01-11 05:51:38 UTC]

I'm using the current stable amd64 version:

$ emerge -pv eselect-postgresql

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

Calculating dependencies... done!
[ebuild   R    ] app-admin/eselect-postgresql-1.2.0  0 kB

Total: 1 package (1 reinstall), Size of downloads: 0 kB

$ eselect postgresql list
Available PostgreSQL Slots
  9.3 *                      server-9.3.2 base-9.3.2 docs-9.3.2



>> Comment 3:

>> How does stuffing it in a tar archive help compression?

I don't understand. It was a huge build log. I was hesitant to even attach it, but also hesitant to hack it to a size that was up-loadable. Should I not attach such large logs in the future? I'm not sure what the accepted practices are.

[Comment 7 Aaron W. Swenson 2014-01-11 11:33:31 UTC]

(In reply to Bob Johnson from comment #6)
> I'm using the current stable amd64 version:
> 
> $ emerge -pv eselect-postgresql
> 
> These are the packages that would be merged, in order:
> 
> Calculating dependencies... done!
> [ebuild   R    ] app-admin/eselect-postgresql-1.2.0  0 kB
> 
> Total: 1 package (1 reinstall), Size of downloads: 0 kB
> 
> $ eselect postgresql list
> Available PostgreSQL Slots
>   9.3 *                      server-9.3.2 base-9.3.2 docs-9.3.2
> 
> 
> 
> >> Comment 3:
> 
> >> How does stuffing it in a tar archive help compression?
> 
> I don't understand. It was a huge build log. I was hesitant to even attach
> it, but also hesitant to hack it to a size that was up-loadable. Should I
> not attach such large logs in the future? I'm not sure what the accepted
> practices are.

Please upgrade to app-admin/eselect-postgresql-1.2.1 and confirm that it resolves your issue.

[Comment 8 Justin Lecher (RETIRED) 2014-01-11 16:57:26 UTC]

I don't have problems with this. Please also try vet version 6.0.0

[Comment 9 Bob Johnson 2014-01-12 02:42:15 UTC]

(In reply to Aaron W. Swenson from comment #7)
> (In reply to Bob Johnson from comment #6)
> > I'm using the current stable amd64 version:
> > 
> > $ emerge -pv eselect-postgresql
> > 
> 
> Please upgrade to app-admin/eselect-postgresql-1.2.1 and confirm that it
> resolves your issue.

Yes. I confirm that eselect-postgresql-1.2.1 fixes the compile issue with vtk-5.10.1 and the postgres USE flag.

[Comment 10 Bob Johnson 2014-01-12 04:16:18 UTC]

(In reply to Justin Lecher from comment #8)
> I don't have problems with this. Please also try vet version 6.0.0

It appears vtk-6.0.0 just hit portage. I confirm that sci-libs/vtk-6.0.0 compiles fine on my system with app-admin/eselect-postgresql-1.2.0 (the current stable version) and the postgres USE flag. However, to do so, I had to keyword not just the new packages that the vtk-6.0.0 ebuild requires, but also x11-libs/gl2ps in order to bring in gl2ps-1.3.8. Any lower gl2ps package generates the following error:

/var/tmp/portage/sci-libs/vtk-6.0.0/work/VTK6.0.0/Rendering/GL2PS/vtkGL2PSUtilit
ies.cxx:580:35: error: ‘gl2psGetFileFormat’ was not declared in this scope
/var/tmp/portage/sci-libs/vtk-6.0.0/work/VTK6.0.0/Rendering/GL2PS/vtkGL2PSUtilit
ies.cxx: In static member function ‘static void vtkGL2PSUtilities::DrawPathSVG(v
tkPath*, double*, double*, unsigned char*, double*, double, float)’:
/var/tmp/portage/sci-libs/vtk-6.0.0/work/VTK6.0.0/Rendering/GL2PS/vtkGL2PSUtilit
ies.cxx:735:35: error: ‘gl2psGetFileFormat’ was not declared in this scope
/usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-libs/vtk-6.0.0/work
/vtk-6.0.0_build/CMakeFiles 
make[2]: *** [Rendering/GL2PS/CMakeFiles/vtkRenderingGL2PS.dir/vtkGL2PSUtilities
.cxx.o] Error 1

This seems to be a known issue:
http://geuz.org/pipermail/gl2ps/2012/000380.html

So it appears vtk-6.0.0 fixes the pg_config_ext.h issue that the new eselect-postgresql ebuild is working around, but the new vtk-6.0.0 ebuild probably needs to depend on gl2ps >= 1.3.8.

[Comment 11 Justin Lecher (RETIRED) 2014-01-12 09:15:45 UTC]

(In reply to Bob Johnson from comment #10)
> So it appears vtk-6.0.0 fixes the pg_config_ext.h issue that the new
> eselect-postgresql ebuild is working around, but the new vtk-6.0.0 ebuild
> probably needs to depend on gl2ps >= 1.3.8.


Thanks for that report, I fixed the version in the deps.

[Comment 12 Aaron W. Swenson 2014-01-14 14:04:50 UTC]

(In reply to Bob Johnson from comment #9)
> (In reply to Aaron W. Swenson from comment #7)
> > (In reply to Bob Johnson from comment #6)
> > > I'm using the current stable amd64 version:
> > > 
> > > $ emerge -pv eselect-postgresql
> > > 
> > 
> > Please upgrade to app-admin/eselect-postgresql-1.2.1 and confirm that it
> > resolves your issue.
> 
> Yes. I confirm that eselect-postgresql-1.2.1 fixes the compile issue with
> vtk-5.10.1 and the postgres USE flag.

Thank you.

The build system of this package is handling discovery of the PostgreSQL header files incorrectly. It should utilize pg_config instead of guessing.

[Comment 13 Justin Lecher (RETIRED) 2014-01-14 14:09:07 UTC]

Perhaps we can use this:

# You may need to manually set:
#  PostgreSQL_INCLUDE_DIR  - the path to where the PostgreSQL include files are.
#  PostgreSQL_LIBRARY_DIR  - The path to where the PostgreSQL library files are.


in combination with pg_config.

[Comment 14 Justin Lecher (RETIRED) 2014-12-26 12:22:50 UTC]

+*vtk-6.1.0 (26 Dec 2014)
+
+  26 Dec 2014; Justin Lecher <[e-mail]> -vtk-5.10.0.ebuild,
+  -vtk-5.10.1.ebuild, vtk-6.0.0.ebuild, +vtk-6.1.0.ebuild,
+  +files/vtk-6.1.0-freetype.patch, +files/vtk-6.1.0-glext.patch,
+  +files/vtk-6.1.0-install.patch, +files/vtk-6.1.0-netcdf.patch,
+  +files/vtk-6.1.0-system.patch, +files/vtk-6.1.0-web.patch, metadata.xml:
+  Version BUmp, #500814; fixes GLintptr declaration problems, #523786; Add slot
+  operators to dependencies, #531040; drop old which obsoletes, #477638,
+  #497224, #520310
+