| Summary: | sci-visualization/hippodraw fails to configure | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Diego Elio Pettenò (RETIRED) <flameeyes> |
| Component: | New packages | Assignee: | Gentoo Science Related Packages <sci> |
| Status: | RESOLVED WORKSFORME | ||
| Severity: | normal | CC: | kredba |
| Priority: | High | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: | Build log | ||
|
Description
Diego Elio Pettenò (RETIRED)
2009-07-08 12:19:34 UTC
Created attachment 197172 [details]
Build log
I have something completely different (not linked openmp library?):
-cut-
Python found
PY_INCLUDE = /usr/include/python2.6
PY_LIB = /usr/lib64/python2.6
configure: checking boost installation with
BOOST_CXXFLAGS=-I/usr/local/include/boost-1_33_1
checking for /usr/local/include/boost-1_33_1/boost/python.hpp... no
configure: checking boost installation with
BOOST_CXXFLAGS=
checking for /usr/include/boost/python.hpp... yes
configure: checking boost installation with
BOOST_LDFLAGS=-L/usr/local/lib -lboost_python-gcc-1_33_1 -R/usr/local/lib
checking for /usr/local/lib/libboost_python-gcc-1_33_1.so... no
configure: checking boost installation with
BOOST_LDFLAGS=-lboost_python
checking for main in -lboost_python... yes
configure: Minuit2 disabled
configure: WARNING: Minuit2 not found
configure: checking Minuit install with
MINUIT_CXXFLAGS=-I/usr/local/include
MINUIT_LDFLAGS=-L/usr/local/lib -llcg_Minuit -R/usr/local/lib
checking for /usr/local/include/Minuit/FCNBase.h... no
checking for /usr/local/lib/liblcg_Minuit.so... no
configure: WARNING: Minuit not found
configure: checking ROOT install with
ROOT_CXXFLAGS=-I/usr/include/root
ROOT_LDFLAGS=-L/usr/lib64/root -lCore -lCint -lTree -lMatrix -lHist -R /usr/lib64/root
checking for /usr/include/root/TTree.h... yes
checking for /usr/lib64/root/libCore.so... yes
checking for /usr/include/root/Minuit2/FCNBase.h... yes
checking for /usr/lib64/root/libMinuit2.so... yes
checking for /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h... yes
Numpy found
checking for Qt... User disabled Qt.
./configure: line 17698: test: too many arguments
configure: checking QT4 install
checking for /usr/include/qt4/QtGui/QAbstractButton... yes
checking for /usr/lib64/qt4/libQtCore.so... yes
./configure: line 17859: test: too many arguments
configure: checking WCSLIB install with
WCSLIB_CXXFLAGS=-Ino
WCSLIB_LDFLAGS=
checking for no/wcslib/wcs.h... no
checking for wcsset in -lwcs... yes
configure: WARNING: WCSLIB not found
configure: checking cfitsio install with
CFITSIO_CXXFLAGS=-I/usr/include
CFITSIO_LDFLAGS=-L/usr/lib64 -lcfitsio -R /usr/lib64
checking for /usr/include/fitsio.h... yes
checking for /usr/lib64/libcfitsio.so... yes
checking sstream usability... yes
checking sstream presence... yes
checking for sstream... yes
checking whether the compiler can use std::distance()... yes
checking whether the compiler can use std::string::clear... (cached) yes
checking whether the compiler can use mem_fun(arg)... yes
configure: creating ./config.status
config.status: creating Makefile
-cut-
...
