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javeree
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Posts: 453

PostPosted: Mon Nov 21, 2011 4:21 pm    Post subject: thunderbird preparation: We've already been run in this tree Reply with quote

I try to emerge thunderbird-7.0.1-r1 and get following output in /var/log/portage/elog/mail-client:thunderbird-7.0.1-r1:20111121-152922.log and get a weird error in the 'prepare' step, followed by a killed ld during the compile. Obviously, this is not a common error (or else the ebuild would have not gone stable), but I could not find any mention of this error in google.

Quote:

LOG: setup
You are enabling official branding. You may not redistribute this build
to any users on your network or the internet. Doing so puts yourself into
a legal problem with Mozilla Foundation
You can disable it by emerging thunderbird _with_ the bindist USE-flag
WARN: prepare
We've already been run in this tree; you should
avoid this if possible (perhaps by filing a bug)
We've already been run in this tree; you should
avoid this if possible (perhaps by filing a bug)
We've already been run in this tree; you should
avoid this if possible (perhaps by filing a bug)
We've already been run in this tree; you should
avoid this if possible (perhaps by filing a bug)
We've already been run in this tree; you should
avoid this if possible (perhaps by filing a bug)
ERROR: compile
ERROR: mail-client/thunderbird-7.0.1-r1 failed (compile phase):
(no error message)

Call stack:
ebuild.sh, line 84: Called src_compile
environment, line 6226: Called die
The specific snippet of code:
emake || die;

If you need support, post the output of 'emerge --info =mail-client/thunderbird-7.0.1-r1',
the complete build log and the output of 'emerge -pqv =mail-client/thunderbird-7.0.1-r1'.
The complete build log is located at '/var/tmp/portage/mail-client/thunderbird-7.0.1-r1/temp/build.log'.
The ebuild environment file is located at '/var/tmp/portage/mail-client/thunderbird-7.0.1-r1/temp/environment'.
S: '/var/tmp/portage/mail-client/thunderbird-7.0.1-r1/work/comm-release'


the build log ends with
Quote:

