'emerge shogun' hangs during configuring at: ... * Applying shogun-1.1.0-respect-ldflags.patch ... [ ok ] * Applying shogun-1.1.0-test-readline.patch ... [ ok ] * Applying shogun-1.1.0-as-needed.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/shogun-2.0.0/work/shogun-2.0.0/src ... Running configure for SHOGUN version 2.0.0 Checking for C Compiler ... ^C root@caiman:/root(39)# gcc -v Using built-in specs. COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.7.2/gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/4.7.2/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /var/tmp/portage/sys-devel/gcc-4.7.2-r1/work/gcc-4.7.2/configure --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.7.2 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.7.2 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.7.2/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.7.2/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/include/g++-v4 --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --disable-altivec --disable-fixed-point --without-ppl --without-cloog --enable-lto --enable-nls --without-included-gettext --with-system-zlib --enable-obsolete --disable-werror --enable-secureplt --enable-multilib --with-multilib-list=m32,m64 --enable-libmudflap --disable-libssp --enable-libgomp --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.7.2/python --enable-checking=release --enable-java-awt=gtk --enable-libstdcxx-time --enable-languages=c,c++,java,objc,fortran --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-targets=all --with-bugurl=http://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.7.2-r1 p1.5, pie-0.5.5' Thread model: posix gcc version 4.7.2 (Gentoo 4.7.2-r1 p1.5, pie-0.5.5) root@caiman:/root(40)# gcc-config -l [1] x86_64-pc-linux-gnu-4.7.2 * This bugs looks similar to bug Bug 462990 and Bug 462672. root@caiman:/root(41)# emerge --info =sci-libs/shogun-2.0.0 Portage 2.1.11.58 (default/linux/amd64/13.0, gcc-4.7.2, glibc-2.16.0, 3.8.2-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.8.2-gentoo-x86_64-AMD_Phenom-tm-_II_X6_1090T_Processor-with-gentoo-2.2 KiB Mem: 16178872 total, 3907524 free KiB Swap: 100663280 total, 100639940 free Timestamp of tree: Mon, 25 Mar 2013 03:00:02 +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 x11 bicatali science sunrise lisp 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-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=amdfam10 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /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/cgi-php5.4/ext-active/ /etc/php/cli-php5.4/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=amdfam10 -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="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j7" 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/x11 /var/lib/layman/bicatali /var/lib/layman/science /var/lib/layman/sunrise /var/lib/layman/lisp /var/lib/layman/sabayon /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowext 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 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 ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx fts3 fuse g3dvl 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 java6 jbig john jpeg jpeg2k kate kdepim kdrive kerberos keymap kpathsea kqemu kvm ladspa lame lapack latex lcms ldap lensfun libffi libkms libnotify libsamplerate live lm_sensors 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 networkmanager nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp overview pam 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 q16 q32 qemu qhull qt3support qt4 quicktime raw readline reiserfs reports rhythmbox rle romio rpc rrdcgi rrdtool sage 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 sse4a ssl stlport subtitles subversion sudo suexec svg svm swig szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus threads thunderbird tidy tiff tk toolbar tools truetype udev udisks unicode usb userlocales utempter v4l vaapi vala vdpau video virt-network virtualbox visio vorbis vpx wav webdav webdav-serf webkit 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="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 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" DRACUT_MODULES="caps lvm mdraid 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" 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="radeon" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON ================================================================= Package Settings ================================================================= sci-libs/shogun-2.0.0 was built with the following: USE="R arpack bzip2 doc examples glpk hdf5 java lapack lua lzo mono octave python readline smp xml -eigen -gzip -json -lpsolve -lzma -nlopt -ruby -snappy -static-libs -superlu -test" LDFLAGS="-Wl,-O1 -Wl,--as-needed -pthread" Reproducible: Always
Created attachment 343232 [details] /var/tmp/portage/sci-libs/shogun-2.0.0/temp/build.log
You may want to do an strace here to see at which call it froze.
