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
@@ -1,64 +1,64 @@
 PORTNAME=	sra-tools
-DISTVERSION=	3.2.1
+DISTVERSION=	3.3.0
 CATEGORIES=	biology java
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	NCBI's toolkit for handling data in INSDC Sequence Read Archives
 WWW=		https://github.com/ncbi/sra-tools
 
 LICENSE=		PD LGPL21+
 LICENSE_COMB=		multi
 LICENSE_FILE_PD=	${WRKSRC}/LICENSE
 LICENSE_DISTFILES_LGPL21+ =
 
 ONLY_FOR_ARCHS=		aarch64 amd64
 ONLY_FOR_ARCHS_REASON=	Upstream explicitly supports specific platforms
 
 # hdf5 is dynamically loaded by some tools, but nothing links to it
 BUILD_DEPENDS=	bash:shells/bash
 RUN_DEPENDS=	hdf5>0:science/hdf5
 
 USES=		bison cmake java shebangfix
 USE_GITHUB=	yes
 USE_LDCONFIG=	${PREFIX}/lib64
 
 # Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
 JAVA_VERSION=	17+
 
 OPTIONS_DEFINE=	EXAMPLES
 
 SHEBANG_GLOB=	*.sh
 GH_ACCOUNT=	ncbi
 # FIXME: At the time this was added, sra-tools build required access to the
 # ncbi-vdb source tree.  Use a separate dependent port if that is no
 # longer the case.  CMakeLists.txt still looks for ../ncbi-vdb in 3.1.1.
 GH_TUPLE+=	ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb
 
 CMAKE_ARGS+=	-DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
 
 PLIST_SUB=	PORTVERSION=${PORTVERSION}
 
 pre-configure:
 	# Reinplaces may follow static patches.  Run "make clean patch"
 	# before updating those patches so reinplaces do not get added to them.
 	@${REINPLACE_CMD} -e 's|"/etc/ncbi"|"${PREFIX}/etc/ncbi"|g' \
 		${WRKSRC}/ncbi-vdb/libs/kfg/config.c
 	@${REINPLACE_CMD} -e 's|/usr/local/bin|${PREFIX}/bin|g' \
 		${WRKSRC}/tools/external/driver-tool/file-path.posix.cpp
 	@${REINPLACE_CMD} -e 's|/../ncbi-vdb|/ncbi-vdb|g' \
 		${WRKSRC}/CMakeLists.txt
 	cd ${WRKSRC}/ncbi-vdb/build && cmake .. && make
 
 # FIXME: Unsure where the jquery version comes from and it differs on
 # amd64 (jquery-3.7.1.min.js) and aarch64 (jquery-3.6.1.min.js).
 # Just hack the version out for now.  Not sure we even need javadoc installed.
 post-stage:
 	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.${DISTVERSION}
 	${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib64/*.${DISTVERSION}
 	${MV} ${STAGEDIR}${JAVASHAREDIR}doc/ngs-doc/script-dir/jquery-[0-9]*.min.js \
 		${STAGEDIR}${JAVASHAREDIR}doc/ngs-doc/script-dir/jquery.min.js
 
