After upgrade to glpk-4.48 revdep-rebuild wants to reemerge octave due missing libglpk.so.0 (/usr/lib/libglpk.so is not generated by 'ldconfig'). Then 'emerge -v1 octave' hangs just after start at: root@lynx2:/root(32)# ll /usr/lib/libglpk.* lrwxrwxrwx 1 root root 17 Mar 23 20:49 /usr/lib/libglpk.so -> libglpk.so.33.0.0* lrwxrwxrwx 1 root root 17 Mar 23 20:49 /usr/lib/libglpk.so.33 -> libglpk.so.33.0.0* -rwxr-xr-x 1 root root 987480 Mar 23 20:49 /usr/lib/libglpk.so.33.0.0* root@lynx2:/root(33)# qfile -v /usr/lib/libglpk.so.33 sci-mathematics/glpk-4.48 (/usr/lib64/libglpk.so.33) root@lynx2:/root(34)# qlist -Iv ocatave root@lynx2:/root(35)# qlist -Iv octave sci-mathematics/octave-3.6.4 root@lynx2:/root(36)# genlop -t glpk | tail * sci-mathematics/glpk Sun Dec 23 17:14:49 2012 >>> sci-mathematics/glpk-4.47 merge time: 33 seconds. Sat Mar 23 20:49:26 2013 >>> sci-mathematics/glpk-4.48 merge time: 40 seconds. root@lynx2:/root(37)# emerge -v1 octave These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-mathematics/octave-3.6.4 USE="X curl doc fftw glpk gnuplot hdf5 imagemagick opengl postscript qhull qrupdate readline sparse zlib -static-libs" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB >>> Verifying ebuild manifests >>> Emerging (1 of 1) sci-mathematics/octave-3.6.4
root@lynx2:/root(38)# emerge --info Portage 2.1.11.58 (default/linux/amd64/13.0/desktop, gcc-4.7.2, glibc-2.16.0, 3.8.3-gentoo-r1 x86_64) ================================================================= System uname: Linux-3.8.3-gentoo-r1-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T7500_@_2.20GHz-with-gentoo-2.2 KiB Mem: 3972832 total, 291520 free KiB Swap: 8008364 total, 7910528 free Timestamp of tree: Sun, 24 Mar 2013 07:30:01 +0000 ld GNU ld (GNU Binutils) 2.23.1 app-shells/bash: 4.2_p45 dev-java/java-config: 2.1.12-r1 dev-lang/python: 2.7.3-r3, 3.2.3-r2 dev-util/cmake: 2.8.10.2-r1 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.11.8 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.6, 1.12.6, 1.13.1 sys-devel/binutils: 2.23.1 sys-devel/gcc: 4.7.2-r1 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.8 (virtual/os-headers) sys-libs/glibc: 2.16.0 Repositories: gentoo sunrise science stuge sabayon x-portage x-cpan x-g-octave ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-10.3 cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -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 /usr/share/gnupg/qualified.txt /usr/share/polkit-1/actions /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-php5.4/ext-active/ /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5.4/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="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch xattr" FFLAGS="-march=native -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LC_ALL="" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j3" 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/sunrise /var/lib/layman/science /var/lib/layman/stuge /var/lib/layman/sabayon /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 ao apache2 apng applet archive armadillo arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit corba cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx fts3 fuse g3dvl garmin gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glib glpk gml gmp gnome gnome-keyring gnome-print gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile harness hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3 id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jabber jadetex java jbig john jpeg jpeg2k kate kde kdepim kdrive kerberos keymap kpathsea kqemu kvm ladspa lame lapack laptop latex lcms ldap lensfun libffi libkms libnotify libsamplerate lirc live lua lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musepack musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp overview pae pam pango pcre pda pdf perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q32 qemu qhull qt3support qt4 quicktime raw readline reiserfs reports rhythmbox rle romio rpc rrdcgi rrdtool samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite sse sse2 ssl ssse3 startup-notification stlport subtitles subversion sudo suexec svg svm swig szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus thinkpad threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb userlocales utempter v4l vaapi vala vdpau video virt-network virtualbox visio vorbis vpx wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xa xattr xcb xemacs xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" 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 auth_digest authn_anon authn_dbd authn_core 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 logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CURL_SSL="nss" DVB_CARDS="usb-wt220u" 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 synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de fr ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="intel" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
At an other system (impala) 'emerge octave' comes until: ... checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for style of include used by make... GNU checking for x86_64-pc-linux-gnu-gcc... mpicc
Created attachment 343164 [details] /var/tmp/portage/sci-mathematics/octave-3.6.4/temp/build.log at impala
Created attachment 343166 [details] /var/tmp/portage/sci-mathematics/octave-3.6.4/work/octave-3.6.4/config.log
See also Bug 462672 and Bug 463220 !
If I mask >=sys-cluster/openmpi-1.6.4 the issue disappears.
*** Bug 463726 has been marked as a duplicate of this bug. ***
*** Bug 462672 has been marked as a duplicate of this bug. ***
*** Bug 463220 has been marked as a duplicate of this bug. ***
But 'mpicc --version' does not hang, if I call it from the command line. It seems, that is hangs only, if it is called by configure: root@orca:/root(11)# qlist -Iv openmpi sys-cluster/openmpi-1.6.4 root@orca:/root(12)# mpicc --version x86_64-pc-linux-gnu-gcc (Gentoo 4.6.3 p1.11, pie-0.5.2) 4.6.3 Copyright (C) 2011 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. root@orca:/root(13)# type mpicc mpicc is hashed (/usr/bin/mpicc) root@orca:/root(14)# ll /usr/bin/mpicc lrwxrwxrwx 1 root root 12 Mar 25 20:02 /usr/bin/mpicc -> opal_wrapper* root@orca:/root(15)# qfile -v /usr/bin/mpicc sys-cluster/openmpi-1.6.4 (/usr/bin/mpicc) root@orca:/root(16)# qfile -v /usr/bin/opal_wrapper sys-cluster/openmpi-1.6.4 (/usr/bin/opal_wrapper)
Hanging is related to sandbox. Compare running 'sandbox mpicc --version' and 'mpicc --version'.
Sandbox maintainers: Could you try to help? 'mpicc --version' hangs only with sandbox enabled.
*** Bug 463646 has been marked as a duplicate of this bug. ***
*** This bug has been marked as a duplicate of bug 462602 ***
