[Bioperl-guts-l] [15489] bioperl-network/branches/branch-1-6: sync with trunk, branch-specific versioning
Christopher John Fields
cjfields at dev.open-bio.org
Sat Jan 31 23:53:22 EST 2009
Revision: 15489
Author: cjfields
Date: 2009-01-31 23:53:22 -0500 (Sat, 31 Jan 2009)
Log Message:
-----------
sync with trunk, branch-specific versioning
Modified Paths:
--------------
bioperl-network/branches/branch-1-6/Build.PL
bioperl-network/branches/branch-1-6/INSTALL
Modified: bioperl-network/branches/branch-1-6/Build.PL
===================================================================
--- bioperl-network/branches/branch-1-6/Build.PL 2009-02-01 04:52:36 UTC (rev 15488)
+++ bioperl-network/branches/branch-1-6/Build.PL 2009-02-01 04:53:22 UTC (rev 15489)
@@ -6,20 +6,23 @@
# Uses a custom subclass of Module::Build called Bio::Root::Build
use strict;
-use Bio::Root::Build;
+my $v = '1.005009_002';
+eval "use Bio::Root::Build $v";
+if ($@) {
+ # using die so wrappers can catch the error message
+ die "BioPerl minimal core version $v is required for BioPerl-network\n";
+}
# Set up the Bio::Root::Build object
my $build = Bio::Root::Build->new(
module_name => 'Bio',
dist_name => 'BioPerl-network',
- dist_version => '1.005009_001',
+ dist_version => $v,
dist_author => 'BioPerl Team <bioperl-l at bioperl.org>',
dist_abstract => 'BioPerl-network - package for biological networks',
license => 'perl',
requires => {'perl' => '5.6.1',
- # this can be bumped to a higher point version if a
- # fix is needed from a core 1.6 point release
- 'Bio::Root::Version' => '1.006000',
+ #'Bio::Root::Version' => '1.006000', # checked above
'Graph' => 0.86 },
recommends => {'XML::Twig' => '3.22/parsing PSI XML/Bio::Graph::IO::psi'},
dynamic_config => 1,
Modified: bioperl-network/branches/branch-1-6/INSTALL
===================================================================
--- bioperl-network/branches/branch-1-6/INSTALL 2009-02-01 04:52:36 UTC (rev 15488)
+++ bioperl-network/branches/branch-1-6/INSTALL 2009-02-01 04:53:22 UTC (rev 15489)
@@ -9,93 +9,94 @@
1. Requirements
- Perl 5.6.1 is required.
+ Perl 5.6.1 is required, but 5.8 or greater is recommended.
The bioperl-network package depends on the core BioPerl package. See
http://www.bioperl.org/wiki/Getting_BioPerl or the BioPerl INSTALL file
- for instructions for downloading and installing BioPerl. You must
- install at least the corresponding version of Bioperl: since this
- is bioperl-network 1.5.2, bioperl 1.5.2 is required.
+ for instructions for downloading and installing BioPerl. You should
+ install at least the corresponding version of Bioperl: since this
+ is bioperl-network 1.6, bioperl 1.6 or greater is recommended.
- bioperl-network also depends on Perl's Graph package. See CPAN at
- www.perl.org for instructions on downloading and installing Graph,
- use Graph version .86 or greater.
+ bioperl-network also depends on Perl's Graph package. See CPAN at
+ www.perl.org for instructions on downloading and installing Graph,
+ use Graph version .86 or greater.
- Reading PSI XML files using bioperl-network requires the XML::Twig
- module. See CPAN at www.perl.org for instructions on downloading
- and installing XML::Twig.
+ Reading PSI XML files using bioperl-network requires the XML::Twig
+ module. See CPAN at www.perl.org for instructions on downloading
+ and installing XML::Twig.
2. Installing bioperl-network (Unix, Mac OS X and Cygwin)
- Installation instructions at the following address apply here:
- http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix
- The following sections summarize the essential points from there.
+ Installation instructions at the following address apply here:
+ http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix
+ The following sections summarize the essential points from there.
- Using CPAN:
- To install using CPAN you will need a recent version (v1.8802 has
- been tested) of it and your prefer_installer conf set to 'MB':
+ Using CPAN:
+
+ To install using CPAN you will need a recent version (v1.8802 has
+ been tested) of it and your prefer_installer conf set to 'MB':
>cpan
cpan>o conf prefer_installer MB
cpan>o conf commit
cpan>q
- Now find the name of the bioperl-network version you want:
+ Now find the name of the bioperl-network version you want:
>cpan
cpan>d /bioperl-network/
Database was generated on Mon, 20 Nov 2006 05:24:36 GMT
- Distribution S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz
+ Distribution C/CJ/CJFIELDS/bioperl-network-1.006000.tar.gz
- Now install:
+ Now install:
- cpan>install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz
+ cpan>install C/CJ/CJFIELDS/bioperl-network-1.006000.tar.gz
- If you've installed everything perfectly then you may pass all the tests
- run in the './Build test' phase.
- It's also possible that you may fail some tests. Possible explanations:
- problems with local Perl installation, previously undetected bug in
- Bioperl, flawed test script and so on. A few failed tests may not affect
- your usage of bioperl-network.
+ If you've installed everything perfectly then you may pass all the tests
+ run in the './Build test' phase.
+ It's also possible that you may fail some tests. Possible explanations:
+ problems with local Perl installation, previously undetected bug in
+ Bioperl, flawed test script and so on. A few failed tests may not affect
+ your usage of bioperl-network.
- If you decide that the failed tests will not affect how you intend to use
- bioperl-network and you'd like to install anyway do:
+ If you decide that the failed tests will not affect how you intend to use
+ bioperl-network and you'd like to install anyway do:
- cpan>force install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz
+ cpan>force C/CJ/CJFIELDS/bioperl-network-1.006000.tar.gz
- This is what most experienced Bioperl users would do. However, if you're
- concerned about a failed test and need assistance or advice then contact
- bioperl-l at bioperl.org.
+ This is what most experienced Bioperl users would do. However, if you're
+ concerned about a failed test and need assistance or advice then contact
+ bioperl-l at bioperl.org.
Manual installation:
+
>gunzip bioperl-network-<release-version>.tar.gz
>tar xvf bioperl-network-<release-version>.tar
>cd bioperl-network
- where <release-version> is the current release.
+ where <release-version> is the current release.
>perl Build.PL
- You can run regression tests and install bioperl-network using the
- following commands:
+ You can run regression tests and install bioperl-network using the
+ following commands:
>./Build test
>./Build install
+ You may have to have root privileges in order to run './Build install'
+ successfully on Unix. See the BioPerl INSTALL file for alternative approaches
+ if you don't have root or administrative privileges.
- You may have to have root privileges in order to run './Build install'
- successfully on Unix. See the BioPerl INSTALL file for alternative approaches
- if you don't have root or administrative privileges.
-
3. Installing bioperl-network (Windows and ActiveState Perl)
- The following page on the BioPerl website has up-to-date
- instructions on how to install bioperl-network on Windows:
+ The following page on the BioPerl website has up-to-date
+ instructions on how to install bioperl-network on Windows:
http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
- (the instructions are aimed at bioperl-core, but apply
- equally to bioperl-network)
+ The instructions are aimed at bioperl-core, but apply
+ equally to bioperl-network.
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