'emerge -uvN scilab' fails with: root@moose:/usr/local/portage/dev-python/python-bibtex(40)# emerge -uvN scilab These are the packages that would be merged, in order: Calculating dependencies - * Missing digest for '/var/lib/layman/science/sci-mathematics/scilab/scilab-5.3.3.ebuild' ... done! Total: 0 packages, Size of downloads: 0 kB * sci-mathematics/scilab >>> Jobs: 0 of 0 complete Load avg: 0.41, 0.18, 0.11 >>> Auto-cleaning packages... >>> No outdated packages were found on your system. Reproducible: Always root@moose:/usr/local/portage/dev-python/python-bibtex(44)# emerge --info scilab Portage 2.1.10.34 (default/linux/amd64/10.0/desktop, gcc-4.5.3, glibc-2.13-r4, 3.1.0-gentoo-r1 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.1.0-gentoo-r1-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9650_@_3.00GHz-with-gentoo-2.1 Timestamp of tree: Wed, 16 Nov 2011 09:30:01 +0000 app-shells/bash: 4.2_p10 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.2-r3::sage-on-gentoo, 3.2.2 dev-util/cmake: 2.8.6-r3 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.1 sys-apps/openrc: 0.9.4 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-r1 sys-devel/binutils: 2.21.1-r1 sys-devel/gcc: 4.5.3-r1 sys-devel/gcc-config: 1.5-r2 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r3 sys-kernel/linux-headers: 2.6.39 (virtual/os-headers) sys-libs/glibc: 2.13-r4 Repositories: gentoo science x11 arcon qting-edge bicatali zugaina sage-on-gentoo java-overlay sunrise x-portage x-cpan g-octave ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft Oracle-BCLA-JavaSE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf /usr/share/openvpn/easy-rsa /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.3/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="-O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="-march=native -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de fr" MAKEOPTS="-j5" 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="/var/lib/layman/science /var/lib/layman/x11 /var/lib/layman/arcon /var/lib/layman/qting-edge /var/lib/layman/bicatali /var/lib/layman/zugaina /var/lib/layman/sage-on-gentoo /var/lib/layman/java-overlay /var/lib/layman/sunrise /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago garmin gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib glpk gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gudev guile harness hddtemp hdf hdf5 hdri http httpd hvm hwdb iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc lm_sensors lua lzo mad mail maildir mapnik math matroska mkl mmx mmxext mng modules mono moonlight motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy nvidia obex objc ocaml ocr octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4 ssl ssse3 startup-notification stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora threads thunderbird tidy tiff tk tools truetype udev unicode usb userlocales utempter v4l2 vaapi video virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xattr xcb xemacs xext xft xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml zlib zvbi" 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_dbm authn_default authn_file 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 log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="canon" 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" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv nouveau vesa" 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 ================================================================= Package Settings ================================================================= sci-mathematics/scilab-5.3.2 was built with the following: USE="doc fftw gui matio (multilib) nls tk umfpack -hdf5 -xcos" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--no-as-needed"
as a workaround you can create your own cd /var/lib/layman/science/sci-mathematics/scilab/ ebuild scilab-5.3.3.ebuild manifest
I do usually: ebuild scilab-5.3.3.ebuild digest .
Two days later, without creating the digest myself, I tried once more 'emerge -vuDN scilab'. It now fails with: root@moose:/root(25)# emerge -vuDN scilab These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild NS ] gnome-extra/polkit-gnome-0.105 [0.102] 0 kB [0] [ebuild U ] sci-libs/hdf5-1.8.8 [1.8.7] USE="cxx examples fortran mpi szip threads zlib -debug -fortran2003% -static-libs" 5,691 kB [0] [ebuild N ] dev-java/hdf-java-2.7 USE="doc examples szip zlib -hdf -test" 12,900 kB [1] [ebuild U ] sci-mathematics/scilab-5.3.3 [5.3.2] USE="doc fftw gui matio nls tk umfpack xcos* -hdf5" 46,146 kB [2=>1] [ebuild U ] dev-vcs/git-1.7.8_rc3 [1.7.8_rc1-r1] USE="blksha1 cgi curl doc emacs gtk iconv perl python subversion threads tk webdav -cvs (-ppcsha1) -xinetd" 5,595 kB [0] [ebuild R ] dev-libs/libusb-0.1.12-r7 USE="cxx%* doc -debug -static-libs (-nocxx%)" 0 kB [0] Total: 6 packages (3 upgrades, 1 new, 1 in new slot, 1 reinstall), Size of downloads: 70,331 kB Portage tree and overlays: [0] /usr/portage [1] /var/lib/layman/science [2] /usr/local/portage >>> Verifying ebuild manifests !!! A file listed in the Manifest could not be found: /var/lib/layman/science/sci-mathematics/scilab/files/bug_9268.diff root@moose:/root(26)# cd /var/lib/layman/science/sci-mathematics/scilab
