From luwe at mail.nih.gov Wed Mar 3 13:24:15 2004 From: luwe at mail.nih.gov (Lu, Wei (NIH/NCI/NCICB)) Date: Tue Mar 9 15:58:56 2004 Subject: [bioped-l] the roundup (long) Message-ID: <8A7350C73265A54587D23E30D15D93800417455F@nihexchange13.nih.gov> Hi, This is Wei, system engineer, from LPG, NCI/NIH. I am trying to install bio-pedigree over the bioperl, but after successfully "make" the module, I got errors on "make test", which showing there is some modules missing as the following. Is there any way I can find these modules? Thanks for you help in advance, Wei Lu PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/DB...............ok t/Draw.............Cannot load GD, skipping tests t/Draw.............ok 2/2 skipped: unable to run all of the Draw tests, check your GD installation t/GD...............cannot load a module GD or Tie::IxHash, skipping tests t/GD...............ok 2/2 skipped: unable to run all of the Draw tests, check your GD installation t/Group............Can't locate Bio/PopGen/PopulationI.pm in @INC (@INC contains: t /opt/progs/bioperl-pedigree/blib/lib /opt/progs/bioperl-pedigree/blib/arch /usr/local/lib/perl5/5.8.2/sun4-solaris-thread-multi /usr/local/lib/perl5/5.8.2 /usr/local/lib/perl5/site_perl/5.8.2/sun4-solaris-thread-multi /usr/local/lib/perl5/site_perl/5.8.2 /usr/local/lib/perl5/site_perl .) at /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/GroupI.pm line 66. BEGIN failed--compilation aborted at /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/GroupI.pm line 66. Compilation failed in require at /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/Group.pm line 82. BEGIN failed--compilation aborted at /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/Group.pm line 82. Compilation failed in require at /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/Pedigree.pm line 101. BEGIN failed--compilation aborted at /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/Pedigree.pm line 101. Compilation failed in require at t/Group.t line 25. BEGIN failed--compilation aborted at t/Group.t line 25. Can't locate Bio/PopGen/Genotype.pm in @INC (@INC contains: t /opt/progs/bioperl-pedigree/blib/lib /opt/progs/bioperl-pedigree/blib/arch /usr/local/lib/perl5/5.8.2/sun4-solaris-thread-multi /usr/local/lib/perl5/5.8.2 /usr/local/lib/perl5/site_perl/5.8.2/sun4-solaris-thread-multi /usr/local/lib/perl5/site_perl/5.8.2 /usr/local/lib/perl5/site_perl .) at t/Person.t line 32. BEGIN failed--compilation aborted at t/Person.t line 32. t/Person...........dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/Relationships....Parameterless "use IO" deprecated at /usr/local/lib/perl5/site_perl/5.8.2/XML/Writer.pm line 16 Can't locate Bio/PopGen/PopulationI.pm in @INC (@INC contains: t /opt/progs/bioperl-pedigree/blib/lib /opt/progs/bioperl-pedigree/blib/arch /usr/local/lib/perl5/5.8.2/sun4-solaris-thread-multi /usr/local/lib/perl5/5.8.2 /usr/local/lib/perl5/site_perl/5.8.2/sun4-solaris-thread-multi /usr/local/lib/perl5/site_perl/5.8.2 /usr/local/lib/perl5/site_perl .) at /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/GroupI.pm line 66. BEGIN failed--compilation aborted at /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/GroupI.pm line 66. Compilation failed in require at /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/Group.pm line 82. BEGIN failed--compilation aborted at /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/Group.pm line 82. Compilation failed in require at t/Relationships.t line 31. BEGIN failed--compilation aborted at t/Relationships.t line 31. From jason at cgt.duhs.duke.edu Tue Mar 9 16:01:09 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 9 16:06:53 2004 Subject: [bioped-l] the roundup (long) In-Reply-To: <8A7350C73265A54587D23E30D15D93800417455F@nihexchange13.nih.gov> References: <8A7350C73265A54587D23E30D15D93800417455F@nihexchange13.nih.gov> Message-ID: Tie::IxHash, GD are from the CPAN archive. Bio::PopGen::PoulationI is part of bioperl-1.4 and beyond