In terminal 1 did: root@caiman:/root(2)# strace -f -o strace_emerge_shogun.log emerge -v1 shogun These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-libs/shogun-2.0.0 USE="R arpack bzip2 doc examples glpk hdf5 java lapack lua lzo mono octave python readline smp xml -eigen -gzip -json -lpsolve -lzma -nlopt -ruby -snappy -static-libs -superlu {-test}" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB >>> Verifying ebuild manifests >>> Emerging (1 of 1) sci-libs/shogun-2.0.0 * shogun-2.0.0.tar.bz2 SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] * shogun-data-0.4.tar.bz2 SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] * Using: sun-jdk-1.6 >>> Unpacking source... >>> Unpacking shogun-2.0.0.tar.bz2 to /var/tmp/portage/sci-libs/shogun-2.0.0/work >>> Unpacking shogun-data-0.4.tar.bz2 to /var/tmp/portage/sci-libs/shogun-2.0.0/work >>> Source unpacked in /var/tmp/portage/sci-libs/shogun-2.0.0/work >>> Preparing source in /var/tmp/portage/sci-libs/shogun-2.0.0/work/shogun-2.0.0/src ... * Applying shogun-1.1.0-respect-ldflags.patch ... [ ok ] * Applying shogun-1.1.0-test-readline.patch ... [ ok ] * Applying shogun-1.1.0-as-needed.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/shogun-2.0.0/work/shogun-2.0.0/src ... Running configure for SHOGUN version 2.0.0 Checking for C Compiler ... In the next terminal I did 'tail -f strace_emerge_shogun.log' I comes to: 30518 mprotect(0x603000, 4096, PROT_READ) = 0 30518 mprotect(0x7f22d0c9e000, 4096, PROT_READ) = 0 30518 munmap(0x7f22d0c25000, 490147) = 0 30518 set_tid_address(0x7f22d0c1f9d0) = 30518 30518 set_robust_list(0x7f22d0c1f9e0, 24) = 0 30518 futex(0x7fff6a79d8d8, FUTEX_WAKE_PRIVATE, 1) = 0 30518 futex(0x7fff6a79d8d8, FUTEX_WAIT_BITSET_PRIVATE|FUTEX_CLOCK_REALTIME, 1, NULL, 7f22d0c1f700) = -1 EAGAIN (Resource temporarily unavailable) 30518 rt_sigaction(SIGRTMIN, {0x7f22d03d57e0, [], SA_RESTORER|SA_SIGINFO, 0x7f22d03dee50}, NULL, 8) = 0 30518 rt_sigaction(SIGRT_1, {0x7f22d03d5860, [], SA_RESTORER|SA_RESTART|SA_SIGINFO, 0x7f22d03dee50}, NULL, 8) = 0 30518 rt_sigprocmask(SIG_UNBLOCK, [RTMIN RT_1], NULL, 8) = 0 30518 getrlimit(RLIMIT_STACK, {rlim_cur=8192*1024, rlim_max=RLIM64_INFINITY}) = 0 30518 stat("/proc/self/status", {st_mode=S_IFREG|0444, st_size=0, ...}) = 0 30518 futex(0x7f22d00200c8, FUTEX_WAKE_PRIVATE, 2147483647) = 0 30518 futex(0x7f22d0a7a340, FUTEX_WAIT_PRIVATE, 2, NULL Then I killed in the first terminal the strace process: Checking for C Compiler ... ^C Exiting on signal 2 sandbox:stop caught signal 2 in pid 30353 sandbox:stop signal already caught and busy still cleaning up! /usr/portage_caiman/sci-libs/shogun/shogun-2.0.0.ebuild: src_configure aborted; exiting. !!! When you file a bug report, please include the following information: GENTOO_VM=sun-jdk-1.6 CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.6.0.43" JAVACFLAGS="-source 1.5 -target 1.5" COMPILER="" and of course, the output of emerge --info root@caiman:/root(3)# The resulting bzip2ed strace.log file has a size of 6 MB
You can find strace_emerge_shogun.log.bz2 at http://141.89.194.24/~rose/strace_emerge_shogun.log.bz2 .
