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
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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
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