[ccp4bb] fink update

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: fink update
From: Nathaniel Echols nathaniel {- dot -} echols {- at -} GMAIL {- dot -} COM
Date: 2009-02-11

Next message:
Subject: Postdoc position in neutron protein crystallography
From: Paul Langan langan_paul {- at -} LANL {- dot -} GOV
Date: 2009-02-11

Subject: fink update
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2009-02-11

Dear Friends,
I incorporated 3 new lines in /sw/etc/apt/sources.list file

deb http://sage.ucsc.edu/fink_intel_10.5_only stable main crypto
deb http://sage.ucsc.edu/fink_intel_10.5_only unstable main crypto
deb http://sage.ucsc.edu/fink_intel_10.5_only local main

and then run 'fink selfupdate' and 'fink update-all' I got some error at the end.
See below:

Last login: Wed Feb 11 14:51:20 on ttys006
anand2:~ rajadey$ fink selfupdate
rsync -az -q rsync://msn.wi.us.finkmirrors.net/finkinfo//TIMESTAMP /sw/fink/TIMESTAMP.tmp
I will now run the rsync command to retrieve the latest package descriptions.
rsync -rtz --delete-after --delete -q --include='10.4/' --include='10.4/stable/' --include='10.4/stable/main/' --include='10.4/stable/main/finkinfo/' --include='10.4/stable/main/finkinfo/*/' --include='10.4/stable/main/finkinfo/*' --include='10.4/stable/main/finkinfo/**/*' --include='10.4/' --include='10.4/stable/' --include='10.4/stable/crypto/' --include='10.4/stable/crypto/finkinfo/' --include='10.4/stable/crypto/finkinfo/*/' --include='10.4/stable/crypto/finkinfo/*' --include='10.4/stable/crypto/finkinfo/**/*' --include='10.4/' --include='10.4/unstable/' --include='10.4/unstable/main/' --include='10.4/unstable/main/finkinfo/' --include='10.4/unstable/main/finkinfo/*/' --include='10.4/unstable/main/finkinfo/*' --include='10.4/unstable/main/finkinfo/**/*' --include='10.4/' --include='10.4/unstable/' --include='10.4/unstable/crypto/' --include='10.4/unstable/crypto/finkinfo/' --include='10.4/unstable/crypto/finkinfo/*/'
--include='10.4/unstable/crypto/finkinfo/*' --include='10.4/unstable/crypto/finkinfo/**/*' --include='VERSION' --include='DISTRIBUTION' --include='README' --exclude='**' 'rsync://msn.wi.us.finkmirrors.net/finkinfo' '/sw/fink/'
Downloading the indexes of available packages in the binary distribution.
/sw/bin/apt-get-lockwait -q update
Hit http://sage.ucsc.edu stable/main Packages
Hit http://sage.ucsc.edu stable/main Release
Hit http://sage.ucsc.edu stable/crypto Packages
Hit http://sage.ucsc.edu stable/crypto Release
Hit http://sage.ucsc.edu unstable/main Packages
Hit http://sage.ucsc.edu unstable/main Release
Hit http://sage.ucsc.edu unstable/crypto Packages
Hit http://sage.ucsc.edu unstable/crypto Release
Hit http://sage.ucsc.edu local/main Packages
Hit http://sage.ucsc.edu local/main Release
Hit http://msn.wi.us.finkmirrors.net 10.5/release/main Packages
Hit http://msn.wi.us.finkmirrors.net 10.5/release/main Release
Hit http://msn.wi.us.finkmirrors.net 10.5/release/crypto Packages
Hit http://msn.wi.us.finkmirrors.net 10.5/release/crypto Release
Hit http://msn.wi.us.finkmirrors.net 10.5/current/main Packages
Hit http://msn.wi.us.finkmirrors.net 10.5/current/main Release
Hit http://msn.wi.us.finkmirrors.net 10.5/current/crypto Packages
Hit http://msn.wi.us.finkmirrors.net 10.5/current/crypto Release
Reading Package Lists...
Building Dependency Tree...
Scanning package description files..........
Information about 7797 packages read in 2 seconds.
No packages to install.

