rpms/perl-bioperl/devel Makefile, 1.2, 1.3 bioperl-1.5.2_102-paths.patch, NONE, 1.1 perl-bioperl.spec, 1.2, 1.3 sources, 1.3, 1.4

Alex Lancaster (alexlan) fedora-extras-commits at redhat.com
Thu Apr 5 11:03:12 UTC 2007 

Author: alexlan

Update of /cvs/extras/rpms/perl-bioperl/devel
In directory cvs-int.fedora.redhat.com:/tmp/cvs-serv5301/devel

Added Files:
	Makefile bioperl-1.5.2_102-paths.patch perl-bioperl.spec 
	sources 
Log Message:
First import of devel branch.



Index: Makefile
===================================================================
RCS file: Makefile
diff -N Makefile
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ Makefile	5 Apr 2007 11:02:34 -0000	1.3
@@ -0,0 +1,21 @@
+# Makefile for source rpm: perl-bioperl
+# $Id$
+NAME := perl-bioperl
+SPECFILE = $(firstword $(wildcard *.spec))
+
+define find-makefile-common
+for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done
+endef
+
+MAKEFILE_COMMON := $(shell $(find-makefile-common))
+
+ifeq ($(MAKEFILE_COMMON),)
+# attept a checkout
+define checkout-makefile-common
+test -f CVS/Root && { cvs -Q -d $$(cat CVS/Root) checkout common && echo "common/Makefile.common" ; } || { echo "ERROR: I can't figure out how to checkout the 'common' module." ; exit -1 ; } >&2
+endef
+
+MAKEFILE_COMMON := $(shell $(checkout-makefile-common))
+endif
+
+include $(MAKEFILE_COMMON)

bioperl-1.5.2_102-paths.patch:

--- NEW FILE bioperl-1.5.2_102-paths.patch ---
diff -u bioperl-1.5.2_102.orig/Build.PL bioperl-1.5.2_102/Build.PL
--- bioperl-1.5.2_102.orig/Build.PL        2007-03-14 03:46:30.000000000 -0700
+++ bioperl-1.5.2_102/Build.PL    2007-03-14 03:46:40.000000000 -0700
@@ -31,8 +31,8 @@
     build_requires      => {
                             'Test::More'                => 0,
                             'Module::Build'             => 0.2805,
-                            'Test::Harness'             => 2.62,
-                            'CPAN'                      => 1.81
+#                            'Test::Harness'             => 2.62,
+#                            'CPAN'                      => 1.81
                            },
     recommends          => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
                             'Ace'                       => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
@@ -63,7 +63,7 @@
                             'XML::DOM::XPath'           => '0.13/parsing interpro features/Bio::FeatureIO::interpro',
                             'XML::Parser'               => '0/parsing xml/Bio::Biblio::IO::medlinexml',
                             'XML::Parser::PerlSAX'      => '0/parsing xml/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp',
-                            'XML::SAX'                  => '0.15/parsing xml/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
+                            'XML::SAX'                  => '0.14/parsing xml/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
                             'XML::SAX::Writer'          => '0/writing xml/Bio::SeqIO::tigrxml',
                             'XML::Twig'                 => '0/parsing xml/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,Bio::DB::Biblio::eutils,Bio::Graph::IO::psi_xml',
                             'XML::Writer'               => '0.4/parsing and writing xml/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,Bio::SearchIO::Writer::BSMLResultWriter'
diff -ru bioperl-1.5.2_102.orig/Bio/Variation/IO.pm bioperl-1.5.2_102/Bio/Variation/IO.pm
--- bioperl-1.5.2_102.orig/Bio/Variation/IO.pm	2003-06-04 04:36:44.000000000 -0400
+++ bioperl-1.5.2_102/Bio/Variation/IO.pm	2005-03-21 20:21:54.000000000 -0500
@@ -83,7 +83,7 @@
 
