Date: Thu, 26 Mar 2026 00:09:46 +0000 From: Jason W. Bacon <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 1dbce6f79e25 - main - biology/sra-tools: Update to 3.4.1 Message-ID: <69c4794a.41fa8.26645500@gitrepo.freebsd.org>
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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.jshome | help
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