 post-stage-EXAMPLES-off:
 	${RM} -r ${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>
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
@@ -1,282 +1,286 @@
 bin/abi-dump
 bin/abi-dump.3
 bin/abi-dump.%%PORTVERSION%%
 bin/align-info
 bin/align-info.3
 bin/align-info.%%PORTVERSION%%
 bin/cache-mgr
 bin/cache-mgr.3
 bin/cache-mgr.%%PORTVERSION%%
 bin/check-corrupt
 bin/check-corrupt.3
 bin/check-corrupt.%%PORTVERSION%%
 bin/fasterq-dump
 bin/fasterq-dump-orig.%%PORTVERSION%%
 bin/fasterq-dump.3
 bin/fasterq-dump.%%PORTVERSION%%
 bin/fastq-dump
 bin/fastq-dump-orig.%%PORTVERSION%%
 bin/fastq-dump.3
 bin/fastq-dump.%%PORTVERSION%%
 bin/illumina-dump
 bin/illumina-dump.3
 bin/illumina-dump.%%PORTVERSION%%
 bin/kdbmeta
 bin/kdbmeta.3
 bin/kdbmeta.%%PORTVERSION%%
 bin/ngs-pileup
 bin/ngs-pileup.3
 bin/ngs-pileup.%%PORTVERSION%%
 bin/prefetch
 bin/prefetch-orig.%%PORTVERSION%%
 bin/prefetch.3
 bin/prefetch.%%PORTVERSION%%
 bin/rcexplain
 bin/rcexplain.3
 bin/rcexplain.%%PORTVERSION%%
 bin/ref-variation
 bin/ref-variation.3
 bin/ref-variation.%%PORTVERSION%%
 bin/sam-dump
 bin/sam-dump-orig.%%PORTVERSION%%
 bin/sam-dump.3
 bin/sam-dump.%%PORTVERSION%%
 bin/sff-dump
 bin/sff-dump.3
 bin/sff-dump.%%PORTVERSION%%
 bin/sra-info
 bin/sra-info.3
 bin/sra-info.%%PORTVERSION%%
 bin/sra-pileup
 bin/sra-pileup-orig.%%PORTVERSION%%
 bin/sra-pileup.3
 bin/sra-pileup.%%PORTVERSION%%
 bin/sra-search
 bin/sra-search.3
 bin/sra-search.%%PORTVERSION%%
 bin/sra-stat
 bin/sra-stat.3
 bin/sra-stat.%%PORTVERSION%%
 bin/srapath
 bin/srapath-orig.%%PORTVERSION%%
 bin/srapath.3
 bin/srapath.%%PORTVERSION%%
 bin/sratools
 bin/sratools.3
 bin/sratools.%%PORTVERSION%%
 bin/test-sra
 bin/test-sra.3
 bin/test-sra.%%PORTVERSION%%
 bin/var-expand
 bin/var-expand.3
 bin/var-expand.%%PORTVERSION%%
 bin/vdb-config
 bin/vdb-config.3
 bin/vdb-config.%%PORTVERSION%%
 bin/vdb-decrypt
 bin/vdb-decrypt.3
 bin/vdb-decrypt.%%PORTVERSION%%
 bin/vdb-dump
 bin/vdb-dump-orig.%%PORTVERSION%%
 bin/vdb-dump.3
 bin/vdb-dump.%%PORTVERSION%%
 bin/vdb-encrypt
 bin/vdb-encrypt.3
 bin/vdb-encrypt.%%PORTVERSION%%
 bin/vdb-validate
 bin/vdb-validate.3
 bin/vdb-validate.%%PORTVERSION%%
 include/ncbi-vdb/NGS.hpp
 include/ngs/Alignment.hpp
 include/ngs/AlignmentIterator.hpp
 include/ngs/ErrorMsg.hpp
 include/ngs/Fragment.hpp
 include/ngs/FragmentIterator.hpp
 include/ngs/Package.hpp
 include/ngs/Pileup.hpp
 include/ngs/PileupEvent.hpp
 include/ngs/PileupEventIterator.hpp
 include/ngs/PileupIterator.hpp
 include/ngs/Read.hpp
 include/ngs/ReadCollection.hpp
 include/ngs/ReadGroup.hpp
 include/ngs/ReadGroupIterator.hpp
 include/ngs/ReadIterator.hpp
 include/ngs/Reference.hpp
 include/ngs/ReferenceIterator.hpp
 include/ngs/ReferenceSequence.hpp
 include/ngs/Statistics.hpp
 include/ngs/StringRef.hpp
 include/ngs/adapter/AlignmentItf.hpp
 include/ngs/adapter/ErrorMsg.hpp
 include/ngs/adapter/FragmentItf.hpp
 include/ngs/adapter/PileupEventItf.hpp
 include/ngs/adapter/PileupItf.hpp
 include/ngs/adapter/ReadCollectionItf.hpp
 include/ngs/adapter/ReadGroupItf.hpp
 include/ngs/adapter/ReadItf.hpp
 include/ngs/adapter/Refcount.hpp
 include/ngs/adapter/ReferenceItf.hpp
 include/ngs/adapter/ReferenceSequenceItf.hpp
 include/ngs/adapter/StatisticsItf.hpp
 include/ngs/adapter/StringItf.hpp
 include/ngs/adapter/defs.h
 include/ngs/inl/Alignment.hpp
 include/ngs/inl/AlignmentIterator.hpp
 include/ngs/inl/Fragment.hpp
 include/ngs/inl/FragmentIterator.hpp