-cut-
make[4]: Leaving directory `/var/tmp/portage/sci-visualization/hippodraw-1.21.3-r1/work/HippoDraw-1.21.3/qt'
Making all in app
make[4]: Entering directory `/var/tmp/portage/sci-visualization/hippodraw-1.21.3-r1/work/HippoDraw-1.21.3/qt/app'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -DQT_THREAD_SUPPORT -I. -I../.. -I../.. -I/usr/include/qt4 -I/usr/include/qt4/Qt -DQT_COMPAT -DQT3_SUPPORT -O2 -g -ggdb -pipe -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cxx
mv -f .deps/main.Tpo .deps/main.Po
/bin/sh ../../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -O2 -g -ggdb -pipe -L/usr/lib64 -lcfitsio -R /usr/lib64 -L/usr/lib64/root -lMinuit2 -lGraf -R/usr/lib64/root -L/usr/lib64/root -lCore -lCint -lTree -lMatrix -lHist -R /usr/lib64/root -u _G__cpp_setup_initializerG__Tree -Wl,-O1 -o hippodraw main.o ../../qt/libhippoqt.la ../../lib/libhippo.la
libtool: link: x86_64-pc-linux-gnu-g++ -O2 -g -ggdb -pipe -u _G__cpp_setup_initializerG__Tree -Wl,-O1 -o .libs/hippodraw main.o -L/usr/lib64 -L/usr/lib64/root ../../qt/.libs/libhippoqt.so -L/usr/lib64/qt4 -L/usr/X11R6/lib -L/usr/lib64/mysql -L/usr/lib /usr/lib64/qt4/libQt3Support.so /usr/lib64/qt4/libQtSql.so /usr/lib64/qt4/libQtXml.so /usr/lib64/qt4/libQtGui.so -laudio /usr/lib64/libXt.so /usr/lib64/libpng12.so /usr/lib64/libgobject-2.0.so /usr/lib64/libSM.so -luuid /usr/lib64/libICE.so /usr/lib64/libXrandr.so /usr/lib64/libXrender.so /usr/lib64/libXinerama.so /usr/lib64/libfontconfig.so /usr/lib64/libfreetype.so /usr/lib64/libexpat.so /usr/lib64/libXext.so /usr/lib64/libX11.so /usr/lib64/libXau.so /usr/lib64/libXdmcp.so /usr/lib64/qt4/libQtNetwork.so /usr/lib64/qt4/libQtCore.so -lz /usr/lib64/libgthread-2.0.so -lrt /usr/lib64/libglib-2.0.so -lpthread -ldl -lQtAssistantClient /var/tmp/portage/sci-visualization/hippodraw-1.21.3-r1/work/HippoDraw-1.21.3/lib/.libs/libhippo.so ../../lib/.libs/libhippo.so -lMinuit2 -lGraf /usr/lib64/libcfitsio.so -lm -lCore -lCint -lTree -lMatrix -lHist -pthread -Wl,-rpath -Wl,/usr/lib64 -Wl,-rpath -Wl,/usr/lib64/root
/usr/lib64/root/libMinuit2.so: undefined reference to `GOMP_parallel_start'
/usr/lib64/root/libMinuit2.so: undefined reference to `omp_get_thread_num'
/usr/lib64/root/libMinuit2.so: undefined reference to `GOMP_parallel_end'
/usr/lib64/root/libMinuit2.so: undefined reference to `omp_get_num_threads'
/usr/lib64/root/libMinuit2.so: undefined reference to `ROOT::Minuit2::Numerical2PGradientCalculator::operator()(std::vector<double, std::allocator<double> > const&) const'
collect2: ld returned 1 exit status
make[4]: *** [hippodraw] Error 1
make[4]: Leaving directory `/var/tmp/portage/sci-visualization/hippodraw-1.21.3-r1/work/HippoDraw-1.21.3/qt/app'
make[3]: *** [all-recursive] Error 1
objdump -T /usr/lib64/root/libMinuit2.so |grep GOMP_parallel
0000000000000000 D *UND* 0000000000000000 GOMP_parallel_start
0000000000000000 D *UND* 0000000000000000 GOMP_parallel_end
other symbols "*UND*" as well.
I have both qt-3.3.8b and 4.5.2 installed.
Maybe the openmp library is not asked at linking time?