i686-pc-linux-gnu-g++ -o nsRDFResource.o -c -I../../dist/stl_wrappers -I../../dist/system_wrappers -include ../../config/gcc_hidden.h -DMOZ_ENABLE_GTK2 -DMOZ_JSDEBUGGER -DMOZ_PREF_EXTENSIONS -DMOZ_AUTH_EXTENSION -DMOZ_PERMISSIONS -DMOZ_UNIVERSALCHARDET -DMOZ_FILEVIEW -DICON_DECODER -DMOZ_SPELLCHECK -DMOZ_ZIPWRITER -DIMPL_XREAPI -DMOZILLA_INTERNAL_API -DMOZ_THUNDERBIRD=1 -DOSTYPE=\"Linux2.6\" -DOSARCH=Linux -D_IMPL_NS_COM -D_IMPL_NS_STRINGAPI -DEXPORT_XPT_API -DEXPORT_XPTC_API -D_IMPL_NS_GFX -D_IMPL_NS_WIDGET -I../../intl/unicharutil/util -I../../intl/unicharutil/src -I../../config -I../../widget/src/windows -I../../widget/src/build -I. -I. -I../../dist/include -I../../dist/include/nsprpub -I/usr/include/nspr -I/usr/include/nss -fPIC -fno-rtti -fno-exceptions -Wall -Wpointer-arith -Woverloaded-virtual -Wsynth -Wno-ctor-dtor-privacy -Wno-non-virtual-dtor -Wcast-align -Wno-invalid-offsetof -Wno-variadic-macros -Werror=return-type -march=pentium4 -pipe -Wno-return-type -w -mno-avx -ffunction-sections -fdata-sections -fno-strict-aliasing -fshort-wchar -pthread -pipe -DNDEBUG -DTRIMMED -g -O2 -DMOZILLA_CLIENT -include ../../mozilla-config.h -MD -MF .deps/nsRDFResource.pp /var/tmp/portage/mail-client/thunderbird-7.0.1-r1/work/comm-release/mozilla/toolkit/library/nsRDFResource.cpp
/var/tmp/portage/mail-client/thunderbird-7.0.1-r1/work/comm-release/mozilla/config/nsinstall -D ../../dist/sdk/lib
rm -f libxul.so
/usr/bin/python2.7 ../../config/pythonpath.py -I../../config ../../config/expandlibs_exec.py --uselist -- i686-pc-linux-gnu-g++ -fno-rtti -fno-exceptions -Wall -Wpointer-arith -Woverloaded-virtual -Wsynth -Wno-ctor-dtor-privacy -Wno-non-virtual-dtor -Wcast-align -Wno-invalid-offsetof -Wno-variadic-macros -Werror=return-type -march=pentium4 -pipe -Wno-return-type -w -mno-avx -ffunction-sections -fdata-sections -fno-strict-aliasing -fshort-wchar -pthread -pipe -DNDEBUG -DTRIMMED -g -O2 -fPIC -shared -Wl,-z,defs -Wl,--gc-sections -Wl,-h,libxul.so -o libxul.so nsStaticXULComponents.o nsUnicharUtils.o nsBidiUtils.o nsRDFResource.o -lpthread -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -Wl,--sort-common -Wl,-rpath-link,/var/tmp/portage/mail-client/thunderbird-7.0.1-r1/work/comm-release/mozilla/dist/bin -Wl,-rpath-link,/usr/lib ../../toolkit/xre/libxulapp_s.a ../../staticlib/components/libnecko.a ../../staticlib/components/libuconv.a ../../staticlib/components/libi18n.a ../../staticlib/components/libchardet.a ../../staticlib/components/libjar50.a ../../staticlib/components/libstartupcache.a ../../staticlib/components/libpref.a ../../staticlib/components/libhtmlpars.a ../../staticlib/components/libimglib2.a ../../staticlib/components/libgkgfx.a ../../staticlib/components/libgklayout.a ../../staticlib/components/libdocshell.a ../../staticlib/components/libembedcomponents.a ../../staticlib/components/libwebbrwsr.a ../../staticlib/components/libnsappshell.a ../../staticlib/components/libtxmgr.a ../../staticlib/components/libcommandlines.a ../../staticlib/components/libtoolkitcomps.a ../../staticlib/components/libpipboot.a ../../staticlib/components/libpipnss.a ../../staticlib/components/libappcomps.a ../../staticlib/components/libjsreflect.a ../../staticlib/components/libcomposer.a ../../staticlib/components/libjetpack_s.a ../../staticlib/components/libtelemetry.a ../../staticlib/components/libjsctypes.a ../../staticlib/components/libjsperf.a ../../staticlib/components/libgkplugin.a ../../staticlib/components/libunixproxy.a ../../staticlib/components/libjsd.a ../../staticlib/components/libautoconfig.a ../../staticlib/components/libauth.a ../../staticlib/components/libcookie.a ../../staticlib/components/libpermissions.a ../../staticlib/components/libuniversalchardet.a ../../staticlib/components/librdf.a ../../staticlib/components/libwindowds.a ../../staticlib/components/libfileview.a ../../staticlib/components/libstoragecomps.a ../../staticlib/components/libplaces.a ../../staticlib/components/libmork.a ../../staticlib/components/libtkautocomplete.a ../../staticlib/components/libsatchel.a ../../staticlib/components/libpippki.a ../../staticlib/components/libwidget_gtk2.a ../../staticlib/components/libsystem-pref.a ../../staticlib/components/libimgicon.a ../../staticlib/components/libaccessibility.a ../../staticlib/components/libremoteservice.a ../../staticlib/components/libspellchecker.a ../../staticlib/components/libzipwriter.a ../../staticlib/components/libservices-crypto.a ../../staticlib/components/libxpautocomplete.a ../../staticlib/components/libmailcomps.a ../../staticlib/components/libmail.a ../../staticlib/components/libmsgsmime.a ../../staticlib/components/libimport.a ../../staticlib/components/libmozldap.a ../../staticlib/libjsipc_s.a ../../staticlib/libdomipc_s.a ../../staticlib/libdomplugins_s.a ../../staticlib/libmozipc_s.a ../../staticlib/libmozipdlgen_s.a ../../staticlib/libipcshell_s.a ../../staticlib/libgfx2d.a ../../staticlib/libgfxipc_s.a ../../staticlib/libxpcom_core.a ../../staticlib/libucvutil_s.a ../../staticlib/libchromium_s.a ../../staticlib/libmozreg_s.a ../../staticlib/libgtkxtbin.a ../../staticlib/libthebes.a ../../staticlib/libycbcr.a ../../staticlib/libangle.a -lsqlite3 -L../../dist/bin -L../../dist/lib -ljpeg -lpng ../../gfx/qcms/libmozqcms.a /var/tmp/portage/mail-client/thunderbird-7.0.1-r1/work/comm-release/mozilla/dist/lib/libjs_static.a -lffi -Wl,-R/usr/lib -L/usr/lib -lssl3 -lsmime3 -lnss3 -lnssutil3 -lcrmf -lcairo -lpixman-1 -lfreetype -lfontconfig -L/usr/lib -lXrender -lcairo -lX11 ../../gfx/harfbuzz/src/libmozharfbuzz.a ../../gfx/ots/src/libmozots.a -L../../dist/bin -L../../dist/lib -lldap60 -lprldap60 -lldif60 -lz -lhunspell-1.3 -L/usr/lib -levent -lasound -L../../dist/bin -L../../dist/lib -Wl,-R/usr/lib -L/usr/lib -lplds4 -lplc4 -lnspr4 -lpthread -ldl ../../dist/lib/libmozalloc.a -ldbus-1 -lpthread -lrt -L/usr/lib -lX11 -lXext -pthread -lpangoft2-1.0 -lfreetype -lfontconfig -lpangocairo-1.0 -lpango-1.0 -lcairo -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lrt -lglib-2.0 -pthread -lgtk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lfreetype -lfontconfig -lgdk-x11-2.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lpango-1.0 -lcairo -lgmodule-2.0 -lgobject-2.0 -lgthread-2.0 -lrt -lglib-2.0 -lXt -lgthread-2.0 -lfreetype -lz -lbz2 -lstartup-notification-1 -ldl -lrt
collect2: ld terminated with signal 9 [Killed]
make[4]: *** [libxul.so] Error 1
make[4]: Leaving directory `/var/tmp/portage/mail-client/thunderbird-7.0.1-r1/work/comm-release/mozilla/toolkit/library'
make[3]: *** [libs_tier_platform] Error 2
make[3]: Leaving directory `/var/tmp/portage/mail-client/thunderbird-7.0.1-r1/work/comm-release/mozilla'
make[2]: *** [tier_platform] Error 2
make[2]: Leaving directory `/var/tmp/portage/mail-client/thunderbird-7.0.1-r1/work/comm-release/mozilla'
make[1]: *** [default] Error 2
make[1]: Leaving directory `/var/tmp/portage/mail-client/thunderbird-7.0.1-r1/work/comm-release/mozilla'
make: *** [default] Error 2