The core packages have been updated. You should now update the other packages
using commands like 'fink update-all'.

anand2:~ rajadey$ fink update-all
Information about 7797 packages read in 0 seconds.
The following 22 packages will be installed or updated:
coot coot-shlibs gnome-themes-glossy-p gnome-vfs2-ssl-shlibs gtk2-engines
gtkglarea2 gtkglarea2-shlibs gtkglext1 gtkglext1-shlibs guile18-gtk
guile18-gtk-dev guile18-gtk-shlibs guile18-gui guile18-www libglade2
libglade2-shlibs libgnomecanvas2-dev libgnomecanvas2-shlibs librsvg2-gtk
librsvg2-shlibs pygtk2-gtk-py25 pygtk2-gtk-py25-dev
The following 4 additional packages will be installed:
gtk+2 gtk+2-dev gtk+2-shlibs guile18-lib
Do you want to continue? [Y/n] Y
Reading buildlock packages...
/sw/bin/dpkg-lockwait -i /sw/var/cache/apt/archives/gnome-vfs2-ssl-shlibs_1%3a2.20.1-1_darwin-i386.deb
(Reading database ... 47557 files and directories currently installed.)
Preparing to replace gnome-vfs2-ssl-shlibs 1:2.15.2-2 (using .../gnome-vfs2-ssl-shlibs_1%3a2.20.1-1_darwin-i386.deb) ...
Unpacking replacement gnome-vfs2-ssl-shlibs ...
Setting up gnome-vfs2-ssl-shlibs (2.20.1-1) ...
Reading buildlock packages...
/sw/bin/dpkg-lockwait -i /sw/var/cache/apt/archives/gtk+2-dev_2.14.7-2_darwin-i386.deb /sw/var/cache/apt/archives/gtk+2_2.14.7-2_darwin-i386.deb /sw/var/cache/apt/archives/gtk+2-shlibs_2.14.7-2_darwin-i386.deb
(Reading database ... 47557 files and directories currently installed.)
Preparing to replace gtk+2-dev 2.14.7-2 (using .../gtk+2-dev_2.14.7-2_darwin-i386.deb) ...
Unpacking replacement gtk+2-dev ...
Preparing to replace gtk+2 2.14.7-2 (using .../gtk+2_2.14.7-2_darwin-i386.deb) ...
Unpacking replacement gtk+2 ...
Preparing to replace gtk+2-shlibs 2.14.7-2 (using .../gtk+2-shlibs_2.14.7-2_darwin-i386.deb) ...
Unpacking replacement gtk+2-shlibs ...
Setting up gtk+2-shlibs (2.14.7-2) ...
dyld: Library not loaded: /usr/X11/lib/libXdamage.1.dylib
Referenced from: /sw/bin/gtk-query-immodules-2.0
Reason: Incompatible library version: gtk-query-immodules-2.0 requires version 3.0.0 or later, but libXdamage.1.dylib provides version 2.0.0
/sw/sbin/update-gtk-immodules-2.0: line 15: 74445 Trace/BPT trap gtk-query-immodules-2.0 > $TMPFILE
/sw/bin/dpkg: error processing gtk+2-shlibs (--install):
subprocess post-installation script returned error exit status 133
dpkg: dependency problems prevent configuration of gtk+2-dev:
gtk+2-dev depends on gtk+2-shlibs (= 2.14.7-2); however:
Package gtk+2-shlibs is not configured yet.
/sw/bin/dpkg: error processing gtk+2-dev (--install):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of gtk+2:
gtk+2 depends on gtk+2-shlibs (= 2.14.7-2); however:
Package gtk+2-shlibs is not configured yet.
/sw/bin/dpkg: error processing gtk+2 (--install):
dependency problems - leaving unconfigured
Errors were encountered while processing:
gtk+2-shlibs
gtk+2-dev
gtk+2
### execution of /sw/bin/dpkg-lockwait failed, exit code 1
Failed: can't batch-install packages: /sw/var/cache/apt/archives/gtk+2-dev_2.14.7-2_darwin-i386.deb /sw/var/cache/apt/archives/gtk+2_2.14.7-2_darwin-i386.deb /sw/var/cache/apt/archives/gtk+2-shlibs_2.14.7-2_darwin-i386.deb
anand2:~ rajadey$

Looking forward to hearing any suggestion...
Raja

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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: fink update
From: Nathaniel Echols nathaniel {- dot -} echols {- at -} GMAIL {- dot -} COM
Date: 2009-02-11

Next message:
Subject: Postdoc position in neutron protein crystallography
From: Paul Langan langan_paul {- at -} LANL {- dot -} GOV
Date: 2009-02-11