W. Augustine Dunn III wrote:
> Firstly thanks your your help!
>
> It doesn't *look* like you should still have a Fink emboss executable.
> What do you get from "which emboss"?
>
> How about posting the output from "fink install emboss" so that
> we can
> see better what's going on in the multi-package failure? For that
> matter, post the output from the recursive remove command that you're
> trying.
>
>
> "which emboss" is empty but "locate emboss" reveals:
> /sw/bin/embossdata
> /sw/bin/embossversion
> /sw/bin/jembossctl
> /sw/bin/runJemboss.csh
> /sw/etc/profile.d/emboss.csh
> /sw/etc/profile.d/emboss.sh
The sh and csh files in /etc _should_ be left behind, because those are
configuration files not removed unless you use the "purge" option. You
can see if the others are orphaned files by running
dpkg -S <filename>
If no package claims a particular file then the maintainer needs to do a
bit of work to make sure that file gets cleaned up. Most of them
everything in /sw/fink/10.4 should be there
The files in /sw/fink/debs indicate that these versions are available
for you to install via apt-get, even if fink doesn't know about them, e.g.
sudo apt-get install emboss=emboss_5.0.0-7
> ... and it goes WAY on
>
> ****** install emboss ******
> big...@earth 09:31:53 ~:
> fink install emboss
> Information about 9593 packages read in 2 seconds.
> The following package will be installed or updated:
> emboss
> The following 3 additional packages will be installed:
> emboss-ajax6-shlibs emboss-nucleus6-shlibs emboss-plplot6-shlibs
> Do you want to continue? [Y/n] y
> Reading buildlock packages...
> /sw/bin/dpkg-lockwait -i
> /sw/fink/dists/unstable/main/binary-darwin-i386/sci/emboss_6.1.0-3_darwin-i386.deb
> /sw/fink/dists/unstable/main/binary-darwin-i386/sci/emboss-ajax6-shlibs_6.1.0-3_darwin-i386.deb
> /sw/fink/dists/unstable/main/binary-darwin-i386/sci/emboss-nucleus6-shlibs_6.1.0-3_darwin-i386.deb
> /sw/fink/dists/unstable/main/binary-darwin-i386/sci/emboss-plplot6-shlibs_6.1.0-3_darwin-i386.deb
> (Reading database ... 160596 files and directories currently installed.)
> Preparing to replace emboss 6.1.0-3 (using
> .../emboss_6.1.0-3_darwin-i386.deb) ...
> Unpacking replacement emboss ...
> Preparing to replace emboss-ajax6-shlibs 6.1.0-3 (using
> .../emboss-ajax6-shlibs_6.1.0-3_darwin-i386.deb) ...
> Unpacking replacement emboss-ajax6-shlibs ...
> Preparing to replace emboss-nucleus6-shlibs 6.1.0-3 (using
> .../emboss-nucleus6-shlibs_6.1.0-3_darwin-i386.deb) ...
> Unpacking replacement emboss-nucleus6-shlibs ...
> Unpacking emboss-plplot6-shlibs (from
> .../emboss-plplot6-shlibs_6.1.0-3_darwin-i386.deb) ...
> /sw/bin/dpkg: error processing
> /sw/fink/dists/unstable/main/binary-darwin-i386/sci/emboss-plplot6-shlibs_6.1.0-3_darwin-i386.deb
> (--install):
> trying to overwrite `/sw/lib/EMBOSS/libeplplot.3.dylib', which is
> also in package emboss-plplot5-shlibs
> /sw/bin/dpkg-deb: subprocess paste killed by signal (Broken pipe)
>
There's the fundamental problem. It looks like the various "5" library
packages were replaced by "6" ones, but unfortunately there's an
overlapping file between emboss-plplot5-shlibs and
emboss-plplot6-shlibs. (maintainer CCed).
>
>
> Thanks again for your help.
> Gus
(Unfortunately, "apt-get -f install" rarely actually helps in a Fink
context. That's a hardcoded message from apt-get that we haven't removed.)
As a workaround, see what you get from
sudo apt-get remove emboss-plplot5-shlibs emboss-nucleus5-shlibs
emboss-ajax5-shlibs
If that works, then try
sudo apt-get install emboss-ajax6-shlibs
(apt-get has some dependency tricks that fink doesn't, and since you
already have the binaries, it will work just fine).
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