Portage 2.1.6.13 (default/linux/amd64/2008.0/desktop, gcc-4.3.3, glibc-2.10.1-r0, 2.6.30-gentoo-r4-4d x86_64)
=================================================================
System uname: Linux-2.6.30-gentoo-r4-4d-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9300_@_2.50GHz-with-gentoo-2.0.1
Timestamp of tree: Tue, 04 Aug 2009 14:30:01 +0000
app-shells/bash: 4.0_p28
dev-java/java-config: 2.1.8-r1
dev-lang/python: 2.6.2-r1, 3.1
dev-util/cmake: 2.6.4-r2
sys-apps/baselayout: 2.0.1
sys-apps/openrc: 0.4.3-r3
sys-apps/sandbox: 2.0
sys-devel/autoconf: 2.13, 2.63-r1
sys-devel/automake: 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11
sys-devel/binutils: 2.19.1-r1
sys-devel/gcc-config: 1.4.1
sys-devel/libtool: 2.2.6a
virtual/os-headers: 2.6.30-r1
ACCEPT_KEYWORDS="amd64 ~amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -g -ggdb -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config /var/bind /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/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 /etc/udev/rules.d"
CXXFLAGS="-O2 -g -ggdb -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks fixpackages nostrip parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="ftp://gentoo.inode.at/source/ ftp://ftp.fi.muni.cz/pub/linux/gentoo/ ftp://gentoo.mirror.web4u.cz/ "
LANG="cs_CZ.UTF-8"
LC_ALL="cs_CZ.UTF-8"
LDFLAGS="-Wl,-O1"
LINGUAS="cs en"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_COMPRESS="echo"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X accessibility acl acpi alsa amd64 arts avahi berkdb bluetooth branding bzip2 cairo cdr cli cracklib crypt cups dbus directfb djvu doc dri dvd dvdr dvdread eds emacs emboss encode epydoc esd evo examples exif fam firefox fontconfig fortran freetds gcj gd gdbm gedit geoip gif gimp glep gmp gnome gnome-keyring gpm gstreamer gtk guile hal htmlhandbook iconv idn ieee1394 isdnlog ithreads jadetex java jpeg jpeg2k kde kdehiddenvisibility kerberos lapack latex lcms ldap libedit libffi libnotify lzma lzo mad mikmod mmx mono mp3 mpeg mudflap multilib mysql nautilus ncurses nls nptl nptlonly objc objc++ objc-gc odbc ogg opengl openmp pam pch pcre pdf perl png portaudio ppds pppd pulseaudio python qt3 qt3support qt4 quicktime readline reflection ruby samba sasl sdl session slang soundex source spell spl sqlite sse sse2 sse3 ssl startup-notification svg sysfs tcl tcpd threads tiff tk truetype unicode usb v4l v4l2 vorbis wmf xinerama xml xorg xpm xulrunner xv zlib" 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" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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 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" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="cs en" LIRC_DEVICES="inputlirc" USERLAND="GNU" VIDEO_CARDS="nvidia nv vesa v4l"
Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Thank you.
(In reply to comment #1) > Created an attachment (id=197172) [details] > Build log Unfortunately, I can't reproduce this on either x86 or amd64. The error message in the log indicates that compilation of a fairly simple qt program fails somehow. Is there anything more instructive in config.log by any chance that would give some indication of what actually fails. Thanks, Markus My compilation fails with: make[4]: Leaving directory `/var/tmp/portage/sci-visualization/hippodraw-1.21.3-r1/work/HippoDraw-1.21.3/qt' Making all in app make[4]: Entering directory `/var/tmp/portage/sci-visualization/hippodraw-1.21.3-r1/work/HippoDraw-1.21.3/qt/app' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -DQT_THREAD_SUPPORT -I. -I../.. -I../.. -I/usr/include/qt4 -I/usr/include/qt4/Qt -DQT_COMPAT -DQT3_SUPPORT -O2 -g -ggdb -pipe -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cxx mv -f .deps/main.Tpo .deps/main.Po /bin/sh ../../libtool --tag=CXX --mode=link x86_64-pc-linux-gnu-g++ -O2 -g -ggdb -pipe -L/usr/lib64 -lcfitsio -R /usr/lib64 -L/usr/lib64/root -lMinuit2 -lGraf -R/usr/lib64/root -L/usr/lib64/root -lCore -lCint -lTree -lMatrix -lHist -R /usr/lib64/root -u _G__cpp_setup_initializerG__Tree -Wl,-O1 -o hippodraw main.o ../../qt/libhippoqt.la ../../lib/libhippo.la libtool: link: x86_64-pc-linux-gnu-g++ -O2 -g -ggdb -pipe -u _G__cpp_setup_initializerG__Tree -Wl,-O1 -o .libs/hippodraw main.o -L/usr/lib64 -L/usr/lib64/root ../../qt/.libs/libhippoqt.so -L/usr/lib64/qt4 -L/usr/X11R6/lib -L/usr/lib64/mysql /usr/lib64/qt4/libQt3Support.so /usr/lib64/qt4/libQtSql.so /usr/lib64/qt4/libQtXml.so /usr/lib64/qt4/libQtGui.so /usr/lib64/qt4/libQtNetwork.so /usr/lib64/qt4/libQtCore.so -lpthread /var/tmp/portage/sci-visualization/hippodraw-1.21.3-r1/work/HippoDraw-1.21.3/lib/.libs/libhippo.so ../../lib/.libs/libhippo.so -lMinuit2 -lGraf /usr/lib64/libcfitsio.so -lm -lCore -lCint -lTree -lMatrix -lHist -lwcs -Wl,-rpath -Wl,/usr/lib64 -Wl,-rpath -Wl,/usr/lib64/root /var/tmp/portage/sci-visualization/hippodraw-1.21.3-r1/work/HippoDraw-1.21.3/lib/.libs/libhippo.so: undefined reference to `ROOT::Minuit2::ModularFunctionMinimizer::Minimize(ROOT::Minuit2::FCNBase const&, std::vector<double, std::allocator<double> > const&, unsigned int, std::vector<double, std::allocator<double> > const&, unsigned int, unsigned int, double) const' /var/tmp/portage/sci-visualization/hippodraw-1.21.3-r1/work/HippoDraw-1.21.3/lib/.libs/libhippo.so: undefined reference to `ROOT::Minuit2::ModularFunctionMinimizer::Minimize(ROOT::Minuit2::FCNGradientBase const&, std::vector<double, std::allocator<double> > const&, unsigned int, std::vector<double, std::allocator<double> > const&, unsigned int, unsigned int, double) const' /var/tmp/portage/sci-visualization/hippodraw-1.21.3-r1/work/HippoDraw-1.21.3/lib/.libs/libhippo.so: undefined reference to `ROOT::Minuit2::ModularFunctionMinimizer::Minimize(ROOT::Minuit2::FCNBase const&, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, unsigned int, unsigned int, double) const' /var/tmp/portage/sci-visualization/hippodraw-1.21.3-r1/work/HippoDraw-1.21.3/lib/.libs/libhippo.so: undefined reference to `ROOT::Minuit2::ModularFunctionMinimizer::Minimize(ROOT::Minuit2::FCNGradientBase const&, std::vector<double, std::allocator<double> > const&, std::vector<double, std::allocator<double> > const&, unsigned int, unsigned int, double) const' collect2: ld returned 1 exit status Info: CPV: sci-visualization/hippodraw- 1.21.3-r1 * USE: amd64 elibc_glibc examples fits kernel_linux multilib numpy qt4 root userland_GNU wcs Portage 2.1.7.14 (default/linux/amd64/10.0/desktop, gcc-4.4.2, glibc-2.11-r1, 2.6.32-gentoo-1d x86_64) ================================================================= System uname: Linux-2.6.32-gentoo-1d-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9300_@_2.50GHz-with-gentoo-2.0.1 Timestamp of tree: Wed, 16 Dec 2009 14:00:01 +0000 app-shells/bash: 4.0_p35 dev-java/java-config: 2.1.10 dev-lang/python: 2.6.4 dev-util/cmake: 2.8.0 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.5.3 sys-apps/sandbox: 2.2 sys-devel/autoconf: 2.13, 2.64 sys-devel/automake: 1.4_p6, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.3, 1.11.1 sys-devel/binutils: 2.20 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -g -ggdb -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/bind /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/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="-O2 -g -ggdb -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests distlocks fixpackages news nostrip parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch" FFLAGS="-O2 -g -ggdb -pipe" GENTOO_MIRRORS="ftp://gentoo.inode.at/source/ ftp://gentoo.mirror.web4u.cz/ " LDFLAGS="-Wl,-O1" LINGUAS="cs en" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" PORTAGE_COMPRESS="echo" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo caps cdr cli consolekit cracklib crypt cups cxx dbus djvu dri dts dvd dvdr eds emboss encode evo examples exif extras fam firefox flac fontconfig fontforge fortran gdbm gif gmp gnome gpm gstreamer gtk hal iconv idn ithreads java jpeg jpeg2k kde kerberos lcms ldap libedit libnotify mad mikmod mmx modules mp3 mp4 mpeg mudflap multilib mysql ncurses nls nptl nptlonly objc objc++ objc-gc odbc ogg openexr opengl openmp pam pch pcre pdf perl png policykit ppds pppd python qt3support qt4 quicktime readline reflection samba sdl session slang spell spl sqlite sse sse2 sse3 ssl startup-notification svg sysfs tcl tcpd threads thunar tiff tk truetype unicode usb utils vorbis x264 xattr xcb xinerama xml xorg xpm xulrunner xv xvid zlib" 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" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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 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" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="cs en" LIRC_DEVICES="inputlirc" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia nv vesa v4l" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY (In reply to comment #4) > My compilation fails with: > David, Could you please file a separate bug since yours has nothing to do with the problem that Diego reported! Otherwise things will become confusing. Thanks, Markus I cannot reproduce that. Please reopen if still exists. |