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
/sw/fink/10.4/stable/main/finkinfo/libs/perlmods/bio-emboss-pm
/sw/fink/10.4/stable/main/finkinfo/sci/emboss-kaptain.info
/sw/fink/10.4/stable/main/finkinfo/sci/emboss.info
/sw/fink/10.4/stable/main/finkinfo/sci/emboss.patch
/sw/fink/10.4/unstable/main/binary-darwin-i386/sci/emboss-ajax5-shlibs_5.0.0-7_darwin-i386.deb
/sw/fink/10.4/unstable/main/binary-darwin-i386/sci/emboss-ajax6-dev_6.1.0-3_darwin-i386.deb
/sw/fink/10.4/unstable/main/binary-darwin-i386/sci/emboss-ajax6-shlibs_6.1.0-3_darwin-i386.deb
/sw/fink/10.4/unstable/main/binary-darwin-i386/sci/emboss-nucleus5-shlibs_5.0.0-7_darwin-i386.deb
/sw/fink/10.4/unstable/main/binary-darwin-i386/sci/emboss-nucleus6-dev_6.1.0-3_darwin-i386.deb
/sw/fink/10.4/unstable/main/binary-darwin-i386/sci/emboss-nucleus6-shlibs_6.1.0-3_darwin-i386.deb
/sw/fink/10.4/unstable/main/binary-darwin-i386/sci/emboss-plplot5-shlibs_5.0.0-7_darwin-i386.deb
/sw/fink/10.4/unstable/main/binary-darwin-i386/sci/emboss-plplot6-dev_6.1.0-3_darwin-i386.deb
/sw/fink/10.4/unstable/main/binary-darwin-i386/sci/emboss-plplot6-shlibs_6.1.0-3_darwin-i386.deb
/sw/fink/10.4/unstable/main/binary-darwin-i386/sci/emboss_5.0.0-7_darwin-i386.deb
/sw/fink/10.4/unstable/main/binary-darwin-i386/sci/emboss_6.1.0-3_darwin-i386.deb
/sw/fink/10.4/unstable/main/finkinfo/libs/perlmods/bio-emboss-pm.info
/sw/fink/10.4/unstable/main/finkinfo/libs/perlmods/bio-emboss-pm.patch
/sw/fink/10.4/unstable/main/finkinfo/sci/emboss-kaptain.info
/sw/fink/10.4/unstable/main/finkinfo/sci/emboss.info
/sw/fink/10.4/unstable/main/finkinfo/sci/emboss.patch
/sw/fink/10.4/unstable/main/finkinfo/sci/embossdb-rebase.info
/sw/fink/10.4/unstable/main/finkinfo/sci/kemboss-qt4.info
/sw/fink/debs/emboss-ajax5-shlibs_5.0.0-7_darwin-i386.deb
/sw/fink/debs/emboss-ajax6-dev_6.1.0-3_darwin-i386.deb
/sw/fink/debs/emboss-ajax6-shlibs_6.1.0-3_darwin-i386.deb
/sw/fink/debs/emboss-nucleus5-shlibs_5.0.0-7_darwin-i386.deb
/sw/fink/debs/emboss-nucleus6-dev_6.1.0-3_darwin-i386.deb
/sw/fink/debs/emboss-nucleus6-shlibs_6.1.0-3_darwin-i386.deb
/sw/fink/debs/emboss-plplot5-shlibs_5.0.0-7_darwin-i386.deb
/sw/fink/debs/emboss-plplot6-dev_6.1.0-3_darwin-i386.deb
/sw/fink/debs/emboss-plplot6-shlibs_6.1.0-3_darwin-i386.deb
/sw/fink/debs/emboss_5.0.0-7_darwin-i386.deb
/sw/fink/debs/emboss_6.1.0-3_darwin-i386.deb
/sw/lib/perl5/5.8.8/Bio/AlignIO/emboss.pm
/sw/lib/perl5/5.8.8/man/man3/Bio::AlignIO::emboss.3pm
/sw/share/EMBOSS/acd/embossdata.acd
/sw/share/EMBOSS/acd/embossversion.acd
/sw/share/EMBOSS/data/Efeatures.emboss
/sw/share/EMBOSS/data/Etags.emboss
/sw/share/EMBOSS/data/embossre.equ
/sw/share/EMBOSS/doc/manuals/emboss.sty
/sw/share/EMBOSS/doc/manuals/emboss_qg.pdf
/sw/share/EMBOSS/doc/manuals/emboss_qg.ps
/sw/share/EMBOSS/doc/programs/html/emboss_icon.gif
/sw/share/EMBOSS/doc/programs/html/emboss_icon.jpg
/sw/share/EMBOSS/doc/programs/html/embossdata.html
/sw/share/EMBOSS/doc/programs/html/embossversion.html
/sw/share/EMBOSS/doc/programs/html/jembossctl.html
/sw/share/EMBOSS/doc/programs/text/embossdata.txt
/sw/share/EMBOSS/doc/programs/text/embossversion.txt
/sw/share/EMBOSS/doc/programs/text/jembossctl.txt
/sw/share/EMBOSS/doc/tutorials/emboss-gcg.ppt
/sw/share/EMBOSS/doc/tutorials/emboss-interfaces.ppt
/sw/share/EMBOSS/doc/tutorials/emboss-talk.ppt
/sw/share/EMBOSS/doc/tutorials/emboss_tut.tar.gz
/sw/share/EMBOSS/emboss.default.template
/sw/share/EMBOSS/jemboss
/sw/share/EMBOSS/jemboss/LICENSE
/sw/share/EMBOSS/jemboss/README
