git: 883c0d3b6207 - main - biology/ncbi-cxx-toolkit: update 27.0.0 → 28.0.0

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=883c0d3b620714610b65cab9f81abcc6c60b9f36

commit 883c0d3b620714610b65cab9f81abcc6c60b9f36
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2024-01-05 09:32:05 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2024-01-05 09:38:14 +0000

    biology/ncbi-cxx-toolkit: update 27.0.0 → 28.0.0
---
 biology/ncbi-cxx-toolkit/Makefile                             |  6 +++---
 biology/ncbi-cxx-toolkit/distinfo                             |  6 +++---
 ...jtools_edit_pubmed__citmatch_Makefile.pubmed__citmatch.app | 11 -----------
 3 files changed, 6 insertions(+), 17 deletions(-)

diff --git a/biology/ncbi-cxx-toolkit/Makefile b/biology/ncbi-cxx-toolkit/Makefile
index 252a5ea5a484..524c59417088 100644
--- a/biology/ncbi-cxx-toolkit/Makefile
+++ b/biology/ncbi-cxx-toolkit/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=	ncbi-cxx-toolkit
 DISTVERSIONPREFIX=	release-
-DISTVERSION=	27.0.0
-PORTREVISION=	1
+DISTVERSION=	28.0.0
 CATEGORIES=	biology science devel
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -13,7 +12,8 @@ LICENSE_FILE=	${WRKSRC}/doc/public/LICENSE
 
 BROKEN_armv6=	platform not defined for FreeBSD arm, see https://github.com/ncbi/ncbi-cxx-toolkit-public/issues/2
 
-LIB_DEPENDS=	libcdd.so:math/cddlib \
+LIB_DEPENDS=	libbz2.so:archivers/bzip2 \
+		libcdd.so:math/cddlib \
 		liblmdb.so:databases/lmdb \
 		libpcre.so:devel/pcre \
 		libunwind.so:devel/libunwind \
diff --git a/biology/ncbi-cxx-toolkit/distinfo b/biology/ncbi-cxx-toolkit/distinfo
index 61f897e153de..d43fffbfce8d 100644
--- a/biology/ncbi-cxx-toolkit/distinfo
+++ b/biology/ncbi-cxx-toolkit/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1687817071
-SHA256 (ncbi-ncbi-cxx-toolkit-public-release-27.0.0_GH0.tar.gz) = c8fb3f99c6fce4f170b381f3a7789c76a2ff1c23c094c9852e2e3de1fdc57277
-SIZE (ncbi-ncbi-cxx-toolkit-public-release-27.0.0_GH0.tar.gz) = 57187775
+TIMESTAMP = 1704429509
+SHA256 (ncbi-ncbi-cxx-toolkit-public-release-28.0.0_GH0.tar.gz) = f0300db41849bbaf690c1dfb9080f3e441fc617a004283acfb2b7b25b32ff885
+SIZE (ncbi-ncbi-cxx-toolkit-public-release-28.0.0_GH0.tar.gz) = 57007980
diff --git a/biology/ncbi-cxx-toolkit/files/patch-src_objtools_edit_pubmed__citmatch_Makefile.pubmed__citmatch.app b/biology/ncbi-cxx-toolkit/files/patch-src_objtools_edit_pubmed__citmatch_Makefile.pubmed__citmatch.app
deleted file mode 100644
index 8781ac4b7d09..000000000000
--- a/biology/ncbi-cxx-toolkit/files/patch-src_objtools_edit_pubmed__citmatch_Makefile.pubmed__citmatch.app
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/objtools/edit/pubmed_citmatch/Makefile.pubmed_citmatch.app.orig	2023-06-26 23:22:57 UTC
-+++ src/objtools/edit/pubmed_citmatch/Makefile.pubmed_citmatch.app
-@@ -2,7 +2,7 @@
- 
- APP = pubmed_citmatch
- SRC = pubmed_citmatch
--LIB = $(OBJEDIT_LIBS) mlacli mla eutils uilist efetch $(SEQ_LIBS) \
-+LIB = $(OBJEDIT_LIBS) mlacli mla eutils uilist efetch seqset $(SEQ_LIBS) \
-       pubmed medlars pub medline biblio general xser xconnect xutil xncbi
- 
- LIBS = $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)