<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/dc5dc332965c312e555780d173e3a1eca970a35b">https://github.com/macports/macports-ports/commit/dc5dc332965c312e555780d173e3a1eca970a35b</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 dc5dc332965 p5-bio-db-ncbihelper: update to version 1.7.7
</span>dc5dc332965 is described below
<span style='display:block; white-space:pre;color:#808000;'>commit dc5dc332965c312e555780d173e3a1eca970a35b
</span>Author: David B. Evans <devans@macports.org>
AuthorDate: Tue Dec 21 14:12:51 2021 -0800
<span style='display:block; white-space:pre;color:#404040;'> p5-bio-db-ncbihelper: update to version 1.7.7
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> Patch test t/Taxonomy.t to work with current NCBI Taxonomy database (20211221).
</span><span style='display:block; white-space:pre;color:#404040;'> See https://www.ncbi.nlm.nih.gov/taxonomy
</span>---
perl/p5-bio-db-ncbihelper/Portfile | 13 +++++++++----
.../files/fix-phygadeuon-ovatus.patch | 22 ++++++++++++++++++++++
.../files/remove-unrecognized-alias.patch | 12 ++++++++++++
3 files changed, 43 insertions(+), 4 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 3ec42fc4dd9..e84bfa41a05 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;'>@@ -4,7 +4,8 @@ PortSystem 1.0
</span> PortGroup perl5 1.0
perl5.branches 5.28 5.30 5.32
<span style='display:block; white-space:pre;background:#ffe0e0;'>-perl5.setup Bio-DB-NCBIHelper 1.7.6 ../../authors/id/C/CJ/CJFIELDS
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+perl5.setup Bio-DB-NCBIHelper 1.7.7 ../../authors/id/C/CJ/CJFIELDS
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span> 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:#e0e0e0;'>@@ -12,9 +13,9 @@ long_description ${description}
</span>
platforms darwin
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 f8dae85114abe0954a88dbe3dcb96c1a95c7879d \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 6475fef8475e9491fec352b4fe3a6249be7b0bee92e7bad62c3f81ca31e3bcc7 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size 45150
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 a651c0a237ed79ca971dbdc564052aa7e4274e4a \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 b90bfbbaaa772c8da023130c2e3f85b5a0cd6decc4973cd615a3334410627b5c \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 45290
</span>
if {${perl5.major} != ""} {
depends_build-append \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -33,5 +34,9 @@ if {${perl5.major} != ""} {
</span> port:p${perl5.major}-uri \
port:p${perl5.major}-xml-twig
<span style='display:block; white-space:pre;background:#e0ffe0;'>+ # fixes for test t/Taxonomy.t
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ patchfiles remove-unrecognized-alias.patch \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ fix-phygadeuon-ovatus.patch
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span> supported_archs noarch
}
<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>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..4d83cca603f
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/perl/p5-bio-db-ncbihelper/files/fix-phygadeuon-ovatus.patch
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,22 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- t/Taxonomy.t.orig 2021-12-21 12:52:06.000000000 -0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ t/Taxonomy.t 2021-12-21 13:42:49.000000000 -0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -166,8 +166,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # 'Chlorella vulgaris' | 3077 | 3077
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # 'Phygadeuon solidus' | 1763951 | 1763951
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # 'Ovatus' | 666060 | 666060
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- # 'Phygadeuon ovatus' | "No hit" | 666060
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- # 'Trimorus ovatus' | "No hit" | 666060
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ # 'Phygadeuon ovatus' | 2890685 | 2890685
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ # 'Trimorus ovatus' | "No hit" | "No hit"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ my @ids;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ @ids = $db->get_taxonids('Lissotriton vulgaris');
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -179,7 +179,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ @ids = $db->get_taxonids('Ovatus');
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ is $ids[0], 666060, 'Correct: Ovatus';
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ @ids = $db->get_taxonids('Phygadeuon ovatus');
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- is $ids[0], 'No hit', 'Correct: No hit';
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ is $ids[0], 2890685, 'Correct: Phygadeuon ovatus';
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ @ids = $db->get_taxonids('Trimorus ovatus');
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ is $ids[0], 'No hit', 'Correct: No hit';
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</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>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..44b4d04f565
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/perl/p5-bio-db-ncbihelper/files/remove-unrecognized-alias.patch
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,12 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- t/Taxonomy.t.orig 2021-12-21 10:45:09.000000000 -0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ t/Taxonomy.t 2021-12-21 10:52:14.000000000 -0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -45,7 +45,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ my %common_names = map { $_ => 1 } $n->common_names;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ cmp_ok keys %common_names, '>=', 3, ref($db).": common names";
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ok exists $common_names{human};
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ok exists $common_names{man};
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++# 'man' is no longer a recognized alias for Homo Sapiens in the Taxonomy database
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++# ok exists $common_names{man};
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ is $n->division, 'Primates';
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ is $n->genetic_code, 1;
</span></pre><pre style='margin:0'>
</pre>