[Bioperl-l] update/install problem

Chris Fields cjfields at uiuc.edu
Tue Feb 13 20:29:03 EST 2007

On Feb 13, 2007, at 4:00 PM, Thomas Keller wrote:

> Could someone suggest a workaround or fix for this error?
> $ sudo fink update bioperl-pm586
> Information about 5850 packages read in 2 seconds.
> The package 'bioperl-pm586' will be built and installed.
> The package 'xml-sax-pm586' will be installed.
> The package 'xml-sax-writer-pm586' will be built and installed.
> The package 'xml-filter-buffertext-pm586' will be built and installed.
> The following package will be installed or updated:
>  bioperl-pm586
> The following 3 additional packages will be installed:
>  xml-filter-buffertext-pm586 xml-sax-pm586 xml-sax-writer-pm586
> Do you want to continue? [Y/n] Y
> /sw/bin/dpkg-lockwait -i
> /sw/fink/dists/unstable/main/binary-darwin-powerpc/libs/perlmods/ 
> xml-sax-pm586_0.13-2_darwin-
> powerpc.deb
> (Reading database ... 48029 files and directories currently  
> installed.)
> Preparing to replace xml-sax-pm586 0.13-2 (using
> .../xml-sax-pm586_0.13-2_darwin-powerpc.deb) ...
> Unpacking replacement xml-sax-pm586 ...
> Setting up xml-sax-pm586 (0.13-2) ...
> update-perl586-sax-parsers: adding Perl SAX parser module info file of
> XML::SAX::PurePerl...
> Can't locate object method "save_parsers_debian" via package  
> "XML::SAX" at
> /sw/sbin/update-perl586-sax-parsers line 96.
> /sw/bin/dpkg: error processing xml-sax-pm586 (--install):
>  subprocess post-installation script returned error exit status 22
> Errors were encountered while processing:
>  xml-sax-pm586
> ### execution of /sw/bin/dpkg-lockwait failed, exit code 1
> Failed: can't install package xml-sax-pm586-0.13-2

The fink installation seems to be hanging on XML::SAX, not bioperl.   
You could try installing XML::SAX (now at v. 0.15) via CPAN using  
'sudo cpan'; I updated just recently w/o problems.

As an aside, you could similarly install bioperl directly from CPAN  
(which I also haven't had any problems with).  The installation  
allows for installing optional modules.


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