As found by Steffen and confirmed below, when module-build is already installed by another package, the bioperl package tries to use that to install. However it fails when using Makefile.PL, so I fixed it by using Build.PL in the info file. But this only works with a newer version of module-build. I have contacted the maintainer of that package to update it. When that's done, I will commit the updated bioperl info file.
cheers, - Koen. On Nov 29, 2007, at 9:17 PM, Alexander K. Hansen wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Koen van der Drift wrote: >> Hi, >> >> A user reported the following error. I have no idea what the first >> error means. Is it a conflict with module-build-pm, or is it >> something that can be fixed in the info or patch file? >> >> I cannot reproduce the second error, but I noticed in his output >> the line "Will try to install symlinks to /sw/sw/bin" - note the >> double / sw. Any ideas? >> >> (I am on a G5 iMac, 10.5.1) >> >> >> thanks, >> >> - Koen. >> >> >> >> >> >> Begin forwarded message: >> >>> From: Steffen Schmidt <[EMAIL PROTECTED]> Date: >>> November 28, 2007 7:51:29 AM EST To: Koen van der Drift >>> <[EMAIL PROTECTED]> Subject: fink bioperl-pm588 >>> problem >>> >>> Hi, >>> >>> thank you for supporting bioperl :-) I experience some problems >>> when installing bioperl-pm588. Do you experience the same >>> problems? My system is OS X (tested on both: Tiger & Leopard) >>> Intel - fink 0.27.9-31 >>> >>> Steffen >>> >>> a) with module-build-pm588 installed: >>> >>> ... patching file ModuleBuildBioperl.pm ARCHFLAGS="" >>> /sw/bin/perl5.8.8 Makefile.PL PERL=/sw/bin/perl5.8.8 PREFIX=/sw >>> INSTALLPRIVLIB=/sw/lib/perl5/5.8.8 INSTALLARCHLIB=/sw/lib/ >>> perl5/5.8.8/darwin-thread-multi-2level INSTALLSITELIB=/sw/lib/ >>> perl5/5.8.8 INSTALLSITEARCH=/sw/lib/perl5/5.8.8/darwin-thread- >>> multi-2level INSTALLMAN1DIR=/sw/share/man/man1 >>> INSTALLMAN3DIR=/sw/ share/man/man3 >>> INSTALLSITEMAN1DIR=/sw/share/man/man1 >>> INSTALLSITEMAN3DIR=/sw/share/man/man3 INSTALLBIN=/sw/bin >>> INSTALLSITEBIN=/sw/bin INSTALLSCRIPT=/sw/bin Sorry, PREFIX is not >>> supported. See the Module::Build documentation for 'destdir' or >>> 'install_base' instead. ### execution of ARCHFLAGS="" failed, >>> exit code 255 ... >>> >>> b) without module-build-pm588: >>> >>> it works until installation: ... Installing >>> /sw/src/fink.build/root-bioperl-pm588-1.5.2-3/sw/share/ >>> man/man3/Bio::Variation::VariantI.3pm Installing >>> /sw/src/fink.build/root-bioperl-pm588-1.5.2-3/sw/share/ >>> man/man3/Bio::WebAgent.3pm Writing >>> /sw/src/fink.build/root-bioperl-pm588-1.5.2-3/sw/lib/ >>> perl5/5.8.8/darwin-thread-multi-2level/auto/Bio/.packlist >>> /sw/bin/perl5.8.8 maintenance/symlink_script.pl Will try to >>> install symlinks to /sw/sw/bin mkdir -p >>> /sw/src/fink.build/root-bioperl-pm588-1.5.2-3/sw/share/ >>> bioperl-pm588 cp -r models examples doc >>> /sw/src/fink.build/root-bioperl- >>> pm588-1.5.2-3/sw/share/bioperl-pm588 mkdir -p >>> /sw/src/fink.build/root-bioperl-pm588-1.5.2-3/sw/share/ >>> bioperl-pm588/t cp -r t/data >>> /sw/src/fink.build/root-bioperl-pm588-1.5.2-3/sw/share/ >>> bioperl-pm588/t mkdir -p >>> /sw/src/fink.build/root-bioperl-pm588-1.5.2-3/sw/lib/ perl5/5.8.8 >>> mv /sw/src/fink.build/root-bioperl-pm588-1.5.2-3/sw/man /sw/src/ >>> fink.build/root-bioperl-pm588-1.5.2-3/sw/lib/perl5/5.8.8 mv: >>> cannot stat `/sw/src/fink.build/root-bioperl-pm588-1.5.2-3/sw/ >>> man': No such file or directory ### execution of mv failed, exit >>> code 1 >>> >>> >> > > I tried this in a clean-build situation (my clean-builder is on OS > 10.4.10, with Xcode 2.4.1, and fink-0.27.9-31), and noticed the > following: > > ... > sudo -u fink-bld [ENV] sh -c/var/tmp/tmp.3.c4k3AF > ARCHFLAGS="" /sw/bin/perl5.8.8 Makefile.PL PERL=/sw/bin/perl5.8.8 > PREFIX=/sw INSTALLPRIVLIB=/sw/lib/perl5/5.8.8 > INSTALLARCHLIB=/sw/lib/perl5/5.8.8/darwin-thread-multi-2level > INSTALLSITELIB=/sw/lib/perl5/5.8.8 > INSTALLSITEARCH=/sw/lib/perl5/5.8.8/darwin-thread-multi-2level > INSTALLMAN1DIR=/sw/share/man/man1 INSTALLMAN3DIR=/sw/share/man/man3 > INSTALLSITEMAN1DIR=/sw/share/man/man1 > INSTALLSITEMAN3DIR=/sw/share/man/man3 INSTALLBIN=/sw/bin > INSTALLSITEBIN=/sw/bin INSTALLSCRIPT=/sw/bin > This module requires Module::Build to install itself. > Install Module::Build now from CPAN? [y] > > It seems un-Finklike to allow a package to install items that Fink > doesn't directly control. > > > If I install module-build-pm588 I get the same error (a) as the > original poster. I'm not going to test (b) because this is my clean > test environment. > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFHT3KhB8UpO3rKjQ8RAi2xAKCYVBMIRox65ZfD8eXbvcJOLXOknwCZAdjD > RS7ygbMeJiLWq+Wh5RUsCP8= > =pFWH > -----END PGP SIGNATURE----- > > > ------------------------------------------------------------------------- > SF.Net email is sponsored by: The Future of Linux Business White Paper > from Novell. From the desktop to the data center, Linux is going > mainstream. 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