git: 0c9f38b3b81f - main - biology/sra-tools: Update to 3.3.0

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=0c9f38b3b81f6cfea7e331318c3cf21f0a50520c

commit 0c9f38b3b81f6cfea7e331318c3cf21f0a50520c
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2025-12-17 16:13:10 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2025-12-17 16:18:23 +0000

    biology/sra-tools: Update to 3.3.0
    
    Several minor enhancements and fixes
    Changes:
        ${WRKSRC}/CHANGES.md
        https://github.com/ncbi/sra-tools/commits/master/
    
    Reported by:    portscout
---
 biology/sra-tools/Makefile                    |  2 +-
 biology/sra-tools/distinfo                    | 10 +++++-----
 biology/sra-tools/files/patch-libs_kxml_xml.c | 11 +++++++++++
 biology/sra-tools/pkg-plist                   |  4 ++++
 4 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile
index 3fa9ae25ebeb..b272f6b61534 100644
--- a/biology/sra-tools/Makefile
+++ b/biology/sra-tools/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	sra-tools
-DISTVERSION=	3.2.1
+DISTVERSION=	3.3.0
 CATEGORIES=	biology java
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/biology/sra-tools/distinfo b/biology/sra-tools/distinfo
index d74965cf7e1a..5897b65aa802 100644
--- a/biology/sra-tools/distinfo
+++ b/biology/sra-tools/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1742507022
-SHA256 (ncbi-sra-tools-3.2.1_GH0.tar.gz) = 2558683c217ad2318833ab7731939617ed91dc79a6b1dee92bf88b56a1dc142a
-SIZE (ncbi-sra-tools-3.2.1_GH0.tar.gz) = 66684089
-SHA256 (ncbi-ncbi-vdb-3.2.1_GH0.tar.gz) = 535511984928ec5bac02a61fc6b4d1ca72a5b69c742f4882eabd32ed3a97621c
-SIZE (ncbi-ncbi-vdb-3.2.1_GH0.tar.gz) = 19061776
+TIMESTAMP = 1765984755
+SHA256 (ncbi-sra-tools-3.3.0_GH0.tar.gz) = 3bfa26c5499a94d3b2a98eb65113bbb902f51dadef767c7c7247fc0175885a9a
+SIZE (ncbi-sra-tools-3.3.0_GH0.tar.gz) = 66485758
+SHA256 (ncbi-ncbi-vdb-3.3.0_GH0.tar.gz) = 36b3467affd53bea794e3eeb5598619d820bc726dc68751a189181ac7973047d
+SIZE (ncbi-ncbi-vdb-3.3.0_GH0.tar.gz) = 19055705
diff --git a/biology/sra-tools/files/patch-libs_kxml_xml.c b/biology/sra-tools/files/patch-libs_kxml_xml.c
new file mode 100644
index 000000000000..76ec7a13fee4
--- /dev/null
+++ b/biology/sra-tools/files/patch-libs_kxml_xml.c
@@ -0,0 +1,11 @@
+--- libs/kxml/xml.c.orig	2025-12-03 13:29:03 UTC
++++ libs/kxml/xml.c
+@@ -171,7 +171,7 @@ rc_t KXMLMgrSchemaValidate ( const KXMLMgr *self,
+ }
+ #endif
+ 
+-static void s_xmlGenericErrorDefaultFunc(void *ctx ATTRIBUTE_UNUSED,
++static void s_xmlGenericErrorDefaultFunc(void *ctx,
+     const char *msg,
+     ...)
+ {
diff --git a/biology/sra-tools/pkg-plist b/biology/sra-tools/pkg-plist
index e047e75fdafd..0bc4898e1af5 100644
--- a/biology/sra-tools/pkg-plist
+++ b/biology/sra-tools/pkg-plist
@@ -181,6 +181,10 @@ jar/ngs-doc.jar
 jar/ngs-examples.jar
 jar/ngs-java.jar
 jar/ngs-src.jar
+lib64/libkapp-static.a
+lib64/libkapp.a
+lib64/libkapp.a.3
+lib64/libkapp.a.%%PORTVERSION%%
 lib64/libncbi-ngs-c++-static.a
 lib64/libncbi-ngs-c++.a
 lib64/libncbi-ngs-c++.a.3