CVS commit: pkgsrc/biology/bioperl

["Thomas Klausner" <wiz%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wiz
Date:           Sun Sep 17 07:48:11 UTC 2017

Modified Files:
        pkgsrc/biology/bioperl: Makefile distinfo

Log Message:
bioperl: update to 1.007002.

Add p5-Text-Diff as test dependency.

1.7.2 - "Entebbe"

    [Bugs]

    * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
    * #245 - Code coverage fixes [zmughal,cjfields]
    * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
    * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
    * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
    * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
    * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
    * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
    * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
    * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
    * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
    * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]

    [Code changes]

    * PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]


To generate a diff of this commit:
cvs rdiff -u -r1.34 -r1.35 pkgsrc/biology/bioperl/Makefile
cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/bioperl/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/bioperl/Makefile
diff -u pkgsrc/biology/bioperl/Makefile:1.34 pkgsrc/biology/bioperl/Makefile:1.35
--- pkgsrc/biology/bioperl/Makefile:1.34        Thu Nov 10 14:00:17 2016
+++ pkgsrc/biology/bioperl/Makefile     Sun Sep 17 07:48:11 2017
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.34 2016/11/10 14:00:17 fhajny Exp $
+# $NetBSD: Makefile,v 1.35 2017/09/17 07:48:11 wiz Exp $
 
-DISTNAME=      BioPerl-1.007001
+DISTNAME=      BioPerl-1.007002
 PKGNAME=       ${DISTNAME:tl}
 CATEGORIES=    biology perl5
 MASTER_SITES=  ${MASTER_SITE_PERL_CPAN:=Bio/}
@@ -49,6 +49,8 @@ DEPENDS+=     p5-libxml-[0-9]*:../../textpro
 
 # Suggested
 DEPENDS+=      p5-XML-DOM>=0:../../textproc/p5-XML-DOM
+# TEST_DEPENDS
+BUILD_DEPENDS+=        p5-Text-Diff-[0-9]*:../../textproc/p5-Text-Diff
 
 USE_TOOLS+=            pax
 

Index: pkgsrc/biology/bioperl/distinfo
diff -u pkgsrc/biology/bioperl/distinfo:1.8 pkgsrc/biology/bioperl/distinfo:1.9
--- pkgsrc/biology/bioperl/distinfo:1.8 Sun Nov  6 08:05:24 2016
+++ pkgsrc/biology/bioperl/distinfo     Sun Sep 17 07:48:11 2017
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.8 2016/11/06 08:05:24 wen Exp $
+$NetBSD: distinfo,v 1.9 2017/09/17 07:48:11 wiz Exp $
 
-SHA1 (BioPerl-1.007001.tar.gz) = 13a3e7a30d68ee32d735921668839eda668771f4
-RMD160 (BioPerl-1.007001.tar.gz) = c433044f47f5827f480836329487bf5780c9f480
-SHA512 (BioPerl-1.007001.tar.gz) = 6ab6af9d8fa74a299870273f2843872af099764997aa1b03f88248502f9ed1b74f4f577b67befa1ae8c18ee2640c029a08a403e2dec5b1cdea41f2b86c82c11b
-Size (BioPerl-1.007001.tar.gz) = 12486953 bytes
+SHA1 (BioPerl-1.007002.tar.gz) = 21ab4653fde8cd8520bd7f59f790535f99358eaa
+RMD160 (BioPerl-1.007002.tar.gz) = 6c38bb83464a36546e22629675f881d42dbda4bd
+SHA512 (BioPerl-1.007002.tar.gz) = d89502dd0561a9a969d816e6d66df7f11e57709934095a87027d2637d16a463f0669f7d7392d95a1c8a9db94bfa8d6ec714668a4b9f81fa8b9b512796138d287
+Size (BioPerl-1.007002.tar.gz) = 12362741 bytes