>>> Emerging (2 of 22) sci-biology/vienna-rna-1.8.5 * ViennaRNA-1.8.5.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking ViennaRNA-1.8.5.tar.gz to /var/tmp/portage/sci-biology/vienna-rna-1.8.5/work >>> Source unpacked in /var/tmp/portage/sci-biology/vienna-rna-1.8.5/work >>> Preparing source in /var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5 ... * Applying vienna-rna-1.6.5-c-fixes.patch ... [ ok ] * Applying vienna-rna-1.7.2-LDFLAGS.patch ... [ ok ] * Applying vienna-rna-1.8.3-gcc4.3.patch ... [ ok ] * Applying vienna-rna-1.8.3-disable-gd.patch ... [ ok ] * Applying vienna-rna-1.8.4-jobserver-fix.patch ... [ ok ] * Applying vienna-rna-1.8.4-bindir.patch ... [ ok ] * Applying vienna-rna-1.8.4-overflows.patch ... [ ok ] * Applying vienna-rna-1.8.4-implicits.patch ... [ ok ] ^C Exiting on signal 2 sandbox:stop caught signal 2 in pid 26731 Hangs there for >30 minutes and doesn't respond properly to ctrl-c Portage 2.2.0_alpha110 (default/linux/amd64/10.0, gcc-4.5.3, glibc-2.15-r2, 3.4.0-vs2.3.3.4 x86_64) ================================================================= System uname: Linux-3.4.0-vs2.3.3.4-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.1 Timestamp of tree: Unknown app-shells/bash: 4.2_p29 dev-lang/python: 2.7.3-r2, 3.2.3-r1 dev-util/cmake: 2.8.8-r2 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.1-r1 sys-apps/openrc: 0.10.3 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.11.5, 1.12.1 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.5.3-r2, 4.6.3 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r3 sys-kernel/linux-headers: 3.4 (virtual/os-headers) sys-libs/glibc: 2.15-r2 Repositories: gentoo Installed sets: ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/qpsmtpd/plugins /usr/share/themes/oxygen-gtk/gtk-2.0 /var/lib/hsqldb /var/spool/torque" CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles news parallel-fetch parse-eapi-ebuild-head preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_GB.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" 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" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X acl amd64 berkdb bzip2 cli cracklib crypt cups cxx dri fontconfig fortran gdbm gpm iconv ipv6 ithreads jpeg mmx modules mudflap multilib ncurses nls nptl openmp pam pcre perl png pppd readline session sse sse2 ssl tcpd tiff truetype unicode xorg 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 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" 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 evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga neomagic nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" 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, LINGUAS, MAKEOPTS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Could that be again a hanger in eatoreconf, similar to your aclocal problems?
could you get us the output of a debug run?
(In reply to comment #2) > could you get us the output of a debug run? What do you mean by debug run? here's an snipplet of htop 11818 root 20 0 8292 2972 1868 S 0.0 0.4 0:01.05 │ ├─ -/bin/zsh 12473 root 20 0 55132 46600 4052 S 0.0 6.1 0:55.75 │ │ └─ /usr/bin/python2.7 /usr/bin/emerge -av1 =sci-biology/vienna-rna-1.8.5 17462 portage 20 0 1988 608 476 S 0.0 0.1 0:00.03 │ │ └─ [sci-biology/vienna-rna-1.8.5] sandbox "/usr/lib/portage/bin/ebuild.sh" prepare 17465 portage 20 0 7440 3436 1612 S 0.0 0.4 0:00.85 │ │ └─ /bin/bash /usr/lib/portage/bin/ebuild.sh prepare 17482 portage 20 0 7572 2888 956 S 0.0 0.4 0:00.46 │ │ └─ /bin/bash /usr/lib/portage/bin/ebuild.sh prepare 17769 portage 20 0 7572 2624 688 S 0.0 0.3 0:00.00 │ │ └─ /bin/bash /usr/lib/portage/bin/ebuild.sh prepare
the base_src_prepare completes, theres an "user patches" in the ebuild-debug.log. The two lines of sed are executed, and they match, but there's no evidence of starting into eautoreconf. Portage 2.1.10.65 (default/linux/powerpc/ppc32/10.0/developer, gcc-4.5.3, glibc-2.14.1-r3, 3.1.6-gentoo-fand.0 ppc) ================================================================= System uname: Linux-3.1.6-gentoo-fand.0-ppc-7400,_altivec_supported-with-gentoo-2.1 Timestamp of tree: Wed, 13 Jun 2012 08:00:01 +0000 ccache version 3.1.7 [disabled] app-shells/bash: 4.2_p20 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.5.4-r4, 2.6.8, 2.7.3-r1, 3.1.5, 3.2.3 dev-util/ccache: 3.1.7 dev-util/cmake: 2.8.7-r5 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.1-r1 sys-apps/openrc: 0.9.8.4 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 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-r2 sys-devel/gcc-config: 1.6 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r1 sys-kernel/linux-headers: 3.1 (virtual/os-headers) sys-libs/glibc: 2.14.1-r3 Repositories: gentoo xmw ACCEPT_KEYWORDS="ppc" ACCEPT_LICENSE="* -@EULA" CBUILD="powerpc-unknown-linux-gnu" CFLAGS="-O2 -mcpu=7400 -maltivec -mabi=altivec -mtune=powerpc -fno-strict-aliasing -pipe" CHOST="powerpc-unknown-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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 -mcpu=7400 -maltivec -mabi=altivec -mtune=powerpc -fno-strict-aliasing -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles multilib-strict news parallel-fetch parse-eapi-ebuild-head protect-owned sandbox sfperms sign strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox" FFLAGS="" GENTOO_MIRRORS="http://lore.xmw.de/gentoo" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de en en_US en_GB" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" 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" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/xmw" SYNC="rsync://lore.xmw.de/gentoo-portage/" USE="X a52 aac acl alsa altivec apache2 bash-completion berkdb bluetooth bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gif git gpm gtk iconv ipv6 jbig jpeg jpeg2k lcms libnotify mad mng modules mp3 mp4 mpeg mudflap ncurses nls nptl ogg opengl openmp pam pango pcre pdf perl png policykit ppc ppds pppd python qt3support qt4 readline sdl session snmp spell sqlite ssl startup-notification subversion svg tcl tcpd threads tiff tk truetype udev udisks unicode upower usb vim-syntax vorbis wxwidgets xcb xml xorg xulrunner xv xvid zlib zsh-completion" 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 sheets stage tables krita karbon braindump" 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="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de en en_US en_GB" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="r128 fbdev" 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" USE_PYTHON="2.5 2.6 2.7 3.1 3.2" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, MAKEOPTS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
(In reply to comment #3) > (In reply to comment #2) > > could you get us the output of a debug run? > > What do you mean by debug run? > ebuild --debug vienna-rna-1.8.5.ebuild prepare
