On Wed, May 9, 2012 at 5:49 PM, Hanspeter Niederstrasser <
[email protected]> wrote:
> On 5/9/2012 6:42 AM, Chris Richardson wrote:
>
>> Hi,
>>
>> I'm trying to install bioperl-run-pm5100. bioperl-pm5100 itself and the
>> two other pre-requisities for bioperl-run install with no problem.
>> bioperl-run dies with the error:
>>
>> Unpacking fink-buildlock-bioperl-run-**pm5100-1.6.1-4 (from
>>> .../fink-buildlock-bioperl-**run-pm5100-1.6.1-4_2012.05.09-**11.32.21_darwin-i386.deb)
>>> ...
>>> Setting up fink-buildlock-bioperl-run-**pm5100-1.6.1-4
>>> (2012.05.09-11.32.21) ...
>>>
>>> /sw/bin/tar --no-same-owner --no-same-permissions -xf
>>> /sw/src/BioPerl-run-1.6.1.tar.**bz2
>>> [ -r
>>> /sw/fink/dists/stable/main/**finkinfo/libs/perlmods/**bioperl-run-pm.patch
>>> ]
>>> patch -p1< /sw/fink/dists/stable/main/**finkinfo/libs/perlmods/**
>>> bioperl-run-pm.patch
>>> patching file Build.PL
>>> ARCHFLAGS="" /usr/bin/arch -i386 perl5.10.0 Build.PL --install_base /sw
>>> --install_path bin=/sw/bin --install_path lib=/sw/lib/perl5/5.10.0
>>> --install_path arch=/sw/lib/perl5/5.10.0/**darwin-thread-multi-2level
>>> --install_path bindoc=/sw/share/man/man1 --install_path
>>> libdoc=/sw/share/man/man3 --install_path script=/sw/bin --destdir
>>> /sw/src/fink.build/root-**bioperl-run-pm5100-1.6.1-4
>>> Invalid prerequisite condition '0/processing XML data/Bio::Tools::Run::*
>>> *EMBOSSacd' for XML::Twig at /sw/lib/perl5/5.10.0/Module/**Build/Base.pm
>>> line 1693.
>>> ### execution of ARCHFLAGS="" failed, exit code 9
>>> Removing runtime build-lock...
>>> Removing build-lock package...
>>> /sw/bin/dpkg-lockwait -r fink-buildlock-bioperl-run-**pm5100-1.6.1-4
>>> (Reading database ... 16020 files and directories currently installed.)
>>> Removing fink-buildlock-bioperl-run-**pm5100-1.6.1-4 ...
>>> Failed: phase compiling: bioperl-run-pm5100-1.6.1-4 failed
>>>
>>
>> This is on a Mac Pro running 10.6.8 and the following:
>>
>> Package manager version: 0.32.6
>> Distribution version: selfupdate-rsync Wed May 9 10:14:52 2012, 10.6,
>> i386
>> Trees: local/main stable/main
>> Xcode: 3.2.6
>> Max. Fink build jobs: 8
>>
>
> This seems to be an incompatibility between bioperl-run 1.6.1 and
> bioperl-1.6.900. I can confirm this build failure with bioperl-1.6.900
> installed. But if I downgrade to bioperl-1.6.1, then bioperl-run builds
> and installs. I've cc'd the bioperl maintainer to this email to see if he
> has suggestions (or perhaps can upgrade bioperl-run to the latest upstream).
>
> For the time being, go to <http://fink.cvs.sourceforge.**
> net/viewvc/fink/dists/10.4/**stable/main/finkinfo/libs/**
> perlmods/bioperl-pm.info?**revision=1.15&view=markup<http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.4/stable/main/finkinfo/libs/perlmods/bioperl-pm.info?revision=1.15&view=markup>>
> and <http://fink.cvs.sourceforge.**net/viewvc/fink/dists/10.4/**
> stable/main/finkinfo/libs/**perlmods/bioperl-pm.patch?**
> revision=1.4&view=markup<http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.4/stable/main/finkinfo/libs/perlmods/bioperl-pm.patch?revision=1.4&view=markup>>,
> download both files there to /sw/fink/dists/local/main/**finkinfo, and
> then run
>
> fink install bioperl-pm5100-1.6.1-5
>
> to downgrade your bioperl, and then try rebuilding bioperl-run.
>
I had the same experience: bioperl-run-pm builds with bioperl-pm version
1.6.1-5, but not 1.6.901-1. I packaged the latest version of
bioperl-run-pm, and that fixes the problem:
https://sourceforge.net/tracker/?func=detail&aid=3525234&group_id=17203&atid=414256
I can't test whether bioperl-run-pm actually works since most of the
programs it wraps aren't on my computer, but at least it builds, which is
an improvement over the current situation. I don't have commit privileges
to add the updated bioperl-run-pm to fink, but hopefully someone can add it
soon.
Dustin
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