git: 1dbce6f79e25 - main - biology/sra-tools: Update to 3.4.1

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From: Jason W. Bacon <jwb_at_FreeBSD.org>
Date: Thu, 26 Mar 2026 00:09:46 UTC
The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=1dbce6f79e2550823b651805b20c4b85faf6d5c5

commit 1dbce6f79e2550823b651805b20c4b85faf6d5c5
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2026-03-26 00:08:17 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2026-03-26 00:08:17 +0000

    biology/sra-tools: Update to 3.4.1
    
    Several minor enhancements and fixes
    Changes:
        https://github.com/ncbi/sra-tools/blob/master/CHANGES.md
        https://github.com/ncbi/sra-tools/commits/master/
    
    Reported by:    portscout
---
 biology/sra-tools/Makefile                    |  5 +--
 biology/sra-tools/distinfo                    | 10 ++---
 biology/sra-tools/files/patch-libs_kxml_xml.c | 11 -----
 biology/sra-tools/pkg-plist                   | 58 ---------------------------
 4 files changed, 6 insertions(+), 78 deletions(-)

diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile
index d5188cf628f3..62686b757250 100644
--- a/biology/sra-tools/Makefile
+++ b/biology/sra-tools/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	sra-tools
-DISTVERSION=	3.3.0
-PORTREVISION=	3
+DISTVERSION=	3.4.1
 CATEGORIES=	biology java
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -58,8 +57,6 @@ pre-configure:
 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}
diff --git a/biology/sra-tools/distinfo b/biology/sra-tools/distinfo
index 5897b65aa802..f663fb69fdbc 100644
--- a/biology/sra-tools/distinfo
+++ b/biology/sra-tools/distinfo
@@ -1,5 +1,5 @@
-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
+TIMESTAMP = 1774483680
+SHA256 (ncbi-sra-tools-3.4.1_GH0.tar.gz) = 7c319c1c71e99f3ab40f8ce26dee7f67bac83c90330985a223adce288aad89e4
+SIZE (ncbi-sra-tools-3.4.1_GH0.tar.gz) = 3260416
+SHA256 (ncbi-ncbi-vdb-3.4.1_GH0.tar.gz) = 2fa0919b2842641ead93eeeb45047e87ca480a543b6e4eda15f94d5187e91c85
+SIZE (ncbi-ncbi-vdb-3.4.1_GH0.tar.gz) = 19106888
diff --git a/biology/sra-tools/files/patch-libs_kxml_xml.c b/biology/sra-tools/files/patch-libs_kxml_xml.c
deleted file mode 100644
index 76ec7a13fee4..000000000000
--- a/biology/sra-tools/files/patch-libs_kxml_xml.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- 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 0bc4898e1af5..b140de4f836a 100644
--- a/biology/sra-tools/pkg-plist
+++ b/biology/sra-tools/pkg-plist
@@ -4,9 +4,6 @@ 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%%
@@ -177,7 +174,6 @@ 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
@@ -230,57 +226,3 @@ lib64/libngs-c++.so.%%PORTVERSION%%
 %%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