 This makes the simplest ever reformatter
 
-    #!/usr/local/bin/perl
+    #!/usr/bin/perl
 
     $format1 = shift;
     $format2 = shift || die "Usage: reformat format1 format2 < input > output";
diff -ru bioperl-1.5.2_102.orig/examples/align/align_on_codons.pl bioperl-1.5.2_102/examples/align/align_on_codons.pl
--- bioperl-1.5.2_102.orig/examples/align/align_on_codons.pl	2003-07-07 14:20:58.000000000 -0400
+++ bioperl-1.5.2_102/examples/align/align_on_codons.pl	2005-03-21 20:24:44.000000000 -0500
@@ -13,10 +13,10 @@
 BEGIN {
     $CODONSIZE = 3; # parametrize everything like a good little programmer
     if( ! defined $ENV{'CLUSTALDIR'} ) { 
-	$ENV{'CLUSTALDIR'} = '/usr/local/bin';
+	$ENV{'CLUSTALDIR'} = '/usr/bin';
     } 
     if( ! defined $ENV{'TCOFFEEDIR'} ) { 
-	$ENV{'TCOFFEEDIR'} = '/usr/local/bin';
+	$ENV{'TCOFFEEDIR'} = '/usr/bin';
     }
     $USAGE = 
 qq{align_on_codons.pl < file.fa
diff -ru bioperl-1.5.2_102.orig/examples/db/dbfetch bioperl-1.5.2_102/examples/db/dbfetch
--- bioperl-1.5.2_102.orig/examples/db/dbfetch	2003-07-15 12:12:16.000000000 -0400
+++ bioperl-1.5.2_102/examples/db/dbfetch	2005-03-21 20:25:01.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -- # -*-Perl-*-
+#!/usr/bin/perl -- # -*-Perl-*-
 
 =head1 NAME
 
diff -ru bioperl-1.5.2_102.orig/examples/db/getGenBank.pl bioperl-1.5.2_102/examples/db/getGenBank.pl
--- bioperl-1.5.2_102.orig/examples/db/getGenBank.pl	2003-07-07 14:20:59.000000000 -0400
+++ bioperl-1.5.2_102/examples/db/getGenBank.pl	2005-03-21 20:24:57.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
 #
 # How to retrieve GenBank entries over the Web
 #
diff -ru bioperl-1.5.2_102.orig/examples/db/get_seqs.pl bioperl-1.5.2_102/examples/db/get_seqs.pl
--- bioperl-1.5.2_102.orig/examples/db/get_seqs.pl	2003-07-07 14:20:59.000000000 -0400
+++ bioperl-1.5.2_102/examples/db/get_seqs.pl	2005-03-21 20:24:53.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
 use strict;
 use vars qw($USAGE);
 use Carp;
diff -ru bioperl-1.5.2_102.orig/examples/generate_random_seq.pl bioperl-1.5.2_102/examples/generate_random_seq.pl
--- bioperl-1.5.2_102.orig/examples/generate_random_seq.pl	2004-11-01 16:09:08.000000000 -0500
+++ bioperl-1.5.2_102/examples/generate_random_seq.pl	2005-03-21 20:27:23.000000000 -0500
@@ -1,4 +1,4 @@
-#!/bin/perl -w
+#!/usr/bin/perl -w
 use strict;
 use vars qw($USAGE);
 
diff -ru bioperl-1.5.2_102.orig/examples/searchio/psiblast_features.pl bioperl-1.5.2_102/examples/searchio/psiblast_features.pl
--- bioperl-1.5.2_102.orig/examples/searchio/psiblast_features.pl	2004-02-21 05:50:34.000000000 -0500
+++ bioperl-1.5.2_102/examples/searchio/psiblast_features.pl	2005-03-21 20:24:30.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl 
+#!/usr/bin/perl 
 
 # Example usage of a SearchIO::psiblast parser of traditional format Blast 
 # and PSI-Blast reports.
diff -ru bioperl-1.5.2_102.orig/examples/structure/structure-io.pl bioperl-1.5.2_102/examples/structure/structure-io.pl
--- bioperl-1.5.2_102.orig/examples/structure/structure-io.pl	2004-11-01 16:09:33.000000000 -0500
+++ bioperl-1.5.2_102/examples/structure/structure-io.pl	2005-03-21 20:27:17.000000000 -0500
@@ -1,4 +1,4 @@
-#!/bin/perl -w
+#!/usr/bin/perl -w
 # Getting  Entry, Chain, Residue, and Atom objects given a PDB file
 
 use Bio::Structure::IO;
diff -ru bioperl-1.5.2_102.orig/examples/tk/hitdisplay.pl bioperl-1.5.2_102/examples/tk/hitdisplay.pl
--- bioperl-1.5.2_102.orig/examples/tk/hitdisplay.pl	2003-07-07 14:20:59.000000000 -0400
+++ bioperl-1.5.2_102/examples/tk/hitdisplay.pl	2005-03-21 20:24:26.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
 #
 # PROGRAM  : hitdisplay.pl
 # PURPOSE  : Demonstrate Bio::Tk::HitDisplay
diff -ru bioperl-1.5.2_102.orig/examples/tools/gb_to_gff.pl bioperl-1.5.2_102/examples/tools/gb_to_gff.pl
--- bioperl-1.5.2_102.orig/examples/tools/gb_to_gff.pl	2003-07-07 14:20:59.000000000 -0400
+++ bioperl-1.5.2_102/examples/tools/gb_to_gff.pl	2005-03-21 20:24:21.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
 use strict;
 
