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<div class="content">

<h3 style="margin-top: 20px; margin-bottom: 10px;">
Aaron M. Ucko pushed to branch master at <a href="https://salsa.debian.org/med-team/ncbi-vdb">Debian Med / ncbi-vdb</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/4dfcc5f61610bd8e6ec85c09d8419bdcb53959b9">4dfcc5f6</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-08-29T21:51:46-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 3.4.1+dfsg</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/8a0a61fe92a1dbafd8cedf50ef4dd8887238c84d">8a0a61fe</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-08-29T21:53:28-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Merge tag upstream/3.4.1+dfsg.

Upstream version 3.4.1(+dfsg).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/731274a654cb30ac2351bdc06924ac24a96a939f">731274a6</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-08-29T22:29:15-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>debian/patches: Update accordingly.

* Consolidate fix_cmake.patch, zstd.patch, and new #include fixups as
  system_compression.patch.
* Formally update remaining patches as needed.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/fc78212a0ce0c1b445a4b56a002bdbc3fc43a658">fc78212a</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-09-06T11:57:55-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>debian/rules: Update libncbi-vdb-dev d-shlibmove invocation.

libvdbapp.a has replaced all of libkapp.a but the main() wrapper,
which kept the kapp name and moved to libngs-c++-dev from sra-sdk, and
libkapp-norsrc.a is gone.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/59f29d0f8de63eeec6ecd22e970fb7ffca2bfc59">59f29d0f</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-09-06T11:59:12-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/rules: Install kapp/version-hash.h from libs for sra-sdk's sake.

Hold off for now on splitting off a private-headers package, which
would be tiny.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/59d436d37e14ea62d2b89336ab28f9b9a4548708">59d436d3</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-09-06T22:41:01-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>debian/rules: Stop passing NO_VDB3 to dh_auto_install

... to accommodate cmake --install (already effectively in play), which
doesn't support that syntax (no longer needed anyway).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/c62f5e765c80cddc1596abc6731d91ddc9d69905">c62f5e76</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-09-06T22:42:05-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/rules: Set the new DYNAMIC_LINK option to ON for futureproofing.

The variables it affects don't actually come into play, at least so far.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/61f20fc0af59c57447304d5a5f6f90392b0af85e">61f20fc0</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-09-06T22:42:09-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Standards-Version: 4.7.4 (routine-update)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/75f927380d62e255ebf69dd098c058fc47e0da18">75f92738</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-09-06T22:42:09-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Changes made by cme
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/7b3999450af0e3bbdc5072c35f9c1215860406b6">7b399945</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-09-06T22:42:09-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Drop 'Rules-Requires-Root: no' from d/control (routine-update)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/b6659d1c4250f6791e215e57df15a6b1bbeb25c7">b6659d1c</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-09-06T22:42:09-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove unused entry from debian/source/include-binaries.

Changes-By: lintian-brush
Fixes: lintian: source: unused-entry-in-debian-source-include-binaries debian/sra-tools.gpg [debian/source/include-binaries:1]
See-also: https://lintian.debian.org/tags/unused-entry-in-debian-source-include-binaries.html
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/5e8ba01e54cd55464a50fbbfb2ddd474822fb3e7">5e8ba01e</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-09-06T22:42:09-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Reformat the Last-Update date as ISO YYYY-MM-DD.

Changes-By: lintian-brush
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/spelling.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/system_compression.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/libsam-extract_shared.patch]
See-also: https://lintian.debian.org/tags/invalid-dep3-format-patch-wrong-last-update.html
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/4c7b69193a08c0f0c42f22ec820f4cd98b8a2f94">4c7b6919</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-09-06T22:42:09-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Avoid explicitly specifying -Wl,--as-needed linker flag.

Changes-By: lintian-brush
Fixes: lintian: source: debian-rules-uses-as-needed-linker-flag [debian/rules]
See-also: https://lintian.debian.org/tags/debian-rules-uses-as-needed-linker-flag.html
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/a9c33c1620ef0b5f61d6d67877e3050b29eada3c">a9c33c16</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-09-06T22:42:09-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>debian/copyright: Note Bison-2.2 exception

... for files otherwise under GPL-3+, per lrc (licenserecon).
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/bbd0293dc328406cb34632bd55b5259674f40e3c">bbd0293d</a></strong>
<div>
<span> by Aaron M. Ucko </span> <i> at 2026-09-27T21:07:34-04:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Finalize ncbi-vdb 3.4.1+dfsg-1 for unstable.
</pre>
</li>
</ul>
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406 changed files:
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LICENSE
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