git: 5230e317c9a8 - main - biology/ncbi-cxx-toolkit: Update 26.0.1 → 27.0.0

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=5230e317c9a8a5b8e49a97736d920ee8295a2a31

commit 5230e317c9a8a5b8e49a97736d920ee8295a2a31
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2023-06-27 03:50:12 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2023-06-27 04:41:39 +0000

    biology/ncbi-cxx-toolkit: Update 26.0.1 → 27.0.0
    
    Reported by:    portscout
---
 biology/ncbi-cxx-toolkit/Makefile                             |  7 ++++---
 biology/ncbi-cxx-toolkit/distinfo                             |  6 +++---
 .../ncbi-cxx-toolkit/files/patch-src_build-system_configure   | 10 ----------
 ...jtools_edit_pubmed__citmatch_Makefile.pubmed__citmatch.app | 11 +++++++++++
 4 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/biology/ncbi-cxx-toolkit/Makefile b/biology/ncbi-cxx-toolkit/Makefile
index 2a24528adfbc..51b51e58add4 100644
--- a/biology/ncbi-cxx-toolkit/Makefile
+++ b/biology/ncbi-cxx-toolkit/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=	ncbi-cxx-toolkit
 DISTVERSIONPREFIX=	release-
-DISTVERSION=	26.0.1
-PORTREVISION=	3
+DISTVERSION=	27.0.0
 CATEGORIES=	biology science devel
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -15,7 +14,9 @@ BROKEN_armv6=	platform not defined for FreeBSD arm, see https://github.com/ncbi/
 
 LIB_DEPENDS=	libcdd.so:math/cddlib \
 		liblmdb.so:databases/lmdb \
-		libpcre.so:devel/pcre
+		libpcre.so:devel/pcre \
+		libunwind.so:devel/libunwind \
+		libzstd.so:archivers/zstd
 RUN_DEPENDS=	bash:shells/bash
 
 USES=		compiler:c++17-lang gmake mysql perl5 python shebangfix ssl xorg
diff --git a/biology/ncbi-cxx-toolkit/distinfo b/biology/ncbi-cxx-toolkit/distinfo
index af7c94b0fa38..61f897e153de 100644
--- a/biology/ncbi-cxx-toolkit/distinfo
+++ b/biology/ncbi-cxx-toolkit/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1643225773
-SHA256 (ncbi-ncbi-cxx-toolkit-public-release-26.0.1_GH0.tar.gz) = aba79da5c8d0407ffc92b7831f4f8f8a8096a15e47a016ada81b6568f9d280cc
-SIZE (ncbi-ncbi-cxx-toolkit-public-release-26.0.1_GH0.tar.gz) = 103933829
+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
diff --git a/biology/ncbi-cxx-toolkit/files/patch-src_build-system_configure b/biology/ncbi-cxx-toolkit/files/patch-src_build-system_configure
deleted file mode 100644
index c6ca30fee2c4..000000000000
--- a/biology/ncbi-cxx-toolkit/files/patch-src_build-system_configure
+++ /dev/null
@@ -1,10 +0,0 @@
---- src/build-system/configure.orig	2020-09-27 04:51:28 UTC
-+++ src/build-system/configure
-@@ -8080,6 +8080,7 @@ case "$compiler:$ncbi_compiler_ver" in
-     ICC:??.?.? | \
-     ICC:??.?.?.* ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)\.\([0-9]\).*/\1\2\3/' ;;
-     *:?.?.?)    ncbi_compiler_sed='s/\([0-9]\)\.\([0-9]\)\.\([0-9]\)/\1\2\3/' ;;
-+    *:??.?.?)   ncbi_compiler_sed='s/\([1-9][0-9]\)\.\([0-9]\)\.\([0-9]\)/\1\2\3/' ;;
-     *:?.??*)    ncbi_compiler_sed='s/\([0-9]\)\.\([0-9][0-9]\).*/\1\2/' ;;
-     *:?.?)      ncbi_compiler_sed='s/\([0-9]\).\([0-9]\)/\1\20/' ;;
-     *:?)        ncbi_compiler_sed='s/\([0-9]\)/\100/' ;;
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
new file mode 100644
index 000000000000..8781ac4b7d09
--- /dev/null
+++ b/biology/ncbi-cxx-toolkit/files/patch-src_objtools_edit_pubmed__citmatch_Makefile.pubmed__citmatch.app
@@ -0,0 +1,11 @@
+--- 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)