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Bug 325561 - Please stable =sci-chemistry/ghemical-2.99.2-r2 (was: =sci-libs/libghemical-2.00 fails to build)
Summary: Please stable =sci-chemistry/ghemical-2.99.2-r2 (was: =sci-libs/libghemical...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Library (show other bugs)
Hardware: x86 Linux
: High normal (vote)
Assignee: Gentoo Chemistry-Related Packages
URL:
Whiteboard:
Keywords: STABLEREQ
: 331169 (view as bug list)
Depends on: 331187
Blocks: 331169
  Show dependency tree
 
Reported: 2010-06-25 19:37 UTC by Myckel Habets
Modified: 2011-05-28 13:56 UTC (History)
2 users (show)

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


Attachments
Build log (build.log,10.50 KB, text/plain)
2010-06-25 19:37 UTC, Myckel Habets
Details
build.log (sci-chemistry:ghemical-2.99.2-r2:20100814-015047.log,88.31 KB, text/plain)
2010-08-14 01:53 UTC, Paweł Hajdan, Jr. (RETIRED)
Details

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Description Myckel Habets 2010-06-25 19:37:16 UTC
I try to build ghemical, which pulls in libghemical.
This one fails during build.

Reproducible: Always

Steps to Reproduce:
1. emerge ghemical
2.
3.

Actual Results:  
Failed build. See build log.

Expected Results:  
Package installed without any problems.

emerge --info
Portage 2.1.8.3 (default/linux/x86/10.0, gcc-4.4.3, glibc-2.11.1-r0, 2.6.32-gentoo-r7 i686)
=================================================================
System uname: Linux-2.6.32-gentoo-r7-i686-Mobile_AMD_Sempron-tm-_Processor_2800+-with-gentoo-1.12.13
Timestamp of tree: Fri, 25 Jun 2010 17:00:18 +0000
distcc 3.1 i686-pc-linux-gnu [disabled]
app-shells/bash:     4.0_p37
dev-java/java-config: 2.1.10
dev-lang/python:     2.6.4-r1, 3.1.2-r3
dev-util/cmake:      2.6.4-r3
sys-apps/baselayout: 1.12.13
sys-apps/sandbox:    1.6-r2
sys-devel/autoconf:  2.13, 2.65
sys-devel/automake:  1.10.3, 1.11.1
sys-devel/binutils:  2.20.1-r1
sys-devel/gcc:       4.4.3-r2
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6b
virtual/os-headers:  2.6.30-r1
ACCEPT_KEYWORDS="x86"
ACCEPT_LICENSE="* -@EULA"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-march=athlon-xp -O2 -pipe -fomit-frame-pointer"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb /var/spool/torque"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /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="-march=athlon-xp -O2 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests collision-protect distlocks fixpackages news nostrip parallel-fetch protect-owned sandbox sfperms strict test unmerge-logs unmerge-orphans userfetch userpriv"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LDFLAGS="-Wl,-O1,--as-needed"
LINGUAS="nl en uk"
MAKEOPTS="-j1"
PKGDIR="/usr/portage/packages"
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"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="7zip X acl acpi alsa avahi berkdb bzip2 cairo cli cracklib crypt cxx dbus dri encode fam ffmpeg flac fortran fts3 gdbm gmp gnutls gpm gtk hal iconv icu imap ipv6 ithreads java5 jpeg libnotify mmx modules mudflap ncurses nls nptl nptlonly ogg openexr opengl openmp pam pcre perl pic player png pppd python rdesktop readline reflection sdl session smime sockets spell spl sqlite sqlite3 sse sse2 ssl startup-notification svg sysfs tcpd theora threads thunar truetype unicode vnc vorbis x86 xcb xcomposite xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="nl en uk" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="radeonhd" 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, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 1 Myckel Habets 2010-06-25 19:37:39 UTC
Created attachment 236549 [details]
Build log
Comment 2 Rafał Mużyło 2010-06-25 20:35:50 UTC
The reason for such failures is quite obvious.
Try one of the more recent versions.

On that note: it seems that about 9 months ago 2.99.1 was released
(and 2.99.2 for ghemical).
Comment 3 Myckel Habets 2010-06-25 21:45:59 UTC
(In reply to comment #2)
> The reason for such failures is quite obvious.
> Try one of the more recent versions.
> 
> On that note: it seems that about 9 months ago 2.99.1 was released
> (and 2.99.2 for ghemical).
> 

This is on stable x86. Is there some more recent version that could be stabilized then? Could 2.96 be a candidate for this?
Comment 4 Justin Lecher (RETIRED) gentoo-dev 2010-06-30 19:45:10 UTC
Will ask for stabling in 3 weeks.
Comment 5 Thomas Kahle (RETIRED) gentoo-dev 2010-08-04 11:36:16 UTC
Hijacking this one:

-) A newer ghemical should be stablized together with libghemical in bug 331169
-) depends on bug 331187

OK?
Comment 6 Myckel Habets 2010-08-13 19:32:09 UTC
I tested bug 325561, bug 331187, bug 331169 and bug 331175 together for stabilization on x86.  All these need to be stabilized together as they depend on each other (and building will fail if any is not stabilized). I was able to get them build against each other. I ran ghemical and tested the bug mentioned in bug 324975. No problems encountered.

Please mark stable for x86.
Comment 7 Paweł Hajdan, Jr. (RETIRED) gentoo-dev 2010-08-14 00:44:45 UTC
Adding archs, this bug pack is going to be tricky...
Comment 8 Paweł Hajdan, Jr. (RETIRED) gentoo-dev 2010-08-14 01:53:46 UTC
Created attachment 242875 [details]
build.log

After emerging all packages from the pack, I have tried different USE flags and got this linking error. Possibly a problem with dependencies.
Comment 9 Thomas Kahle (RETIRED) gentoo-dev 2010-08-14 08:25:28 UTC
(In reply to comment #8)
> Created an attachment (id=242875) [details]
> build.log
> 
> After emerging all packages from the pack, I have tried different USE flags and
> got this linking error. Possibly a problem with dependencies.

The undefined references are to be found in sci-chemistry/mpqc which is a dependency. Can you track back the exact USE-combination triggering this problem, and maybe try -Wl,--no-as-needed on mpqc, libghemical and ghemical, just to be sure.
Comment 10 Markos Chandras (RETIRED) gentoo-dev 2010-08-14 12:20:12 UTC
*** Bug 331169 has been marked as a duplicate of this bug. ***
Comment 11 Christian Faulhammer (RETIRED) gentoo-dev 2010-08-23 12:00:25 UTC
(In reply to comment #9)
> (In reply to comment #8)
> > Created an attachment (id=242875) [details] [details]
> > build.log
> > 
> > After emerging all packages from the pack, I have tried different USE flags and
> > got this linking error. Possibly a problem with dependencies.
> 
> The undefined references are to be found in sci-chemistry/mpqc which is a
> dependency. Can you track back the exact USE-combination triggering this
> problem, and maybe try -Wl,--no-as-needed on mpqc, libghemical and ghemical,
> just to be sure.

 With the -r2 of mqpc those errors disappear, but a new one occurs.