releases. http://bioperl.org/DIST/bioperl-1.4.tar.gz should have what you need. I've since cleaned up the code from the last bioperl-pedigree release - I will have to see if I can't make another tarball - you may find doing a CVS checkout will be less painful to insure things work. It may be helpful to describe what you want to do with the modules as they have been typically used for some specific tasks. -jason On Wed, 3 Mar 2004, Lu, Wei (NIH/NCI/NCICB) wrote: > Hi, > This is Wei, system engineer, from LPG, NCI/NIH. I am trying to install > bio-pedigree over the bioperl, but after successfully "make" the module, I > got errors on "make test", which showing there is some modules missing as > the following. Is there any way I can find these modules? > > Thanks for you help in advance, > Wei Lu > > > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/DB...............ok > > t/Draw.............Cannot load GD, skipping tests > t/Draw.............ok > > 2/2 skipped: unable to run all of the Draw tests, check your GD > installation > t/GD...............cannot load a module GD or Tie::IxHash, skipping tests > t/GD...............ok > > 2/2 skipped: unable to run all of the Draw tests, check your GD > installation > t/Group............Can't locate Bio/PopGen/PopulationI.pm in @INC (@INC > contains: t /opt/progs/bioperl-pedigree/blib/lib > /opt/progs/bioperl-pedigree/blib/arch > /usr/local/lib/perl5/5.8.2/sun4-solaris-thread-multi > /usr/local/lib/perl5/5.8.2 > /usr/local/lib/perl5/site_perl/5.8.2/sun4-solaris-thread-multi > /usr/local/lib/perl5/site_perl/5.8.2 /usr/local/lib/perl5/site_perl .) at > /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/GroupI.pm line 66. > BEGIN failed--compilation aborted at > /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/GroupI.pm line 66. > Compilation failed in require at > /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/Group.pm line 82. > BEGIN failed--compilation aborted at > /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/Group.pm line 82. > Compilation failed in require at > /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/Pedigree.pm line 101. > BEGIN failed--compilation aborted at > /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/Pedigree.pm line 101. > Compilation failed in require at t/Group.t line 25. > BEGIN failed--compilation aborted at t/Group.t line 25. > > Can't locate Bio/PopGen/Genotype.pm in @INC (@INC contains: t > /opt/progs/bioperl-pedigree/blib/lib /opt/progs/bioperl-pedigree/blib/arch > /usr/local/lib/perl5/5.8.2/sun4-solaris-thread-multi > /usr/local/lib/perl5/5.8.2 > /usr/local/lib/perl5/site_perl/5.8.2/sun4-solaris-thread-multi > /usr/local/lib/perl5/site_perl/5.8.2 /usr/local/lib/perl5/site_perl .) at > t/Person.t line 32. > BEGIN failed--compilation aborted at t/Person.t line 32. > t/Person...........dubious > > Test returned status 2 (wstat 512, 0x200) > after all the subtests completed successfully > t/Relationships....Parameterless "use IO" deprecated at > /usr/local/lib/perl5/site_perl/5.8.2/XML/Writer.pm line 16 > Can't locate Bio/PopGen/PopulationI.pm in @INC (@INC contains: t > /opt/progs/bioperl-pedigree/blib/lib /opt/progs/bioperl-pedigree/blib/arch > /usr/local/lib/perl5/5.8.2/sun4-solaris-thread-multi > /usr/local/lib/perl5/5.8.2 > /usr/local/lib/perl5/site_perl/5.8.2/sun4-solaris-thread-multi > /usr/local/lib/perl5/site_perl/5.8.2 /usr/local/lib/perl5/site_perl .) at > /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/GroupI.pm line 66. > BEGIN failed--compilation aborted at > /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/GroupI.pm line 66. > Compilation failed in require at > /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/Group.pm line 82. > BEGIN failed--compilation aborted at > /opt/progs/bioperl-pedigree/blib/lib/Bio/Pedigree/Group.pm line 82. > Compilation failed in require at t/Relationships.t line 31. > BEGIN failed--compilation aborted at t/Relationships.t line 31. > > > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu