Broken dependencies: perl-B-Hooks-OP-Check
by Fedora Koji Build System
perl-B-Hooks-OP-Check has broken dependencies in the development tree:
On ppc:
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc requires perl(warnings)
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc requires perl >= 0:5.008001
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc requires perl(:MODULE_COMPAT_5.10.0)
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc requires rtld(GNU_HASH)
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc requires libc.so.6
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc requires libc.so.6(GLIBC_2.0)
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc requires libc.so.6(GLIBC_2.1.3)
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc requires perl(strict)
On ppc64:
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc64 requires perl(warnings)
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc64 requires libc.so.6()(64bit)
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc64 requires perl >= 0:5.008001
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc64 requires perl(:MODULE_COMPAT_5.10.0)
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc64 requires rtld(GNU_HASH)
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc64 requires libc.so.6(GLIBC_2.3)(64bit)
perl-B-Hooks-OP-Check-0.17-2.fc12.ppc64 requires perl(strict)
Please resolve this as soon as possible.
14 years, 5 months
Broken dependencies: perl-XXX
by Fedora Koji Build System
perl-XXX has broken dependencies in the development tree:
On ppc:
perl-XXX-0.12-3.fc12.noarch requires perl(warnings)
perl-XXX-0.12-3.fc12.noarch requires perl(:MODULE_COMPAT_5.10.0)
perl-XXX-0.12-3.fc12.noarch requires perl >= 0:5.006001
perl-XXX-0.12-3.fc12.noarch requires perl(base)
perl-XXX-0.12-3.fc12.noarch requires perl(strict)
On ppc64:
perl-XXX-0.12-3.fc12.noarch requires perl(warnings)
perl-XXX-0.12-3.fc12.noarch requires perl(:MODULE_COMPAT_5.10.0)
perl-XXX-0.12-3.fc12.noarch requires perl >= 0:5.006001
perl-XXX-0.12-3.fc12.noarch requires perl(base)
perl-XXX-0.12-3.fc12.noarch requires perl(strict)
Please resolve this as soon as possible.
14 years, 5 months
Broken dependencies: perl-WebService-Validator-CSS-W3C
by Fedora Koji Build System
perl-WebService-Validator-CSS-W3C has broken dependencies in the development tree:
On ppc:
perl-WebService-Validator-CSS-W3C-0.2-2.fc12.noarch requires perl(warnings)
perl-WebService-Validator-CSS-W3C-0.2-2.fc12.noarch requires perl(:MODULE_COMPAT_5.10.0)
perl-WebService-Validator-CSS-W3C-0.2-2.fc12.noarch requires perl(Carp)
perl-WebService-Validator-CSS-W3C-0.2-2.fc12.noarch requires perl(base)
perl-WebService-Validator-CSS-W3C-0.2-2.fc12.noarch requires perl(strict)
On ppc64:
perl-WebService-Validator-CSS-W3C-0.2-2.fc12.noarch requires perl(warnings)
perl-WebService-Validator-CSS-W3C-0.2-2.fc12.noarch requires perl(:MODULE_COMPAT_5.10.0)
perl-WebService-Validator-CSS-W3C-0.2-2.fc12.noarch requires perl(Carp)
perl-WebService-Validator-CSS-W3C-0.2-2.fc12.noarch requires perl(base)
perl-WebService-Validator-CSS-W3C-0.2-2.fc12.noarch requires perl(strict)
Please resolve this as soon as possible.
14 years, 5 months
Broken dependencies: perl-Clipboard
by Fedora Koji Build System
perl-Clipboard has broken dependencies in the development tree:
On ppc:
perl-Clipboard-0.09-2.fc12.noarch requires perl(:MODULE_COMPAT_5.10.0)
perl-Clipboard-0.09-2.fc12.noarch requires /usr/bin/perl
perl-Clipboard-0.09-2.fc12.noarch requires perl(strict)
On ppc64:
perl-Clipboard-0.09-2.fc12.noarch requires perl(:MODULE_COMPAT_5.10.0)
perl-Clipboard-0.09-2.fc12.noarch requires /usr/bin/perl
perl-Clipboard-0.09-2.fc12.noarch requires perl(strict)
Please resolve this as soon as possible.
14 years, 5 months
Broken dependencies: perl-Catalyst-Plugin-Session-Store-File
by Fedora Koji Build System
perl-Catalyst-Plugin-Session-Store-File has broken dependencies in the development tree:
On ppc:
perl-Catalyst-Plugin-Session-Store-File-0.18-1.fc13.noarch requires perl(warnings)
perl-Catalyst-Plugin-Session-Store-File-0.18-1.fc13.noarch requires perl(:MODULE_COMPAT_5.10.0)
perl-Catalyst-Plugin-Session-Store-File-0.18-1.fc13.noarch requires perl(base)
perl-Catalyst-Plugin-Session-Store-File-0.18-1.fc13.noarch requires perl(strict)
On ppc64:
perl-Catalyst-Plugin-Session-Store-File-0.18-1.fc13.noarch requires perl(warnings)
perl-Catalyst-Plugin-Session-Store-File-0.18-1.fc13.noarch requires perl(:MODULE_COMPAT_5.10.0)
perl-Catalyst-Plugin-Session-Store-File-0.18-1.fc13.noarch requires perl(base)
perl-Catalyst-Plugin-Session-Store-File-0.18-1.fc13.noarch requires perl(strict)
Please resolve this as soon as possible.
14 years, 5 months
rpms/perl-Event/EL-4 perl-Event.spec,1.14,1.15 sources,1.7,1.8
by stevetraylen
Author: stevetraylen
Update of /cvs/pkgs/rpms/perl-Event/EL-4
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv32681
Modified Files:
perl-Event.spec sources
Log Message:
First EPEL4 version.
Index: perl-Event.spec
===================================================================
RCS file: /cvs/pkgs/rpms/perl-Event/EL-4/perl-Event.spec,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -p -r1.14 -r1.15
--- perl-Event.spec 1 Sep 2009 07:55:11 -0000 1.14
+++ perl-Event.spec 13 Nov 2009 20:08:29 -0000 1.15
@@ -1,5 +1,5 @@
Name: perl-Event
-Version: 1.12
+Version: 1.13
Release: 1%{?dist}
Summary: Event loop processing
@@ -15,7 +15,7 @@ BuildRequires: /usr/bin/iconv
BuildRequires: perl(ExtUtils::MakeMaker)
BuildRequires: perl(Time::HiRes)
BuildRequires: perl(Test) >= 1
-
+BuildRequires: groff
Requires: perl(Time::HiRes)
%{?perl_default_filter}
@@ -35,9 +35,9 @@ perldoc perlgpl > LICENSE.GPL
perldoc perlartistic > LICENSE.Artistic
# appease rpmlint :)
-find . -type f -exec chmod -c -x {} +
+find . -type f -print -exec chmod -c -x {} \;
%{_fixperms} demo util
-find t/ -type f -exec perl -pi -e 's|^#!\./perl|#!%{__perl}|' {} +
+find t/ -type f -print -exec perl -pi -e 's|^#!\./perl|#!%{__perl}|' {} \;
# fix some other interperter issues..
cd demo
@@ -63,9 +63,9 @@ mv Event.3pm.new Event.3pm
rm -rf %{buildroot}
make pure_install PERL_INSTALL_ROOT=%{buildroot}
-find %{buildroot} -type f -name .packlist -exec rm -f {} +
-find %{buildroot} -type f -name '*.bs' -a -size 0 -exec rm -f {} +
-find %{buildroot} -type d -depth -exec rmdir --ignore-fail-on-non-empty {} +
+find %{buildroot} -type f -name .packlist -exec rm -f {} \;
+find %{buildroot} -type f -name '*.bs' -a -size 0 -exec rm -f {} \;
+find %{buildroot} -type d -depth -exec rmdir --ignore-fail-on-non-empty {} \;
%{_fixperms} %{buildroot}/*
@@ -88,6 +88,9 @@ rm -rf %{buildroot}
%changelog
+* Fri Nov 13 2009 Steve Traylen <steve.traylen(a)cern.ch> 1.13-1
+- New upstream version 1.13
+- Add BR of groff, needed for EPEL4.
* Tue Sep 01 2009 Chris Weyl <cweyl(a)alumni.drew.edu> 1.12-1
- add perl_default_filter
- auto-update to 1.12 (by cpan-spec-update 0.01)
Index: sources
===================================================================
RCS file: /cvs/pkgs/rpms/perl-Event/EL-4/sources,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -p -r1.7 -r1.8
--- sources 1 Sep 2009 07:55:12 -0000 1.7
+++ sources 13 Nov 2009 20:08:29 -0000 1.8
@@ -1 +1 @@
-f09285ef0388be739fbb83bc3a221977 Event-1.12.tar.gz
+88cf5bb6b4b06e016072a5ff2ff8fa1a Event-1.13.tar.gz
14 years, 5 months
rpms/perl-Event/EL-5 .cvsignore, 1.3, 1.4 perl-Event.spec, 1.6, 1.7 sources, 1.5, 1.6
by stevetraylen
Author: stevetraylen
Update of /cvs/pkgs/rpms/perl-Event/EL-5
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv28249
Modified Files:
.cvsignore perl-Event.spec sources
Log Message:
First EPEL5 build.
Index: .cvsignore
===================================================================
RCS file: /cvs/pkgs/rpms/perl-Event/EL-5/.cvsignore,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -p -r1.3 -r1.4
--- .cvsignore 16 Oct 2006 04:37:26 -0000 1.3
+++ .cvsignore 13 Nov 2009 19:47:56 -0000 1.4
@@ -1 +1 @@
-Event-1.07.tar.gz
+Event-1.13.tar.gz
Index: perl-Event.spec
===================================================================
RCS file: /cvs/pkgs/rpms/perl-Event/EL-5/perl-Event.spec,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -p -r1.6 -r1.7
--- perl-Event.spec 1 Jun 2007 21:11:11 -0000 1.6
+++ perl-Event.spec 13 Nov 2009 19:47:56 -0000 1.7
@@ -1,10 +1,10 @@
Name: perl-Event
-Version: 1.09
+Version: 1.13
Release: 1%{?dist}
Summary: Event loop processing
Group: Development/Libraries
-License: Artistic or GPL
+License: GPL+ or Artistic
URL: http://search.cpan.org/dist/Event/
Source0: http://search.cpan.org/CPAN/authors/id/J/JP/JPRIT/Event-%{version}.tar.gz
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
@@ -86,6 +86,10 @@ rm -rf %{buildroot}
%changelog
+* Fri Nov 13 2009 Steve Traylen <steve.traylen(a)cern.ch> 1.13-1
+- Update to 1.13
+- Reformat license string to pass rpmlint
+
* Fri Jun 01 2007 Chris Weyl <cweyl(a)alumni.drew.edu> 1.09-1
- update to 1.09
- add t/ to doc
Index: sources
===================================================================
RCS file: /cvs/pkgs/rpms/perl-Event/EL-5/sources,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -p -r1.5 -r1.6
--- sources 1 Jun 2007 21:11:11 -0000 1.5
+++ sources 13 Nov 2009 19:47:56 -0000 1.6
@@ -1 +1 @@
-3700789e6af2595925a6fe2ce3d5d052 Event-1.09.tar.gz
+88cf5bb6b4b06e016072a5ff2ff8fa1a Event-1.13.tar.gz
14 years, 5 months
rpms/netcdf-perl/devel netcdf-perl.spec,1.9,1.10
by Orion Poplawski
Author: orion
Update of /cvs/pkgs/rpms/netcdf-perl/devel
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv31296
Modified Files:
netcdf-perl.spec
Log Message:
* Thu Nov 11 2009 Orion Poplawski <orion(a)cora.nwra.com> - 1.2.4-3
- Rebuild for netcdf 4.1.0
Index: netcdf-perl.spec
===================================================================
RCS file: /cvs/pkgs/rpms/netcdf-perl/devel/netcdf-perl.spec,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -p -r1.9 -r1.10
--- netcdf-perl.spec 25 Jul 2009 18:03:53 -0000 1.9
+++ netcdf-perl.spec 12 Nov 2009 16:47:19 -0000 1.10
@@ -1,6 +1,6 @@
Name: netcdf-perl
Version: 1.2.4
-Release: 2%{?dist}
+Release: 3%{?dist}
Summary: Perl extension module for scientific data access via the netCDF API
Group: Development/Libraries
@@ -71,6 +71,9 @@ rm -rf $RPM_BUILD_ROOT
%changelog
+* Thu Nov 11 2009 Orion Poplawski <orion(a)cora.nwra.com> - 1.2.4-3
+- Rebuild for netcdf 4.1.0
+
* Sat Jul 25 2009 Fedora Release Engineering <rel-eng(a)lists.fedoraproject.org> - 1.2.4-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild
14 years, 5 months
rpms/perl-Math-Pari/devel .cvsignore, 1.11, 1.12 perl-Math-Pari.spec, 1.21, 1.22 sources, 1.11, 1.12
by Paul Howarth
Author: pghmcfc
Update of /cvs/pkgs/rpms/perl-Math-Pari/devel
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv11383
Modified Files:
.cvsignore perl-Math-Pari.spec sources
Log Message:
Update to 2.01080602 (see Changes for details)
No longer need to fix test suite for 64-bit builds
Index: .cvsignore
===================================================================
RCS file: /cvs/pkgs/rpms/perl-Math-Pari/devel/.cvsignore,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -p -r1.11 -r1.12
--- .cvsignore 6 Nov 2009 09:11:19 -0000 1.11
+++ .cvsignore 12 Nov 2009 10:50:04 -0000 1.12
@@ -1,2 +1,2 @@
-Math-Pari-2.010806.tar.gz
+Math-Pari-2.01080602.tar.gz
pari-2.3.4.tar.gz
Index: perl-Math-Pari.spec
===================================================================
RCS file: /cvs/pkgs/rpms/perl-Math-Pari/devel/perl-Math-Pari.spec,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -p -r1.21 -r1.22
--- perl-Math-Pari.spec 6 Nov 2009 09:11:19 -0000 1.21
+++ perl-Math-Pari.spec 12 Nov 2009 10:50:04 -0000 1.22
@@ -10,14 +10,16 @@
%global pari_version 2.3.4
%global pari_int_version %(echo %{pari_version} | %{__perl} -pi -e 's/(\\d+)\\.(\\d+)\\.(\\d+)/sprintf("%d%03d%03d",$1,$2,$3)/e')
+%global extraversion 02
+
Summary: Perl interface to PARI
Name: perl-Math-Pari
Version: 2.010806
-Release: 1%{?dist}
+Release: 2%{?dist}
License: GPL+ or Artistic
Group: Development/Libraries
Url: http://search.cpan.org/dist/Math-Pari/
-Source0: http://search.cpan.org/CPAN/authors/id/I/IL/ILYAZ/modules/Math-Pari-%{ver...
+Source0: http://search.cpan.org/CPAN/authors/id/I/IL/ILYAZ/modules/Math-Pari-%{ver...
Source1: http://pari.math.u-bordeaux.fr/pub/pari/unix/pari-%{pari_version}.tar.gz
Patch0: perl-Math-Pari-2.010802-no-fake-version.patch
Patch1: perl-Math-Pari-2.010802-docs-and-testsuite.patch
@@ -40,18 +42,11 @@ scientific/ number-theoretic calculation
as Perl functions, and (almost) seamless merging of PARI and Perl data.
%prep
-%setup -q -n Math-Pari-%{version} -a 1
+%setup -q -n Math-Pari-%{version}%{extraversion} -a 1
# Remove spurious executable permission bits
%{__chmod} -x Changes README Pari.pm PariInit.pm func_codes.h Pari.xs
-# If 64-bit test results missing, they should be copied from 32-bit test results
-cd pari-%{pari_version}/src/test/in
-for test in *; do
- [ ! -f ../64/${test} ] && %{__cp} -a ../32/${test} ../64/${test}
-done
-cd -
-
# Don't use a fake version number when we can use a real one
%patch0 -p1
%{__sed} -i -e s/@@@OUR-PARI-VERSION@@@/%{pari_int_version}/ Makefile.PL
@@ -94,6 +89,10 @@ cd -
%exclude %{_mandir}/man3/Math::libPARI.dumb.3pm*
%changelog
+* Thu Nov 12 2009 Paul Howarth <paul(a)city-fan.org> - 2.010806-2
+- Update to 2.01080602 (see Changes for details)
+- No longer need to fix test suite for 64-bit builds
+
* Fri Nov 6 2009 Paul Howarth <paul(a)city-fan.org> - 2.010806-1
- Update to 2.010806
Index: sources
===================================================================
RCS file: /cvs/pkgs/rpms/perl-Math-Pari/devel/sources,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -p -r1.11 -r1.12
--- sources 6 Nov 2009 09:11:19 -0000 1.11
+++ sources 12 Nov 2009 10:50:04 -0000 1.12
@@ -1,2 +1,2 @@
-59a92c209ba1e3a0e908f8110cbd0223 Math-Pari-2.010806.tar.gz
+3148a58fe17ebe4c54e28b2a6ba19ab8 Math-Pari-2.01080602.tar.gz
35c896266e4257793387ba22d5d76078 pari-2.3.4.tar.gz
14 years, 5 months
rpms/perl-bioperl/F-11 bioperl-1.6.1-paths.patch, NONE, 1.1 .cvsignore, 1.8, 1.9 perl-bioperl.spec, 1.21, 1.22 sources, 1.9, 1.10
by alexlan
Author: alexlan
Update of /cvs/extras/rpms/perl-bioperl/F-11
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv26675
Modified Files:
.cvsignore perl-bioperl.spec sources
Added Files:
bioperl-1.6.1-paths.patch
Log Message:
Sync with F_11 branch: Update to latest upstream 1.6.1
bioperl-1.6.1-paths.patch:
BioPerl-1.6.1.mod/Bio/Variation/IO.pm | 2 +-
BioPerl-1.6.1.mod/Bio/Variation/IO.pm.orig |only
BioPerl-1.6.1.mod/Build.PL | 6 +++---
BioPerl-1.6.1.mod/examples/align/align_on_codons.pl | 4 ++--
BioPerl-1.6.1.mod/examples/db/dbfetch | 2 +-
BioPerl-1.6.1.mod/examples/db/getGenBank.pl | 2 +-
BioPerl-1.6.1.mod/examples/db/get_seqs.pl | 2 +-
BioPerl-1.6.1.mod/examples/generate_random_seq.pl | 2 +-
BioPerl-1.6.1.mod/examples/searchio/psiblast_features.pl | 2 +-
BioPerl-1.6.1.mod/examples/structure/structure-io.pl | 2 +-
BioPerl-1.6.1.mod/examples/tk/hitdisplay.pl | 2 +-
BioPerl-1.6.1.mod/examples/tools/gb_to_gff.pl | 2 +-
BioPerl-1.6.1.mod/examples/tools/gff2ps.pl | 2 +-
BioPerl-1.6.1/MANIFEST | 15 ---------------
14 files changed, 15 insertions(+), 30 deletions(-)
--- NEW FILE bioperl-1.6.1-paths.patch ---
diff -u -r BioPerl-1.6.1/Bio/Variation/IO.pm BioPerl-1.6.1.mod/Bio/Variation/IO.pm
--- BioPerl-1.6.1/Bio/Variation/IO.pm 2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.mod/Bio/Variation/IO.pm 2008-09-25 02:03:26.000000000 -0700
@@ -86,7 +86,7 @@
This makes the simplest ever reformatter
- #!/usr/local/bin/perl
+ #!/usr/bin/perl
$format1 = shift;
$format2 = shift;
Only in BioPerl-1.6.1.mod/Bio/Variation: IO.pm.orig
diff -u -r BioPerl-1.6.1/Build.PL BioPerl-1.6.1.mod/Build.PL
--- BioPerl-1.6.1/Build.PL 2009-09-29 12:33:45.000000000 -0400
+++ BioPerl-1.6.1.mod/Build.PL 2009-11-11 22:23:17.000000000 -0500
@@ -31,13 +31,13 @@
'DB_File' => 0,
'Data::Stag' => 0.11, # Bio::SeqIO::swiss, we can change to 'recommend' if needed
'Scalar::Util' => 0, # not in Perl 5.6.1, arrived in core in 5.7.3
- 'ExtUtils::Manifest' => '1.52', # allows spaces in file names
+# 'ExtUtils::Manifest' => '1.52', # allows spaces in file names
},
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',
diff -u -r BioPerl-1.6.1/examples/align/align_on_codons.pl BioPerl-1.6.1.mod/examples/align/align_on_codons.pl
--- BioPerl-1.6.1/examples/align/align_on_codons.pl 2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/align/align_on_codons.pl 2008-09-25 02:03:26.000000000 -0700
@@ -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';
}
$USAGE =
qq{align_on_codons.pl < file.fa
diff -u -r BioPerl-1.6.1/examples/db/dbfetch BioPerl-1.6.1.mod/examples/db/dbfetch
--- BioPerl-1.6.1/examples/db/dbfetch 2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/db/dbfetch 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -- # -*-Perl-*-
+#!/usr/bin/perl -- # -*-Perl-*-
=head1 NAME
diff -u -r BioPerl-1.6.1/examples/db/getGenBank.pl BioPerl-1.6.1.mod/examples/db/getGenBank.pl
--- BioPerl-1.6.1/examples/db/getGenBank.pl 2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/db/getGenBank.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
#
# How to retrieve GenBank entries over the Web
#
diff -u -r BioPerl-1.6.1/examples/db/get_seqs.pl BioPerl-1.6.1.mod/examples/db/get_seqs.pl
--- BioPerl-1.6.1/examples/db/get_seqs.pl 2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/db/get_seqs.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use vars qw($USAGE);
use Carp;
diff -u -r BioPerl-1.6.1/examples/generate_random_seq.pl BioPerl-1.6.1.mod/examples/generate_random_seq.pl
--- BioPerl-1.6.1/examples/generate_random_seq.pl 2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/generate_random_seq.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use vars qw($USAGE);
diff -u -r BioPerl-1.6.1/examples/searchio/psiblast_features.pl BioPerl-1.6.1.mod/examples/searchio/psiblast_features.pl
--- BioPerl-1.6.1/examples/searchio/psiblast_features.pl 2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/searchio/psiblast_features.pl 2008-09-25 02:03:26.000000000 -0700
@@ -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 -u -r BioPerl-1.6.1/examples/structure/structure-io.pl BioPerl-1.6.1.mod/examples/structure/structure-io.pl
--- BioPerl-1.6.1/examples/structure/structure-io.pl 2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/structure/structure-io.pl 2008-09-25 02:03:26.000000000 -0700
@@ -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 -u -r BioPerl-1.6.1/examples/tk/hitdisplay.pl BioPerl-1.6.1.mod/examples/tk/hitdisplay.pl
--- BioPerl-1.6.1/examples/tk/hitdisplay.pl 2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/tk/hitdisplay.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
#
# PROGRAM : hitdisplay.pl
# PURPOSE : Demonstrate Bio::Tk::HitDisplay
diff -u -r BioPerl-1.6.1/examples/tools/gb_to_gff.pl BioPerl-1.6.1.mod/examples/tools/gb_to_gff.pl
--- BioPerl-1.6.1/examples/tools/gb_to_gff.pl 2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/tools/gb_to_gff.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use Bio::Tools::GFF;
diff -u -r BioPerl-1.6.1/examples/tools/gff2ps.pl BioPerl-1.6.1.mod/examples/tools/gff2ps.pl
--- BioPerl-1.6.1/examples/tools/gff2ps.pl 2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/tools/gff2ps.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
=head1 NAME
--- BioPerl-1.6.1/MANIFEST.orig 2008-12-27 20:29:43.000000000 -0700
+++ BioPerl-1.6.1/MANIFEST 2008-12-27 20:31:23.000000000 -0700
@@ -424,15 +424,6 @@
Bio/Phenotype/OMIM/OMIMparser.pm
Bio/Phenotype/Phenotype.pm
Bio/Phenotype/PhenotypeI.pm
-Bio/PhyloNetwork.pm
-Bio/PhyloNetwork/Factory.pm
-Bio/PhyloNetwork/FactoryX.pm
-Bio/PhyloNetwork/GraphViz.pm
-Bio/PhyloNetwork/muVector.pm
-Bio/PhyloNetwork/RandomFactory.pm
-Bio/PhyloNetwork/TreeFactory.pm
-Bio/PhyloNetwork/TreeFactoryMulti.pm
-Bio/PhyloNetwork/TreeFactoryX.pm
Bio/PopGen/Genotype.pm
Bio/PopGen/GenotypeI.pm
Bio/PopGen/HtSNP.pm
@@ -1994,12 +1985,6 @@
t/Tools/tRNAscanSE.t
t/Tree/Compatible.t
t/Tree/Node.t
-t/Tree/PhyloNetwork/Factory.t
