<pre style='margin:0'>
David B. Evans (dbevans) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/0b3078b739a0ed39ac2b9131dc3f1eeb45656cad">https://github.com/macports/macports-ports/commit/0b3078b739a0ed39ac2b9131dc3f1eeb45656cad</a></p>
<pre style="white-space: pre; background: #F8F8F8">The following commit(s) were added to refs/heads/master by this push:
<span style='display:block; white-space:pre;color:#404040;'> new 0b3078b739a p5-bio-db-ncbihelper: update to version 1.7.8
</span>0b3078b739a is described below
<span style='display:block; white-space:pre;color:#808000;'>commit 0b3078b739a0ed39ac2b9131dc3f1eeb45656cad
</span>Author: David B. Evans <devans@macports.org>
AuthorDate: Mon Dec 18 15:22:08 2023 -0800
<span style='display:block; white-space:pre;color:#404040;'> p5-bio-db-ncbihelper: update to version 1.7.8
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> Drop patches now encorporated upstream.
</span>---
perl/p5-bio-db-ncbihelper/Portfile | 14 +++++---------
.../files/fix-phygadeuon-ovatus.patch | 22 ----------------------
.../files/remove-unrecognized-alias.patch | 12 ------------
3 files changed, 5 insertions(+), 43 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/perl/p5-bio-db-ncbihelper/Portfile b/perl/p5-bio-db-ncbihelper/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 594908cb4cf..fb3f1458d51 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/perl/p5-bio-db-ncbihelper/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/perl/p5-bio-db-ncbihelper/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -4,19 +4,19 @@ PortSystem 1.0
</span> PortGroup perl5 1.0
perl5.branches 5.28 5.30 5.32 5.34
<span style='display:block; white-space:pre;background:#ffe0e0;'>-perl5.setup Bio-DB-NCBIHelper 1.7.7 ../../authors/id/C/CJ/CJFIELDS
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+perl5.setup Bio-DB-NCBIHelper 1.7.8 ../../authors/id/C/CJ/CJFIELDS
</span> revision 0
license {Artistic-1 GPL}
maintainers {devans @dbevans} openmaintainer
description Bio::DB::NCBIHelper - A collection of routines useful for queries to NCBI databases
<span style='display:block; white-space:pre;background:#ffe0e0;'>-long_description ${description}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description {*}${description}
</span>
platforms {darwin any}
supported_archs noarch
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 a651c0a237ed79ca971dbdc564052aa7e4274e4a \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 b90bfbbaaa772c8da023130c2e3f85b5a0cd6decc4973cd615a3334410627b5c \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size 45290
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 38e1f7dc4a8fef60221e7b7f4235d12eee212eb6 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 f8e2a739c872608a24003a642a686b6e9c72af59a3bc0aceea6e5a5c2ea5ecbf \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 45770
</span>
if {${perl5.major} != ""} {
depends_build-append \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -34,8 +34,4 @@ if {${perl5.major} != ""} {
</span> port:p${perl5.major}-lwp-protocol-https \
port:p${perl5.major}-uri \
port:p${perl5.major}-xml-twig
<span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # fixes for test t/Taxonomy.t
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- patchfiles remove-unrecognized-alias.patch \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- fix-phygadeuon-ovatus.patch
</span> }
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/perl/p5-bio-db-ncbihelper/files/fix-phygadeuon-ovatus.patch b/perl/p5-bio-db-ncbihelper/files/fix-phygadeuon-ovatus.patch
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 4d83cca603f..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/perl/p5-bio-db-ncbihelper/files/fix-phygadeuon-ovatus.patch
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,22 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- t/Taxonomy.t.orig 2021-12-21 12:52:06.000000000 -0800
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ t/Taxonomy.t 2021-12-21 13:42:49.000000000 -0800
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -166,8 +166,8 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # 'Chlorella vulgaris' | 3077 | 3077
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # 'Phygadeuon solidus' | 1763951 | 1763951
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # 'Ovatus' | 666060 | 666060
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- # 'Phygadeuon ovatus' | "No hit" | 666060
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- # 'Trimorus ovatus' | "No hit" | 666060
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ # 'Phygadeuon ovatus' | 2890685 | 2890685
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ # 'Trimorus ovatus' | "No hit" | "No hit"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- my @ids;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- @ids = $db->get_taxonids('Lissotriton vulgaris');
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -179,7 +179,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- @ids = $db->get_taxonids('Ovatus');
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- is $ids[0], 666060, 'Correct: Ovatus';
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- @ids = $db->get_taxonids('Phygadeuon ovatus');
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- is $ids[0], 'No hit', 'Correct: No hit';
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ is $ids[0], 2890685, 'Correct: Phygadeuon ovatus';
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- @ids = $db->get_taxonids('Trimorus ovatus');
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- is $ids[0], 'No hit', 'Correct: No hit';
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/perl/p5-bio-db-ncbihelper/files/remove-unrecognized-alias.patch b/perl/p5-bio-db-ncbihelper/files/remove-unrecognized-alias.patch
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 44b4d04f565..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/perl/p5-bio-db-ncbihelper/files/remove-unrecognized-alias.patch
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,12 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- t/Taxonomy.t.orig 2021-12-21 10:45:09.000000000 -0800
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ t/Taxonomy.t 2021-12-21 10:52:14.000000000 -0800
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -45,7 +45,8 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- my %common_names = map { $_ => 1 } $n->common_names;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- cmp_ok keys %common_names, '>=', 3, ref($db).": common names";
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ok exists $common_names{human};
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ok exists $common_names{man};
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+# 'man' is no longer a recognized alias for Homo Sapiens in the Taxonomy database
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+# ok exists $common_names{man};
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- is $n->division, 'Primates';
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- is $n->genetic_code, 1;
</span></pre><pre style='margin:0'>
</pre>