If I create a new digest, 'emerge -vuDN scilab' fails with: ... >>> Emerging (1 of 2) sci-mathematics/scilab-5.3.3 from science >>> Failed to emerge sci-mathematics/scilab-5.3.3, Log file: >>> '/var/tmp/portage/sci-mathematics/scilab-5.3.3/temp/build.log' >>> Jobs: 0 of 2 complete, 1 failed Load avg: 1.26, 0.69, 0.40 * Package: sci-mathematics/scilab-5.3.3 * Repository: science * USE: amd64 doc elibc_glibc fftw gui kernel_linux matio multilib nls tk umfpack userland_GNU xcos * FEATURES: sandbox * Checking for at least 512 mebibytes RAM ... [ ok ] >>> Unpacking source... >>> Unpacking scilab-5.3.3-src.tar.gz to /var/tmp/portage/sci-mathematics/scilab-5.3.3/work >>> Source unpacked in /var/tmp/portage/sci-mathematics/scilab-5.3.3/work >>> Preparing source in /var/tmp/portage/sci-mathematics/scilab-5.3.3/work/scilab-5.3.3 ... * Applying java-heap-5.3.3.patch ... [ ok ] * Applying scilab-5.3.3-scilib-fix.patch ... [ ok ] * Cannot find $EPATCH_SOURCE! Value for $EPATCH_SOURCE is: * * /var/lib/layman/science/sci-mathematics/scilab/files/bug_9268.diff * ( bug_9268.diff ) * ERROR: sci-mathemati/var/lib/layman/science/sci-mathematics/scilab/files/cs/scilab-5.3.3 failed (prepare phase): It seems that the file /var/lib/layman/science/sci-mathematics/scilab/files/bug_9268.diff is really necessary. I do not have it: root@moose:/var/lib/layman/science/sci-mathematics/scilab(33)# ll files/ total 28 -rw-r--r-- 1 root root 1425 Nov 16 10:40 disablebuildhelp.patch -rw-r--r-- 1 root root 562 Nov 16 10:40 java-heap-5.3.3.patch -rw-r--r-- 1 root root 746 Sep 20 09:49 scilab-5.3.2-allow-hdf-1.8.7.patch -rw-r--r-- 1 root root 368 Jun 29 14:18 scilab-5.3.2-scilib-fix.patch -rw-r--r-- 1 root root 746 Nov 16 10:40 scilab-5.3.3-allow-hdf-1.8.7.patch -rw-r--r-- 1 root root 368 Nov 16 10:40 scilab-5.3.3-scilib-fix.patch -rw-r--r-- 1 root root 432 Sep 20 09:49 scilab.xml
Neither 'layman -S' nor 'layman -s science' did add the bug_9268.diff to the /var/lib/layman/science/sci-mathematics/scilab/files directory. Only 'layman -d science; layman -a science' created the missing files. It seems that something with layman is out of order. But also with this fresh installed overlay 'emerge scilab' fails, now with "ACCESS VIOLATION": --------------------------- ACCESS VIOLATION SUMMARY --------------------------- LOG FILE "/var/log/sandbox/sandbox-28064.log" VERSION 1.0 FORMAT: F - Function called FORMAT: S - Access Status FORMAT: P - Path as passed to function FORMAT: A - Absolute Path (not canonical) FORMAT: R - Canonical Path FORMAT: C - Command Line F: open_wr S: deny P: /proc/self/coredump_filter A: /proc/self/coredump_filter R: /proc/28998/coredump_filter C: /usr/lib64/icedtea7/bin/javac -g conftest.java F: open_wr S: deny P: /proc/self/coredump_filter A: /proc/self/coredump_filter R: /proc/29016/coredump_filter C: /usr/lib64/icedtea7/bin/javac -g conftest.java F: open_wr S: deny P: /proc/self/coredump_filter A: /proc/self/coredump_filter R: /proc/29033/coredump_filter C: /usr/lib64/icedtea7/bin/javac -g conftest.java ... on the first system, with: --------------------------- ACCESS VIOLATION SUMMARY --------------------------- LOG FILE "/var/log/sandbox/sandbox-22430.log" VERSION 1.0 FORMAT: F - Function called FORMAT: S - Access Status FORMAT: P - Path as passed to function FORMAT: A - Absolute Path (not canonical) FORMAT: R - Canonical Path FORMAT: C - Command Line F: mkdir S: deny P: /root/.java A: /root/.java R: /root/.java C: /usr/lib64/icedtea7/jre/bin/java -classpath /var/tmp/portage_standard/dev-java/jlatexmath-0.9.4/work/jlatexmath-0.9.4/examples/Macros:/var/tmp/portage_standard/dev-java/jlatexmath-0.9.4/work/jlatexmath-0.9.4/examples/Macros/Foo.jar:/var/tmp/portage_standard/dev-java/jlatexmath-0.9.4/work/jlatexmath-0.9.4/dist/jlatexmath-0.9.4.jar Main F: mkdir S: deny P: /root/.java A: /root/.java R: /root/.java C: /usr/lib64/icedtea7/jre/bin/java -classpath /var/tmp/portage_standard/dev-java/jlatexmath-0.9.4/work/jlatexmath-0.9.4/examples/Macros:/var/tmp/portage_standard/dev-java/jlatexmath-0.9.4/work/jlatexmath-0.9.4/examples/Macros/Foo.jar:/var/tmp/portage_standard/dev-java/jlatexmath-0.9.4/work/jlatexmath-0.9.4/dist/jlatexmath-0.9.4.jar Main F: mkdir S: deny P: /root/.java A: /root/.java R: /root/.java C: /usr/lib64/icedtea7/jre/bin/java -classpath /var/tmp/portage_standard/dev-java/jlatexmath-0.9.4/work/jlatexmath-0.9.4/examples/Basic:/var/tmp/portage_standard/dev-java/jlatexmath-0.9.4/work/jlatexmath-0.9.4/dist/jlatexmath-0.9.4.jar Main F: mkdir S: deny P: /root/.java A: /root/.java R: /root/.java C: /usr/lib64/icedtea7/jre/bin/java -classpath /var/tmp/portage_standard/dev-java/jlatexmath-0.9.4/work/jlatexmath-0.9.4/examples/Basic:/var/tmp/portage_standard/dev-java/jlatexmath-0.9.4/work/jlatexmath-0.9.4/dist/jlatexmath-0.9.4.jar Main on the second system.