 use Bio::Tools::GFF;
diff -ru bioperl-1.5.2_102.orig/examples/tools/gff2ps.pl bioperl-1.5.2_102/examples/tools/gff2ps.pl
--- bioperl-1.5.2_102.orig/examples/tools/gff2ps.pl	2003-07-07 14:20:59.000000000 -0400
+++ bioperl-1.5.2_102/examples/tools/gff2ps.pl	2005-03-21 20:24:17.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
 
 
 =head1 NAME
diff -ru bioperl-1.5.2_102.orig/t/Promoterwise.t bioperl-1.5.2_102/t/Promoterwise.t
--- bioperl-1.5.2_102.orig/t/Promoterwise.t	2003-03-10 13:21:03.000000000 -0500
+++ bioperl-1.5.2_102/t/Promoterwise.t	2005-03-21 20:24:04.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
 # -*-Perl-*-
 ## Bioperl Test Harness Script for Modules
 
diff -ru bioperl-1.5.2_102.orig/t/testformats.pl bioperl-1.5.2_102/t/testformats.pl
--- bioperl-1.5.2_102.orig/t/testformats.pl	2001-06-29 17:17:02.000000000 -0400
+++ bioperl-1.5.2_102/t/testformats.pl	2005-03-21 20:24:00.000000000 -0500
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
 use strict;
 
 use Bio::SeqIO;