'emerge --info =mail-client/thunderbird-7.0.1-r1'
Quote:

Portage 2.2.0_alpha76 (default/linux/x86/10.0/desktop/kde, gcc-4.5.3, glibc-2.12.2-r0, 2.6.39-gentoo-r3 i686)
=================================================================
System Settings
=================================================================
System uname: Linux-2.6.39-gentoo-r3-i686-Intel-R-_Pentium-R-_4_CPU_3.00GHz-with-gentoo-2.0.3
Timestamp of tree: Mon, 21 Nov 2011 12:00:01 +0000
app-shells/bash: 4.1_p9
dev-lang/python: 2.7.2-r3, 3.1.4-r3
dev-util/cmake: 2.8.4-r1
dev-util/pkgconfig: 0.26
sys-apps/baselayout: 2.0.3
sys-apps/openrc: 0.8.3-r1
sys-apps/sandbox: 2.5
sys-devel/autoconf: 2.13::<unknown repository>, 2.68
sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils: 2.21.1-r1
sys-devel/gcc: 4.5.3-r1
sys-devel/gcc-config: 1.4.1-r1
sys-devel/libtool: 2.4-r1
sys-devel/make: 3.82-r1
sys-kernel/linux-headers: 2.6.39 (virtual/os-headers)
sys-libs/glibc: 2.12.2
Repositories: gentoo sabayon portage-overlay-for-all-PCs
Installed sets: @system
ACCEPT_KEYWORDS="x86"
ACCEPT_LICENSE="* -@EULA"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-march=pentium4 -O2 -pipe -fomit-frame-pointer -D_FILE_OFFSET_BITS=64"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/xsessions"
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=pentium4 -O2 -pipe -fomit-frame-pointer -D_FILE_OFFSET_BITS=64"
DISTDIR="/mnt/portage/distfiles"
EMERGE_DEFAULT_OPTS="--keep-going"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS=""
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="nl_BE.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -Wl,--sort-common"
LINGUAS="en en_US en_UK en_GB nl"
MAKEOPTS="-j3"
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="/mnt/portage/portage"
PORTDIR_OVERLAY="/var/lib/layman/sabayon /mnt/portage/overlay"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac acpi alsa avahi bash-completion berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus declarative dri dts dv dvd dvdr emboss encode exif fam fat ffmpeg firefox flac fortran gdbm gdu gif glibc-omitfp gtk iconv ieee1394 inotify ipod jpeg kde kipi lcms libnotify lirc mad matroska mdnsresponder-compat mmap mmx mmxext mng modules moznopango mp3 mp4 mpeg ncurses nls nokia nptl nptlonly ntfs ogg opengl openmp pam pango pcre pdf phonon plasma png policykit ppds pppd pulseaudio qt3support qt4 radio readline samba scanner sdl semantic-desktop session smp sndfile spell sse sse2 ssl startup-notification svg sysfs system-sqlite systemd systray tcpd teletext threads thumbnail tiff truetype udev unicode usb v4l vim-syntax vorbis wma x264 x86 xcb xcomposite xinerama xml xorg xscreensaver xulrunner xv xvid zeroconf zlib" ALSA_CARDS="intel8x0 emu10k1 ens1371" 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 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 stage tables krita karbon braindump" CAMERAS="canon 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="evdev virtualbox synaptics" KERNEL="linux" LINGUAS="en en_US en_UK en_GB nl" LIRC_DEVICES="atiusb" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" SANE_BACKENDS="mustek_pp" USERLAND="GNU" VIDEO_CARDS="vesa nv nouveau 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"
Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
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Aquous
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Joined: 08 Jan 2011
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PostPosted: Mon Nov 21, 2011 6:02 pm    Post subject: Reply with quote

