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Bug 373367 - [science overlay] sci-chemistry/jmol-12.0.45-r1 fails to emerge due to missing digest
Summary: [science overlay] sci-chemistry/jmol-12.0.45-r1 fails to emerge due to missin...
Status: RESOLVED OBSOLETE
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2011-06-28 16:02 UTC by Juergen Rose
Modified: 2012-06-01 00:26 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


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Description Juergen Rose 2011-06-28 16:02:11 UTC
The mol-12.0.45-r1.ebuild of the science overlay is not executed: 

rose@lynx:/home/rose(16)$ emerge -pvD jmol  

These are the packages that would be merged, in order:

Calculating dependencies / * Missing digest for '/var/lib/layman/science/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild'
... done!
[ebuild   R    ] sci-chemistry/jmol-12.0.45  USE="-client-only -vhosts" 0 kB

Total: 1 package (1 reinstall), Size of downloads: 0 kB
Comment 1 Juergen Rose 2011-06-28 16:34:48 UTC
If I create the digest, 'emerge -v jmol' fails as jmol-12.0.45, see https://bugs.gentoo.org/show_bug.cgi?id=373359:
...
 * Running /usr/sbin/webapp-config -U -h localhost -u root -d /jmol jmol 12.0.45-r1
Traceback (most recent call last):
  File "/usr/sbin/webapp-config-2.7", line 44, in <module>
    main()
  File "/usr/sbin/webapp-config-2.7", line 41, in main
    config.run()
  File "/usr/lib64/python2.7/site-packages/WebappConfig/config.py", line 1335, in run
    old['WEB_CATEGORY'] + old['WEB_PN']):
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'

 * Running /usr/sbin/webapp-cleaner -p -C jmol
 * Package name must be in the form CATEGORY/PN
 * ERROR: sci-chemistry/jmol-12.0.45-r1 failed (postinst phase):
Comment 2 Justin Lecher (RETIRED) gentoo-dev 2011-07-09 11:59:48 UTC
should be fixed now. Please restetst and close bug.
Comment 3 Juergen Rose 2011-07-13 10:11:17 UTC
'emerge -v1 jmol' still fails for me:

root@lynx:/root(24)# emerge -pv1 jmol

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild   R    ] sci-chemistry/jmol-12.0.45-r1  USE="-client-only -vhosts" 0 kB [1]

Total: 1 package (1 reinstall), Size of downloads: 0 kB
Portage tree and overlays:
 [0] /usr/portage
 [1] /var/lib/layman/science


root@lynx:/root(25)# emerge -v1 jmol

These are the packages that would be merged, in order:
...

--- replaced dir /usr
>>> Regenerating /etc/ld.so.cache...
>>> Original instance of package unmerged safely.

 * vhosts USE flag not set - auto-installing using webapp-config
 * This is an upgrade
 * jmol-11.6 is already installed - upgrading
 * Running /usr/sbin/webapp-config -U -h localhost -u root -d /jmol jmol 12.0.45-r1
Traceback (most recent call last):
  File "/usr/sbin/webapp-config-2.7", line 44, in <module>
    main()
  File "/usr/sbin/webapp-config-2.7", line 41, in main
    config.run()
  File "/usr/lib64/python2.7/site-packages/WebappConfig/config.py", line 1335, in run
    old['WEB_CATEGORY'] + old['WEB_PN']):
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'

 * Running /usr/sbin/webapp-cleaner -p -C jmol
 * Package name must be in the form CATEGORY/PN
 * ERROR: sci-chemistry/jmol-12.0.45-r1 failed (postinst phase):
 *   webapp_pkg_postinst failed
Comment 4 Juergen Rose 2011-07-13 10:12:09 UTC
root@lynx:/root(26)# emerge --info =sci-chemistry/jmol-12.0.45-r1
Portage 2.1.10.5 (default/linux/amd64/10.0/desktop, gcc-4.5.2, glibc-2.13-r3, 2.6.39.3 x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-2.6.39.3-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-2.0.3
Timestamp of tree: Wed, 13 Jul 2011 05:30:01 +0000
app-shells/bash:          4.2_p10
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2, 3.2
dev-util/cmake:           2.8.5
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, 2.68
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.1-r1
sys-devel/binutils:       2.21.1
sys-devel/gcc:            4.5.2
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 2.6.38 (virtual/os-headers)
sys-libs/glibc:           2.13-r3
Repositories: gentoo lordvan x11 java-overlay sunrise arcon qting-edge ibormuth bicatali proaudio science local x-cpan g-octave
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft"
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/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.2/ext-active/ /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.2/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.2/ext-active/ /etc/php/cli-php5.3/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=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-march=native -O2 -pipe"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo ftp://ftp.easynet.nl/mirror/gentoo/ "
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de fr"
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="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/lordvan /var/lib/layman/x11 /var/lib/layman/java-overlay /var/lib/layman/sunrise /var/lib/layman/arcon /var/lib/layman/qting-edge /var/lib/layman/ibormuth /var/lib/layman/bicatali /var/lib/layman/pro-audio /var/lib/layman/science /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 audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding bzip2 cairo cardbus 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 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 laptop latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc 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 obex objc ocaml 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 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 thinkpad threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 video virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xattr xcb xemacs xext 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="braindump flow karbon kexi kpresenter krita tables words" CAMERAS="canon" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" 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" 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 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm 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-chemistry/jmol-12.0.45-r1 was built with the following:
USE="(multilib) -client-only -vhosts"



root@lynx:/root(27)# emerge -pqv =sci-chemistry/jmol-12.0.45-r1
[ebuild   R   ] sci-chemistry/jmol-12.0.45-r1  USE="-client-only -vhosts"
Comment 5 François Bissey 2011-07-13 13:01:57 UTC
It looks like what you see now is really bug #355295 Juergen. Someone posted some kind of work around in that other bug.
Comment 6 Jeffrey Gardner (RETIRED) gentoo-dev 2012-06-01 00:26:00 UTC
Newer version in portage does not have this problem.