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<h3>
Aaron M. Ucko pushed to branch master
at <a href="https://salsa.debian.org/med-team/sra-sdk">Debian Med / sra-sdk</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/648f0b0de126db0ab7a8ac7b15ec34fee338606b">648f0b0d</a></strong>
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<span>by Aaron M. Ucko</span>
<i>at 2021-10-14T16:23:45-04:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix_libngs_linkage.patch (new): Substitute ngs-c++ for absent ngs.
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<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/8b630244e7e1071868df80ea76b80b9a14bb6db1">8b630244</a></strong>
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<span>by Aaron M. Ucko</span>
<i>at 2021-10-14T16:27:48-04:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/rules: Stop renaming kget now that it's retired altogether.
The historical rename addressed a file conflict, #851219.
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<h4>4 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#7bd2ac29921940ab85c08bbb61e68dfa4d862bf1">
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+
debian/patches/fix_libngs_linkage.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/dc201cc5cb985642eed919d69867b80feb7b9ce9...8b630244e7e1071868df80ea76b80b9a14bb6db1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">sra-sdk (2.11.2+dfsg-1) UNRELEASED; 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"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Bump versioned Build-Depends: libngs-sdk-dev (>= 2.11.2)</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 13 Oct 2021 15:54:35 +0200</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> [ Aaron M. Ucko ]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * d/p/fix_libngs_linkage.patch (new): Substitute ngs-c++ library for</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> absent ngs library.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * debian/rules: Stop renaming kget (to avoid a file conflict, #851219)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> now that it's retired altogether.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> -- Aaron M. Ucko <ucko@debian.org> Thu, 14 Oct 2021 16:27:47 -0400</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">sra-sdk (2.10.9+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<li id="7bd2ac29921940ab85c08bbb61e68dfa4d862bf1">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/dc201cc5cb985642eed919d69867b80feb7b9ce9...8b630244e7e1071868df80ea76b80b9a14bb6db1#7bd2ac29921940ab85c08bbb61e68dfa4d862bf1"><strong>debian/patches/fix_libngs_linkage.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Aaron M. Ucko <ucko@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Changed: Thu, 14 Oct 2021 16:23:45 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Substitute ngs-c++ library for absent ngs library.</span></span>
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4
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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">Index: b/tools/vdb-sql/Makefile</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/vdb-sql/Makefile</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/vdb-sql/Makefile</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -80,7 +80,7 @@</span> VDB_SQL_SRC = \</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> VDB_SQL_LIB = \</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> -svdb-sqlite \</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -sngs \</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -sngs-c++ \</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> -sncbi-vdb \</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> -lm \</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> -lpthread</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -100,7 +100,7 @@</span> FASTCONV_LIB = \</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> -skapp \</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> -stk-version \</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> -svdb-sqlite \</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -sngs \</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -sngs-c++ \</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> -sncbi-vdb \</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> -lm \</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> -lpthread</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: b/tools/ngs-pileup/Makefile</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></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/tools/ngs-pileup/Makefile</span></span>
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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/tools/ngs-pileup/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="p">@@ -73,7 +73,6 @@</span> NGS_PILEUP_OBJ = \</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> NGS_PILEUP_LIBS = \</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> -sncbi-ngs-c++ \</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> -sngs-c++ \</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -sngs \</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> -sncbi-vdb \</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> -skapp \</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> -stk-version \</span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/dc201cc5cb985642eed919d69867b80feb7b9ce9...8b630244e7e1071868df80ea76b80b9a14bb6db1#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -20,3 +20,4 @@ python3</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">use_exposed_headers.patch</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">#reenable_legacy_schema_in_sra_load.patch</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">skip_broken_loaders.patch</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">fix_libngs_linkage.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/dc201cc5cb985642eed919d69867b80feb7b9ce9...8b630244e7e1071868df80ea76b80b9a14bb6db1#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -68,8 +68,6 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> # remove susipcious file which is not executable and conflicts with package magic</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> rm -f debian/*/usr/bin/magic</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> # rename kget which conflicts with kget download manager (see #851219)</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> mv debian/$(pkg)/usr/bin/kget debian/$(pkg)/usr/bin/vdb-get</span>
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73
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"> # Formally supply a standard installation ID to satisfy sratools</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> echo '/LIBS/GUID = "$(DEBIAN_GUID)"' >debian/$(pkg)/etc/ncbi/debian.kfg</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"></span>
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