Index: perl-bioperl.spec
===================================================================
RCS file: perl-bioperl.spec
diff -N perl-bioperl.spec
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ perl-bioperl.spec	5 Apr 2007 11:02:34 -0000	1.3
@@ -0,0 +1,141 @@
+Name:           perl-bioperl
+Version:        1.5.2_102
+Release:        5%{?dist}
+Summary:        A package of Perl tools for computational molecular biology
+
+Group:          Development/Libraries
+License:        GPL or Artistic
+URL:            http://bioperl.org
+Source0:        http://bioperl.org/DIST/bioperl-%{version}.tar.bz2
+Patch0:         bioperl-1.5.2_102-paths.patch
+BuildRoot:      %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+
+BuildArch:      noarch
+BuildRequires:  perl(Ace)
+BuildRequires:  perl(Class::AutoClass) >= 1
+BuildRequires:  perl(Clone)
+BuildRequires:  perl(Convert::Binary::C)
+BuildRequires:  perl(Data::Stag::XMLWriter)
+BuildRequires:  perl(DBD::mysql)
+BuildRequires:  perl(DBD::Pg)
+BuildRequires:  perl(GD) >= 1.3
+BuildRequires:  perl(GD::SVG)
+BuildRequires:  perl(Graph)
+BuildRequires:  perl(HTML::Entities)
+BuildRequires:  perl(HTML::Parser)
+BuildRequires:  perl(HTTP::Request::Common)
+BuildRequires:  perl(IO::Stringy)
+BuildRequires:  perl(IO::String)
+BuildRequires:  perl(LWP::UserAgent)
+BuildRequires:  perl(PostScript::TextBlock)
+BuildRequires:  perl(Set::Scalar)
+BuildRequires:  perl(SOAP::Lite)
+BuildRequires:  perl(Spreadsheet::ParseExcel)
+BuildRequires:  perl(Storable)
+BuildRequires:  perl(SVG) >= 2.26
+BuildRequires:  perl(SVG::Graph) >= 0.01
+BuildRequires:  perl(Text::Shellwords)
+BuildRequires:  perl(URI::Escape)
+BuildRequires:  perl(XML::DOM::XPath) >= 0.13
+BuildRequires:  perl(XML::Parser)
+BuildRequires:  perl(XML::Parser::PerlSAX)
+BuildRequires:  perl(XML::SAX) >= 0.14
+BuildRequires:  perl(XML::SAX::Writer)
+BuildRequires:  perl(XML::Twig)
+BuildRequires:  perl(XML::Writer) > 0.4
+BuildRequires:  perl(Module::Build)
+Requires:  perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version))
+
+%description
+Bioperl is a package of Perl tools for computational molecular
+biology.
+
+%prep
+%setup -q -n bioperl-%{version}
+%patch0 -p1 
+
+# remove all execute bits from the doc stuff
+find examples -type f -exec chmod -x {} 2>/dev/null ';'
+##find doc -type f -exec chmod -x {} 2>/dev/null ';'
+##find scripts -type f -exec chmod -x {} 2>/dev/null ';'
+
+%build
+%{__perl} Build.PL --installdirs vendor << EOF
+n
+n
+EOF
+
+./Build
+
+# make sure the man page is UTF-8...
+cd blib/libdoc
+for i in Bio::Tools::GuessSeqFormat.3pm Bio::Tools::Geneid.3pm; do
+    iconv --from=ISO-8859-1 --to=UTF-8 $i > new
+    mv new $i
+done
+
+
+%install
+rm -rf $RPM_BUILD_ROOT
+#make pure_install PERL_INSTALL_ROOT=$RPM_BUILD_ROOT
+perl Build pure_install --destdir=$RPM_BUILD_ROOT
+find $RPM_BUILD_ROOT -type f -a \( -name .packlist \
+  -o \( -name '*.bs' -a -empty \) \) -exec rm -f {} ';'
+find $RPM_BUILD_ROOT -type d -depth -exec rmdir {} 2>/dev/null ';'
+# remove errant execute bit from the .pm's
+find $RPM_BUILD_ROOT -type f -name '*.pm' -exec chmod -x {} 2>/dev/null ';'
+# correct all binaries in /usr/bin to be 0755
+# disable since we aren't building scripts currently
+##find $RPM_BUILD_ROOT/%{_bindir} -type f -name '*.pl' -exec chmod 0755 {} 2>/dev/null ';'
+
+%check
+%{?_with_check:./Build test || :}
+
+%clean
+rm -rf $RPM_BUILD_ROOT
+
+
+%files
+%defattr(-,root,root,-)
+## don't distribute "doc" "scripts" subdirectories, they don't contain docs
+%doc examples models 
+%doc AUTHORS BUGS Changes DEPRECATED  INSTALL LICENSE PLATFORMS README
+%{perl_vendorlib}/*
+%{_mandir}/man3/*.3*    
+## disable scripts for now
+##%{_bindir}/*
+##%{_mandir}/man1/*.1*
+
+%changelog
+* Tue Apr 03 2007 Alex Lancaster <alexl at users.sourceforge.net> 1.5.2_102-5
+- Fix changelog
+
+* Tue Apr 03 2007 Alex Lancaster <alexl at users.sourceforge.net> 1.5.2_102-4
+- Disable tests because many of them require network access, add
+  _with_check macro so they can be enabled during testing.
+
+* Mon Apr 02 2007 Alex Lancaster <alexl at users.sourceforge.net> 1.5.2_102-3
+- Remove BuildRequires: perl(Bio::ASN1::EntrezGene), creates a
+  circular dependency, the dependency is still found at install-time.
+
+* Thu Mar 29 2007 Alex Lancaster <alexl at users.sourceforge.net> 1.5.2_102-2
+- Add all BRs listed as 'recommends' in Build.PL so that it never
+  needs to get packages from CPAN.
+- Remove unnecessary filtering of Requires
+
+* Wed Mar 23 2007 Alex Lancaster <alexl at users.sourceforge.net> 1.5.2_102-1
+- Update to 1.5.2_102
+- Review suggestions from Steven Pritchard
+- BR: perl(IO::String)
+- Disable scripts for now as they require bioperl-run (not yet packaged)
+- Don't mark non-documentation files as documentation.
+
+* Wed Apr 06 2005 Hunter Matthews <thm at duke.edu> 1.5.0-3
+- Review suggestions from José Pedro Oliveira
+
+* Mon Apr 01 2005 Hunter Matthews <thm at duke.edu> 1.5.0-2
+- Added buildrequires and improved documention entries from FE mailing list.
+
+* Mon Mar 21 2005 Hunter Matthews <thm at duke.edu> 1.5.0-1
+- Initial build. I started with the biolinux.org rpm, but broke out 
+  most of the deps and built them seperately.


Index: sources
===================================================================
RCS file: sources
diff -N sources
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ sources	5 Apr 2007 11:02:34 -0000	1.4
@@ -0,0 +1 @@
+71f22246979ee5d6e19d547319962eea  bioperl-1.5.2_102.tar.bz2

More information about the scm-commits mailing list