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> and <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. Hanspeter ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Fink-users mailing list [email protected] List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