/sw/share/EMBOSS/jemboss/api
/sw/share/EMBOSS/jemboss/api/allclasses-frame.html
/sw/share/EMBOSS/jemboss/api/deprecated-list.html
/sw/share/EMBOSS/jemboss/api/getClasses.pl
/sw/share/EMBOSS/jemboss/api/help-doc.html
/sw/share/EMBOSS/jemboss/api/index-all.html
/sw/share/EMBOSS/jemboss/api/index.html
/sw/share/EMBOSS/jemboss/api/makeDocs.csh
/sw/share/EMBOSS/jemboss/api/org
/sw/share/EMBOSS/jemboss/api/org/emboss
... 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)
dpkg: dependency problems prevent configuration of emboss:
emboss depends on emboss-plplot6-shlibs (>= 6.1.0-3); however:
Package emboss-plplot6-shlibs is not installed.
/sw/bin/dpkg: error processing emboss (--install):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of emboss-ajax6-shlibs:
emboss-ajax6-shlibs depends on emboss-plplot6-shlibs (>= 6.1.0-3); however:
Package emboss-plplot6-shlibs is not installed.
/sw/bin/dpkg: error processing emboss-ajax6-shlibs (--install):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of emboss-nucleus6-shlibs:
emboss-nucleus6-shlibs depends on emboss-ajax6-shlibs (>= 6.1.0-3);
however:
Package emboss-ajax6-shlibs is not configured yet.
/sw/bin/dpkg: error processing emboss-nucleus6-shlibs (--install):
dependency problems - leaving unconfigured
Errors were encountered while processing:
/sw/fink/dists/unstable/main/binary-darwin-i386/sci/emboss-plplot6-shlibs_6.1.0-3_darwin-i386.deb
emboss
emboss-ajax6-shlibs
emboss-nucleus6-shlibs
### execution of /sw/bin/dpkg-lockwait failed, exit code 1
Failed: can't batch-install packages:
/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
***** recursive remove example *****
fink remove --recursive emboss-ajax5-shlibs
Information about 9593 packages read in 2 seconds.
/sw/bin/apt-get-lockwait remove emboss-ajax5-shlibs
Reading Package Lists... Done
Building Dependency Tree... Done
You might want to run `apt-get -f install' to correct these:
Sorry, but the following packages have unmet dependencies:
emboss: Depends: emboss-plplot6-shlibs (>= 6.1.0-3) but it is not going to
be installed
emboss-ajax6-shlibs: Depends: emboss-plplot6-shlibs (>= 6.1.0-3) but it is
not going to be installed
emboss-nucleus5-shlibs: Depends: emboss-ajax5-shlibs (>= 5.0.0-7) but it
is not going to be installed
E: Unmet dependencies. Try 'apt-get -f install' with no packages (or specify
a solution).
### execution of /sw/bin/apt-get-lockwait failed, exit code 100
Failed: can't remove package emboss-ajax5-shlibs
***** apt-get -f install suggested by remove error return*****
big...@earth 09:39:35 ~:
sudo apt-get -f install
Reading Package Lists... Done
Building Dependency Tree... Done
Correcting dependencies... Done
The following extra packages will be installed:
emboss-plplot6-shlibs
The following NEW packages will be installed:
emboss-plplot6-shlibs
0 packages upgraded, 1 newly installed, 0 to remove and 15 not upgraded.
3 packages not fully installed or removed.
Need to get 0B/194kB of archives. After unpacking 479kB will be used.
Do you want to continue? [Y/n] y
(Reading database ... 160596 files and directories currently installed.)
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
(--unpack):
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)
Errors were encountered while processing:
/sw/fink/dists/unstable/main/binary-darwin-i386/sci/emboss-plplot6-shlibs_6.1.0-3_darwin-i386.deb
E: Sub-process /sw/bin/dpkg returned an error code (1)
Thanks again for your help.
Gus
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