 include/ngs/inl/Package.hpp
 include/ngs/inl/Pileup.hpp
 include/ngs/inl/PileupEvent.hpp
 include/ngs/inl/PileupEventIterator.hpp
 include/ngs/inl/PileupIterator.hpp
 include/ngs/inl/Read.hpp
 include/ngs/inl/ReadCollection.hpp
 include/ngs/inl/ReadGroup.hpp
 include/ngs/inl/ReadGroupIterator.hpp
 include/ngs/inl/ReadIterator.hpp
 include/ngs/inl/Reference.hpp
 include/ngs/inl/ReferenceIterator.hpp
 include/ngs/inl/ReferenceSequence.hpp
 include/ngs/inl/Statistics.hpp
 include/ngs/inl/StringRef.hpp
 include/ngs/itf/AlignmentItf.h
 include/ngs/itf/AlignmentItf.hpp
 include/ngs/itf/ErrBlock.h
 include/ngs/itf/ErrBlock.hpp
 include/ngs/itf/ErrorMsg.hpp
 include/ngs/itf/FragmentItf.h
 include/ngs/itf/FragmentItf.hpp
 include/ngs/itf/PackageItf.hpp
 include/ngs/itf/PileupEventItf.h
 include/ngs/itf/PileupEventItf.hpp
 include/ngs/itf/PileupItf.h
 include/ngs/itf/PileupItf.hpp
 include/ngs/itf/ReadCollectionItf.h
 include/ngs/itf/ReadCollectionItf.hpp
 include/ngs/itf/ReadGroupItf.h
 include/ngs/itf/ReadGroupItf.hpp
 include/ngs/itf/ReadItf.h
 include/ngs/itf/ReadItf.hpp
 include/ngs/itf/Refcount.h
 include/ngs/itf/Refcount.hpp
 include/ngs/itf/ReferenceItf.h
 include/ngs/itf/ReferenceItf.hpp
 include/ngs/itf/ReferenceSequenceItf.h
 include/ngs/itf/ReferenceSequenceItf.hpp
 include/ngs/itf/StatisticsItf.h
 include/ngs/itf/StatisticsItf.hpp
 include/ngs/itf/StringItf.h
 include/ngs/itf/StringItf.hpp
 include/ngs/itf/VTable.h
 include/ngs/itf/VTable.hpp
 include/ngs/itf/defs.h
 include/ngs/unix/arm64/atomic32.h
 include/ngs/unix/fat86/atomic32.h
 include/ngs/unix/i386/atomic32.h
 include/ngs/unix/x86_64/atomic32.h
 include/ngs/win/atomic32.h
 include/ngs/win/stdbool.h
 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
 lib64/libncbi-ngs-c++.a.%%PORTVERSION%%
 lib64/libncbi-ngs-static.a
 lib64/libncbi-ngs.a
 lib64/libncbi-ngs.a.3
 lib64/libncbi-ngs.a.%%PORTVERSION%%
 lib64/libncbi-ngs.so
 lib64/libncbi-ngs.so.3
 lib64/libncbi-ngs.so.%%PORTVERSION%%
 lib64/libngs-c++-static.a
 lib64/libngs-c++.a
 lib64/libngs-c++.a.3
 lib64/libngs-c++.a.%%PORTVERSION%%
 lib64/libngs-c++.so
 lib64/libngs-c++.so.3
 lib64/libngs-c++.so.%%PORTVERSION%%
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignSliceTest.cpp
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignTest.cpp
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DumpReferenceFASTA.cpp
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/FragTest.cpp
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Makefile
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/PileupTest.cpp
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/RefTest.cpp
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/expected.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/Makefile
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/AlignSliceTest.java
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/AlignTest.java
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/DumpReferenceFASTA.java
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/FragTest.java
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/PileupTest.java
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/ReadGroupTest.java
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/examples/RefTest.java
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/expected.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/AlignSliceTest.py
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/AlignTest.py