-t/Tree/PhyloNetwork/GraphViz.t
-t/Tree/PhyloNetwork/MuVector.t
-t/Tree/PhyloNetwork/PhyloNetwork.t
-t/Tree/PhyloNetwork/RandomFactory.t
-t/Tree/PhyloNetwork/TreeFactory.t
t/Tree/RandomTreeFactory.t
t/Tree/Tree.t
t/Tree/TreeIO.t
Index: .cvsignore
===================================================================
RCS file: /cvs/extras/rpms/perl-bioperl/F-11/.cvsignore,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -p -r1.8 -r1.9
--- .cvsignore 26 Jan 2009 07:28:04 -0000 1.8
+++ .cvsignore 12 Nov 2009 06:33:39 -0000 1.9
@@ -1 +1 @@
-BioPerl-1.6.0.tar.bz2
+BioPerl-1.6.1.tar.bz2
Index: perl-bioperl.spec
===================================================================
RCS file: /cvs/extras/rpms/perl-bioperl/F-11/perl-bioperl.spec,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -p -r1.21 -r1.22
--- perl-bioperl.spec 27 Feb 2009 05:03:51 -0000 1.21
+++ perl-bioperl.spec 12 Nov 2009 06:33:39 -0000 1.22
@@ -1,13 +1,13 @@
Name: perl-bioperl
-Version: 1.6.0
-Release: 2%{?dist}
+Version: 1.6.1
+Release: 1%{?dist}
Summary: Perl tools for computational molecular biology
Group: Development/Libraries
License: GPL+ or Artistic
URL: http://www.bioperl.org/
Source0: http://bioperl.org/DIST/BioPerl-%{version}.tar.bz2
-Patch0: bioperl-1.5.9-paths.patch
+Patch0: bioperl-1.6.1-paths.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildArch: noarch
@@ -18,6 +18,7 @@ BuildRequires: perl(Convert::Binary::C)
BuildRequires: perl(Data::Stag::XMLWriter)
BuildRequires: perl(DBD::mysql)
BuildRequires: perl(DBD::Pg)
+BuildRequires: perl(DBD::SQLite)
BuildRequires: perl(GD) >= 1.3
BuildRequires: perl(GD::SVG)
BuildRequires: perl(Graph)
@@ -41,6 +42,7 @@ BuildRequires: perl(XML::Parser)
BuildRequires: perl(XML::Parser::PerlSAX)
BuildRequires: perl(XML::SAX) >= 0.14
BuildRequires: perl(XML::SAX::Writer)
+BuildRequires: perl(XML::Simple)
BuildRequires: perl(XML::Twig)
BuildRequires: perl(XML::Writer) > 0.4
BuildRequires: perl(Module::Build)
@@ -122,13 +124,22 @@ rm -rf $RPM_BUILD_ROOT
%defattr(-,root,root,-)
## don't distribute "doc" subdirectory, doesn't contain docs
%doc examples models
-%doc AUTHORS BUGS Changes DEPRECATED INSTALL LICENSE PLATFORMS README
+%doc AUTHORS BUGS Changes DEPRECATED INSTALL LICENSE README
%{_bindir}/*
%{perl_vendorlib}/*
%{_mandir}/man1/*.1*
%{_mandir}/man3/*.3*
%changelog
+* Wed Nov 4 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.6.1-1
+- Update to latest upstream 1.6.1
+- Add BR: perl(XML::Simple), perl(DBD:SQLite) for new modules
+- Disable ExtUtils::Manifest build requirement, don't require a MANIFEST
+- Fix doc distributed
+
+* Sun Jul 26 2009 Fedora Release Engineering <rel-eng(a)lists.fedoraproject.org> - 1.6.0-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild
+
* Thu Feb 26 2009 Fedora Release Engineering <rel-eng(a)lists.fedoraproject.org> - 1.6.0-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild
Index: sources
===================================================================
RCS file: /cvs/extras/rpms/perl-bioperl/F-11/sources,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -p -r1.9 -r1.10
--- sources 26 Jan 2009 07:28:04 -0000 1.9
+++ sources 12 Nov 2009 06:33:39 -0000 1.10
@@ -1 +1 @@
-b5bc873aa990892651c3092d7e504397 BioPerl-1.6.0.tar.bz2
+d629dbdb3efca353f8f52108f41c09e0 BioPerl-1.6.1.tar.bz2
14 years, 5 months