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<h3>
Aaron M. Ucko pushed to branch master
at <a href="https://salsa.debian.org/med-team/ncbi-vdb">Debian Med / ncbi-vdb</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/545d1b2f4a72efe4118cfb347cd6ee26ecab17fe">545d1b2f</a></strong>
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<span>by Aaron M. Ucko</span>
<i>at 2021-11-22T22:34:52-05:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">zstd.patch: Adopt dynamic system zstd more fully.
* Comment out ZSTD_STATIC_LINKING_ONLY to enforce use of stable APIs.
* Actually link libncbi-(w)vdb and libvdb-sqlite against libzstd.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/c4a37fff5a97087245c7d6b179754f541a7d7d7b">c4a37fff</a></strong>
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<span>by Aaron M. Ucko</span>
<i>at 2021-11-22T22:38:25-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Have libncbi-vdb2 break sra-toolkit (<< 2.11) anyway.
Even with zstd linkage fixed, sra-toolkit 2.10.x's autopkgtest will
still fail over dropped support for protected repository configuration.
</pre>
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<strong><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/6566a48576b6eafaf1cbd15c6b3b36363a066c50">6566a485</a></strong>
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<span>by Aaron M. Ucko</span>
<i>at 2021-11-22T22:39:27-05:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Finalize ncbi-vdb 2.11.2+dfsg-4 for unstable.
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#f1960eb11d100e5d1f2dbf5e0c94c39bce85b17b">
debian/patches/zstd.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/182e49d87c8912f3311376f0455ce968ce8a9a40...6566a48576b6eafaf1cbd15c6b3b36363a066c50#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ncbi-vdb (2.11.2+dfsg-4) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * zstd.patch: Adopt dynamic system zstd more fully.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> - Comment out ZSTD_STATIC_LINKING_ONLY to enforce use of stable APIs.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> - Actually link libncbi-(w)vdb and libvdb-sqlite against libzstd.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Have libncbi-vdb2 break sra-toolkit (<< 2.11) anyway -- even with zstd</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> linkage fixed, sra-toolkit 2.10.x's autopkgtest will still fail over</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> dropped support for protected repository configuration.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Aaron M. Ucko <ucko@debian.org> Mon, 22 Nov 2021 22:39:27 -0500</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">ncbi-vdb (2.11.2+dfsg-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Leave mbedtls quirk handling to d-shlibs (>= 0.104). (Closes: #999788.)</span>
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<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/182e49d87c8912f3311376f0455ce968ce8a9a40...6566a48576b6eafaf1cbd15c6b3b36363a066c50#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +28,7 @@ Architecture: amd64 arm64 i386 x32</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Section: libs</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Breaks: sra-toolkit (<< 2.11~)</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Description: libraries for using data in the INSDC Sequence Read Archives</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> NGS is a new, domain-specific API for accessing reads, alignments and</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> pileups produced from Next Generation Sequencing. The API itself is</span>
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<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/182e49d87c8912f3311376f0455ce968ce8a9a40...6566a48576b6eafaf1cbd15c6b3b36363a066c50#f1960eb11d100e5d1f2dbf5e0c94c39bce85b17b"><strong>debian/patches/zstd.patch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, <span class="idiff left right">11 Oct 2021 11:37:20 +02</span>00</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org><span class="idiff left right">, Aaron Ucko <ucko@debian.org></span></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, <span class="idiff left right">22 Nov 2021 22:14:57 -05</span>00</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Use Debian packaged libzstd</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/libs/vxf/zstd.c</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/vxf/zstd.c</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -32,7 +32,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -31,8 +31,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #include <klib/log.h></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> #include <vdb/xform.h></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="idiff left right"> </span>#define ZSTD_STATIC_LINKING_ONLY</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span>#define ZSTD_STATIC_LINKING_ONLY</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <ext/zstd.h></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/* #define ZSTD_STATIC_LINKING_ONLY */</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <zstd.h></span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> #ifndef ZSTD_MIN_LEVEL</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,3 +26,34 @@ Description: Use Debian packaged libzstd</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> #include <klib/rc.h></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> #include <vdb/xform.h></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libs/ncbi-vdb/Makefile</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/ncbi-vdb/Makefile</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="p">@@ -152,7 +152,7 @@</span> VDB_OBJ = \</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> $(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RD)))</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> VDB_LIB = \</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(addprefix -s,$(VDB_LIB_RD)) -lmbedx509 -lmbedtls -lmbedcrypto</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(addprefix -s,$(VDB_LIB_RD)) -lmbedx509 -lmbedtls -lmbedcrypto -lzstd</span></span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> $(LIBDIR)/libncbi-vdb.$(LIBX): $(VDB_OBJ)</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> $(LD) --slib --vers $(SRCDIR)/libncbi-vdb.vers -o $@ $(VDB_LIB)</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -178,7 +178,7 @@</span> WVDB_OBJ = \</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> $(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RDWR)))</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> WVDB_LIB = \</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(addprefix -s,$(VDB_LIB_RDWR)) -lmbedx509 -lmbedtls -lmbedcrypto</span></span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(addprefix -s,$(VDB_LIB_RDWR)) -lmbedx509 -lmbedtls -lmbedcrypto -lzstd</span></span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> $(LIBDIR)/libncbi-wvdb.$(LIBX): $(WVDB_OBJ)</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> $(LD) --slib --vers $(SRCDIR)/libncbi-vdb.vers -o $@ $(WVDB_LIB)</span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libs/vdb-sqlite/Makefile</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/vdb-sqlite/Makefile</span></span>
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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -85,7 +85,7 @@</span> VDB_SQLITE_OBJ = \</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> $(addsuffix .$(LOBX),$(VDB_SQLITE_SRC))</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> VDB_SQLITE_LIB = \</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -sncbi-vdb -lmbedx509 -lmbedtls -lmbedcrypto -lz -lbz2</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -sncbi-vdb -lmbedx509 -lmbedtls -lmbedcrypto -lzstd -lz -lbz2</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> VDB_SQLITE_VERS = \</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> $(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers</span></pre>
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