Nobody else has this issue? For me 'revdep-rebuild -- --keep-going' hangs on all of my systems (12 PCs) due to this bug and I have manually to kill the corresponding processes.
I cannot reproduce this here. As you reported numerous other reports with compiler error I would think there is a problem on your systems.
(In reply to comment #6) > I cannot reproduce this here. As you reported numerous other reports with > compiler error I would think there is a problem on your systems. So far as I see, there are two other reports Bug 462990 and Bug 462672, where the issue seems to be compiler related, and Bug 462672 was not started by me. I tried to switch back to gcc-4.6.3, reemerged cmake, but it did not help. The issue happens for me with gcc-4.6.3 and gcc-4.7.2 on 32- and 64-Bit systems, with Intel and AMD processors and corresponding CFLAGS: CFLAGS="-march=amdfam10 -O2 -pipe" CFLAGS="-march=native -O2 -pipe" CFLAGS="-O2 -march=pentium4 -fomit-frame-pointer" If I go to /var/tmp/portage/sci-libs/shogun-2.0.0/work/shogun-2.0.0/src and run manually './configure --disable-cpudetection --destdir="/var/tmp/portage/sci-libs/shogun-2.0.0/image/" --prefix="/usr" --mandir="/usr/share/man" --libdir="/usr/lib64" --cc="mpicc" --cxx="mpicxx" --target="" --interfaces=java_modular,lua_modular,octave_modular,python_modular,csharp_modular,r_modular --enable-arpack --enable-bzip2 --enable-doxygen --disable-eigen3 --enable-glpk --disable-gzip --enable-hdf5 --disable-json --enable-lapack --disable-lpsolve --disable-lzma --enable-lzo --disable-nlopt --enable-readline --enable-hmm-parallel --disable-snappy --disable-static --disable-superlu --enable-xml', I do not have serious problems: root@impala:/var/tmp/portage/sci-libs/shogun-2.0.0/work/shogun-2.0.0/src(27)# ./configure --disable-cpudetection --destdir="/var/tmp/portage/sci-libs/shogun-2.0.0/image/" --prefix="/usr" --mandir="/usr/share/man" --libdir="/usr/lib64" --cc="mpicc" --cxx="mpicxx" --target="" --interfaces=java_modular,lua_modular,octave_modular,python_modular,csharp_modular,r_modular --enable-arpack --enable-bzip2 --enable-doxygen --disable-eigen3 --enable-glpk --disable-gzip --enable-hdf5 --disable-json --enable-lapack --disable-lpsolve --disable-lzma --enable-lzo --disable-nlopt --enable-readline --enable-hmm-parallel --disable-snappy --disable-static --disable-superlu --enable-xml Running configure for SHOGUN version 2.0.0 Checking for C Compiler ... gcc 4.7.2, ok Checking for C Compiler flags ... -fPIC -g Checking for C++ Compiler ... gcc 4.7.2, ok Checking for C++ Compiler flags ... -fPIC -g Detected Operating System: Linux Detected Host Architecture: x86_64 Checking for makedepend ... gcc -MM ... Checking for Ruby NArray ... not detected Checking for Lua ... Package lua5.1 was not found in the pkg-config search path. Perhaps you should add the directory containing `lua5.1.pc' to the PKG_CONFIG_PATH environment variable No package 'lua5.1' found 5.1.5 ... SHOGUN was configured for libshogun and the following interfaces: cmdline_static python_static octave_static octave_modular python_modular java_modular csharp_modular lua_modular interface(s) with the following configure options It will support the following data types bool,char,uint8_t,uint16_t,int32_t,int64_t,uint64_t,float32_t,float64_t. type "make" now to compile root@impala:/var/tmp/portage/sci-libs/shogun-2.0.0/work/shogun-2.0.0/src(28)# echo $? 0 What could I else check?
did you do any changes to your configuration lately? try to select again the profile.
(In reply to comment #8) > did you do any changes to your configuration lately? try to select again the > profile. Do you mean gcc-profile?