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/FragTest.py
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/Makefile
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/PileupTest.py
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/RefTest.py
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/expected.txt
 %%JAVASHAREDIR%%doc/ngs-doc/allclasses-index.html
 %%JAVASHAREDIR%%doc/ngs-doc/allpackages-index.html
 %%JAVASHAREDIR%%doc/ngs-doc/constant-values.html
 %%JAVASHAREDIR%%doc/ngs-doc/element-list
 %%JAVASHAREDIR%%doc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html
 %%JAVASHAREDIR%%doc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html
 %%JAVASHAREDIR%%doc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html
 %%JAVASHAREDIR%%doc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html
 %%JAVASHAREDIR%%doc/ngs-doc/help-doc.html
 %%JAVASHAREDIR%%doc/ngs-doc/index-all.html
 %%JAVASHAREDIR%%doc/ngs-doc/index.html
 %%JAVASHAREDIR%%doc/ngs-doc/jquery-ui.overrides.css
 %%JAVASHAREDIR%%doc/ngs-doc/legal/ADDITIONAL_LICENSE_INFO
 %%JAVASHAREDIR%%doc/ngs-doc/legal/ASSEMBLY_EXCEPTION
 %%JAVASHAREDIR%%doc/ngs-doc/legal/LICENSE
 %%JAVASHAREDIR%%doc/ngs-doc/legal/jquery.md
 %%JAVASHAREDIR%%doc/ngs-doc/legal/jqueryUI.md
 %%JAVASHAREDIR%%doc/ngs-doc/member-search-index.js
 %%JAVASHAREDIR%%doc/ngs-doc/module-search-index.js
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/Alignment.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/AlignmentIterator.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/ErrorMsg.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/Fragment.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/FragmentIterator.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/Package.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/Pileup.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/PileupEvent.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/PileupEventIterator.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/PileupIterator.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/Read.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/ReadCollection.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/ReadGroup.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/ReadGroupIterator.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/ReadIterator.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/Reference.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/ReferenceIterator.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/ReferenceSequence.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/Statistics.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/package-summary.html
 %%JAVASHAREDIR%%doc/ngs-doc/ngs/package-tree.html
 %%JAVASHAREDIR%%doc/ngs-doc/overview-summary.html
 %%JAVASHAREDIR%%doc/ngs-doc/overview-tree.html
 %%JAVASHAREDIR%%doc/ngs-doc/package-search-index.js
 %%JAVASHAREDIR%%doc/ngs-doc/resources/glass.png
 %%JAVASHAREDIR%%doc/ngs-doc/resources/x.png
 %%JAVASHAREDIR%%doc/ngs-doc/script-dir/jquery-ui.min.css
 %%JAVASHAREDIR%%doc/ngs-doc/script-dir/jquery-ui.min.js
 %%JAVASHAREDIR%%doc/ngs-doc/script-dir/jquery.min.js
 %%JAVASHAREDIR%%doc/ngs-doc/script.js
 %%JAVASHAREDIR%%doc/ngs-doc/search.js
 %%JAVASHAREDIR%%doc/ngs-doc/serialized-form.html
 %%JAVASHAREDIR%%doc/ngs-doc/stylesheet.css
 %%JAVASHAREDIR%%doc/ngs-doc/tag-search-index.js
 %%JAVASHAREDIR%%doc/ngs-doc/type-search-index.js