You're running out of memory during the build. Add more swap.
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Hu
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PostPosted: Tue Nov 22, 2011 2:52 am    Post subject: Reply with quote

The "We've already been run in this tree" warning appears even if the build succeeds. It is probably not a good sign to have that, given that it explicitly tells you to file a bug.
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javeree
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PostPosted: Tue Nov 22, 2011 9:12 am    Post subject: Reply with quote

@Aquous

Yes, adding swap helped. What made it so clear to you that swap was the culprit ? I have had previously builds going wrong without clear indication of the problem because my workspace on disk was growing too small, but that was one of the things I had checked.

Was it a guess, was it because you had the same problem and are sharing experience, or is there something one can learn from the way the build dies ?

@Hu
You suggest a bug with the gentoo team. Shouldn't that be a bug upstream ? Or is it customary that build problems are first examined by gentoo team and then if they think it is needed sent upstream ?
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Hu
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PostPosted: Wed Nov 23, 2011 3:16 am    Post subject: Reply with quote

javeree wrote:
@Hu
You suggest a bug with the gentoo team. Shouldn't that be a bug upstream ? Or is it customary that build problems are first examined by gentoo team and then if they think it is needed sent upstream ?
The output you provided appears to have been generated by the Gentoo build system. Otherwise, it would not be so nicely isolated as messages that occurred in the src_prepare phase. If I am correct that it is generated by the Gentoo build scripts, then the Gentoo maintainers need to look at it. If I am wrong, then taking it upstream would be more appropriate.
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Aquous
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Joined: 08 Jan 2011
Posts: 700

PostPosted: Wed Nov 23, 2011 8:16 am    Post subject: Reply with quote

javeree wrote:
What made it so clear to you that swap was the culprit ?

Two things:
1) the build was linking libxul.so which is a huge library (and when linking all of it needs to be loaded into RAM)
2) this line:
Code:
collect2: ld terminated with signal 9 [Killed]

IIRC, signal 9 = segmentation fault = memory-related problem

so it looks like the OOM killer got your ld :)
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javeree
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PostPosted: Wed Nov 23, 2011 9:15 am    Post subject: Reply with quote

Thanks for the enlightment. You deserve your 'Guru' status.
It's good to know what kind of info is hidden behind the 'signal' info.
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Gentree
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PostPosted: Sat Nov 26, 2011 8:05 am    Post subject: Reply with quote

Nice detective work Aquous.

Javeree you should probably file a gentoo bug since that original output about being out if it's tree is amazingly unhelpful and confusing.

Clearly the error trapping needs to be improved in this area. It seems to be catching any error at this stage and attibuting it to a specific cause which is not necessarily the correct one.

That thunderbird triggered this is probably mainly coincidence. I would imagine from the diagnostic that any build of a similar size would trigger the same false error message, hence it is a broader problem in portage that should probably get fixed.
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raygun
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PostPosted: Wed Nov 30, 2011 12:33 am    Post subject: Reply with quote

Gentree wrote:
I would imagine from the diagnostic that any build of a similar size would trigger the same false error message


On the other hand, sometimes the error message is reporting exactly what it claims to be: a part of the build process that is inadvertently being run twice.

It's interesting, though, that a Google search on this error message shows it cropping up in various contexts, but all of them from within the past week or so. (This thread, started on Nov 21, is the oldest I found.) This implies a fairly recent change at the root of all these occurrences.
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twalter
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PostPosted: Wed Nov 30, 2011 4:50 pm    Post subject: Not just swap related Reply with quote

FWIW, I have 6Gb allocated to swap and 0% was in use when emerging libsoup-gnome so it's definitely not just OOM killer. There was a circular dependency with libsoup and libsoup-gnome that couldn't resolve itself; I had to emerge it explicitly which never ends well with libraries.

* Should also add I've never seen this message before until recently so I'm wondering if the latest version of portage is the culprit.
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JohnLM
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PostPosted: Thu Dec 01, 2011 10:41 pm    Post subject: Reply with quote

I'm also having this "bug" message on quite a lot of ebuilds
Code:
We've already been run in this tree; you should
avoid this if possible (perhaps by filing a bug)


This is apparently a new thing and I've no idea what does the message mean.
No apparent detrimental effect is seen, and no package build fails. Cryptic...

I've had this both on amd64 and x86 machines, former having gentoo for long time and the latter a fresh install.
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