I mean the gentoo profile > eselect profile
root@impala:/var/tmp/portage/sci-libs/shogun-2.0.0/work/shogun-2.0.0/src(53)# eselect profile list Available profile symlink targets: [1] default/linux/amd64/13.0 * [2] default/linux/amd64/13.0/selinux [3] default/linux/amd64/13.0/desktop ... root@impala:/var/tmp/portage/sci-libs/shogun-2.0.0/work/shogun-2.0.0/src(54)# eselect profile set 1 root@impala:/var/tmp/portage/sci-libs/shogun-2.0.0/work/shogun-2.0.0/src(55)# eselect profile list Available profile symlink targets: [1] default/linux/amd64/13.0 * [2] default/linux/amd64/13.0/selinux ... root@impala:/var/tmp/portage/sci-libs/shogun-2.0.0/work/shogun-2.0.0/src(56) exit I open a new terminal window and run again 'emerge -v1 shogun'. It is now running from local overlay, because I add one echo statement to the ebuild to see the options of configure: root@impala:/root(2)# emerge -v1 shogun These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-libs/shogun-2.0.0::x-portage [2.0.0::gentoo] USE="R arpack bzip2 doc examples glpk hdf5 java lapack lua lzo mono octave python readline smp xml -eigen -gzip -json -lpsolve -lzma -nlopt -ruby -snappy -static-libs -superlu {-test}" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB >>> Verifying ebuild manifests >>> Emerging (1 of 1) sci-libs/shogun-2.0.0 from x-portage * shogun-2.0.0.tar.bz2 SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] * shogun-data-0.4.tar.bz2 SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] * Using: sun-jdk-1.6 >>> Unpacking source... >>> Unpacking shogun-2.0.0.tar.bz2 to /var/tmp/portage/sci-libs/shogun-2.0.0/work >>> Unpacking shogun-data-0.4.tar.bz2 to /var/tmp/portage/sci-libs/shogun-2.0.0/work >>> Source unpacked in /var/tmp/portage/sci-libs/shogun-2.0.0/work >>> Preparing source in /var/tmp/portage/sci-libs/shogun-2.0.0/work/shogun-2.0.0/src ... * Applying shogun-1.1.0-respect-ldflags.patch ... [ ok ] * Applying shogun-1.1.0-test-readline.patch ... [ ok ] * Applying shogun-1.1.0-as-needed.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/shogun-2.0.0/work/shogun-2.0.0/src ... before './configure --disable-cpudetection --destdir="/var/tmp/portage/sci-libs/shogun-2.0.0/image/" --prefix="/usr" --mandir="/usr/share/man" --libdir="/usr/lib64" --cc="mpicc" --cxx="mpicxx" --target="" --interfaces=java_modular,lua_modular,octave_modular,python_modular,csharp_modular,r_modular --enable-arpack --enable-bzip2 --enable-doxygen --disable-eigen3 --enable-glpk --disable-gzip --enable-hdf5 --disable-json --enable-lapack --disable-lpsolve --disable-lzma --enable-lzo --disable-nlopt --enable-readline --enable-hmm-parallel --disable-snappy --disable-static --disable-superlu --enable-xml' Running configure for SHOGUN version 2.0.0 Checking for C Compiler ... ^C Exiting on signal 2 sandbox:stop caught signal 2 in pid 28385 sandbox:stop signal already caught and busy still cleaning up! /usr/local/portage/sci-libs/shogun/shogun-2.0.0.ebuild: src_configure aborted; exiting. !!! When you file a bug report, please include the following information: GENTOO_VM=sun-jdk-1.6 CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.6.0.43" JAVACFLAGS="-source 1.5 -target 1.5" COMPILER="" and of course, the output of emerge --info It is hanging at the same point.
Created attachment 343405 [details] the output of 'env | sort' Is something wrong with my environment?
I can't spot anything.
If I mask >=sys-cluster/openmpi-1.6.4, I can emerge shogun without problems. Justin, which version of openmpi do you use?
I am using mpich2
*** This bug has been marked as a duplicate of bug 462990 ***