libtool: link: i686-pc-linux-gnu-g++ -O2 -march=athlon-xp -pipe -msse3 -Wl,-O1 -Wl,--hash-style=gnu -o ghemical fileio.o filetrans.o custom_app.o custo
m_camera.o custom_lights.o project.o spline.o pangofont_wcl.o oglview_wcl.o ac_stor_wcl.o p1dview_wcl.o p2dview_wcl.o eldview_wcl.o rcpview_wcl.o gpcvi
ew_wcl.o ogl_plane.o ogl_surface.o ogl_ribbon.o gtk_simple_dialogs.o gtk_glade_dialog.o gtk_file_export_dialog.o gtk_file_import_dialog.o gtk_geomopt_d
ialog.o gtk_moldyn_dialog.o gtk_progress_dialog.o gtk_setup_dialog.o gtk_stereo_dialog.o gtk_trajview_dialog.o gtk_wnd.o gtk_oglview_wnd.o gtk_p1dview_
wnd.o gtk_p2dview_wnd.o gtk_eldview_wnd.o gtk_rcpview_wnd.o gtk_gpcview_wnd.o gtk_app.o gtk_project.o gtk_main.o -pthread -pthread -Wl,--export-dynamic
  -Wl,--as-needed -L/usr/X11R6/lib /usr/lib/libgtkglext-x11-1.0.so /usr/lib/libgdkglext-x11-1.0.so /usr/lib/libXmu.so /usr/lib/libXext.so /usr/lib/libXt.so /usr/lib/libSM.so -luuid /usr/lib/libICE.so /usr/lib/libpangox-1.0.so /usr/lib/libglade-2.0.so /usr/lib/libgtk-x11-2.0.so /usr/lib/libxml2.so /usr/lib/libgdk-x11-2.0.so /usr/lib/libatk-1.0.so /usr/lib/libgdk_pixbuf-2.0.so /usr/lib/libgio-2.0.so -lresolv /usr/lib/libpangocairo-1.0.so /usr/lib/libpangoft2-1.0.so /usr/lib/libcairo.so /usr/lib/libpixman-1.so /usr/lib/libdirectfb.so /usr/lib/libfusion.so /usr/lib/libdirect.so /usr/lib/libglitz-glx.so /usr/lib/libglitz.so /usr/lib/libpng14.so /usr/lib/libxcb-render-util.so /usr/lib/libxcb-render.so /usr/lib/libXrender.so /usr/lib/libX11.so /usr/lib/libxcb.so /usr/lib/libXau.so /usr/lib/libXdmcp.so /usr/lib/libpango-1.0.so /usr/lib/libfontconfig.so /usr/lib/libfreetype.so /usr/lib/libexpat.so /usr/lib/libgobject-2.0.so /usr/lib/libgmodule-2.0.so /usr/lib/libgthread-2.0.so -lrt /usr/lib/libglib-2.0.so /usr/lib/libopenbabel.so -lz -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.3 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.3/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.3/../../.. /usr/lib/libghemical.so -L/usr/lib /usr/lib/libSCoptions.so /usr/lib/libSCpsi.so /usr/lib/libSCmbpt.so /usr/lib/libSCscf.so /usr/lib/libSCwfn.so /usr/lib/libSCdft.so /usr/lib/libSCintv3.so /usr/lib/libSCbasis.so /usr/lib/libSCoint3.so /usr/lib/libSCsolvent.so /usr/lib/libSCmolecule.so /usr/lib/libSCsymmetry.so /usr/lib/libSCisosurf.so /usr/lib/libSCoptimize.so /usr/lib/libSCscmat.so /usr/lib/libSCgroup.so /usr/lib/libSCrender.so /usr/lib/libSCmisc.so /usr/lib/libSCstate.so /usr/lib/libSCkeyval.so /usr/lib/libSCclass.so /usr/lib/libSCcontainer.so /usr/lib/libSCref.so /usr/lib/libmpi.so /usr/lib/libopen-rte.so /usr/lib/libopen-pal.so -lnsl -lutil -lfl -ldl -lpthread -llapack -lblas /usr/lib/gcc/i686-pc-linux-gnu/4.4.3/libgfortranbegin.a /usr/lib/gcc/i686-pc-linux-gnu/4.4.3/libgfortran.so -lgcc_s /usr/lib/libmopac7.so -lm -lGL -lGLU /usr/lib/liboglappth.so -pthread
/usr/lib/libghemical.so: undefined reference to `sc::MTMPIMemoryGrp::MTMPIMemoryGrp(sc::Ref<sc::KeyVal> const&)'
collect2: ld returned 1 exit status

Will try with --as-needed disabled.
Comment 12 Christian Faulhammer (RETIRED) gentoo-dev 2010-08-23 12:45:40 UTC
Building libghemical and mqpc with --no-as-needed helps.
Comment 13 Christian Faulhammer (RETIRED) gentoo-dev 2010-09-06 13:52:42 UTC
stable x86, thanks Myckel and Thomas. Sorted out the as-needed problems with Xarthisius with a newer version of mpqc
Comment 14 Markos Chandras (RETIRED) gentoo-dev 2010-10-10 11:16:34 UTC
amd64 done
Comment 15 Brent Baude (RETIRED) gentoo-dev 2011-05-28 13:56:04 UTC
ppc done; closing as last arch