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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/ncbi-vdb">Debian Med / ncbi-vdb</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/58549c5a620e7b0cd9699ed80c3686802067130a">58549c5a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-25T06:56:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Move around kfg files to the place where it used to be in version 2.x
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/6df7f300667253d1d9c5a66b2ca10d7a02233bf6">6df7f300</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-25T08:24:23+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove now unused patches which all were targeting the old build system
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/07729f6af113e22c15bf032120dcf9fcb0888bb9">07729f6a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-25T10:13:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Library libvdb-sqlite is not provided by upstream any more which builds libsam-extract as new library. Binary packages are adapted accordingly
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-vdb/-/commit/d0082b21b63b51bcfb224e693db943cc6db11290">d0082b21</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-25T10:15:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DEP3
</pre>
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<h4>14 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#703cbbd48f14f0278f020aea76f9b5a278218975">
<span class="deleted-file">
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debian/libncbi-vdb3.install
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<a href="#85c2372f08a82474c265a322ee882abe8e807cc2">
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debian/patches/add_-msse2.patch
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<a href="#4eca8ae1f2f2fa6d260ecc047b7525738be8be87">
<span class="deleted-file">
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debian/patches/find_hdf5_serial.patch
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<li class="file-stats">
<a href="#919c97d0a2231ce347c61944400cf020c46dd04e">
<span class="deleted-file">
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debian/patches/find_ngs-sdk.patch
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<a href="#b69b1866479a98f00ebf85934c0848ff4f8a3f87">
<span class="deleted-file">
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debian/patches/fix_install_target.patch
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<a href="#b40efade8b4eeecdda8e2910182402b1fab4f90d">
<span class="new-file">
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debian/patches/libsam-extract_shared.patch
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<a href="#ee2e66eb47c649999baaffe018301cb40c0c3bc3">
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debian/patches/remove_-m64_flag.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="#7900bbc7deb8691929abfe4314ae83c60f651c15">
<span class="deleted-file">
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debian/patches/skip_failing_test.patch
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<a href="#009708d204ad3859ac4f374f0a54ff90f3e158f2">
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debian/patches/use_debian_packaged_libmbedx.patch
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<li class="file-stats">
<a href="#966bb4d5dd1abaf8ad19f277388bf088d452d07d">
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debian/patches/use_debian_packaged_zlib.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" 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="3" 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">@@ -3,6 +3,9 @@ ncbi-vdb (3.0.0+dfsg-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<td class="new_line diff-line-num" data-linenumber="4" 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">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Switch to cmake build system</span>
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<td class="old_line diff-line-num" data-linenumber="5" 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">
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<td class="new_line diff-line-num" data-linenumber="5" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Reflect SONAME bump in package names</span>
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<td class="old_line diff-line-num new" data-linenumber="6" 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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<td class="new_line diff-line-num new" data-linenumber="6" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Library libvdb-sqlite is not provided by upstream any more which</span>
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<td class="old_line diff-line-num new" data-linenumber="6" 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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<td class="new_line diff-line-num new" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> builds libsam-extract as new library. Binary packages are adapted</span>
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<td class="new_line diff-line-num new" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> accordingly</span>
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<td class="new_line diff-line-num" data-linenumber="9" 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">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num" data-linenumber="7" 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">
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<td class="new_line diff-line-num" data-linenumber="10" 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">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sat, 19 Feb 2022 11:53:03 +0100</span>
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<td class="new_line diff-line-num" data-linenumber="11" 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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<br>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="147" 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="147" 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">@@ -147,12 +147,12 @@ Description: virtual layer update modul of ncbi-vdb library (devel)</td>
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<td class="old_line diff-line-num" data-linenumber="147" 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">
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext"> .</span>
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<td class="new_line diff-line-num" data-linenumber="148" 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">
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext"> This is the development package.</span>
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<td class="old_line diff-line-num" data-linenumber="149" 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">
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="plaintext">Package: lib<span class="idiff left right">vdb-sqlite2</span></span>
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<td class="old_line diff-line-num new" data-linenumber="151" 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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<td class="new_line diff-line-num new" data-linenumber="150" 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="LC150" class="line" lang="plaintext">Package: lib<span class="idiff left right">sam-extract3</span></span>
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<td class="old_line diff-line-num" data-linenumber="151" 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">
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext">Architecture: amd64 arm64 i386 x32</span>
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<td class="old_line diff-line-num" data-linenumber="152" 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">
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext">Section: libs</span>
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<td class="old_line diff-line-num" data-linenumber="153" 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">
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext">Description: s<span class="idiff left right">qlite</span> modul of ncbi-vdb library</span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">Description: s<span class="idiff left right">am-extract</span> modul of ncbi-vdb library</span>
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<pre style="margin: 0;"> <span id="LC156" 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="LC157" class="line" lang="plaintext"> pileups produced from Next Generation Sequencing. The API itself is</span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext"> independent from any particular back-end implementation, and supports</span>
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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">@@ -160,15 +160,15 @@ Description: sqlite modul of ncbi-vdb library</td>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext"> building new back-end "engines". The engine for accessing SRA data is</span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext"> contained within the sister repository ncbi-vdb.</span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext"> This library is part of the ncbi-vdb package and provides a<span class="idiff left right"> sqlit</span>e</span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext"> <span class="idiff left right">interface</span>.</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> This library is part of the ncbi-vdb package and provides a<span class="idiff left right">n interfac</span>e</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> <span class="idiff left right">to extrat sam files</span>.</span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext">Package: lib<span class="idiff left right">vdb-sqlite</span>-dev</span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">Package: lib<span class="idiff left right">sam-extract</span>-dev</span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext">Architecture: amd64 arm64 i386 x32</span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="plaintext">Section: libdevel</span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="plaintext"> lib<span class="idiff left right">vdb-sqlite2</span> (= ${binary:Version})</span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"> lib<span class="idiff left right">sam-extract3</span> (= ${binary:Version})</span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="plaintext">Description: sqlite modul of ncbi-vdb library (devel)</span>
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<pre style="margin: 0;"> <span id="LC173" 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="LC174" class="line" lang="plaintext"> pileups produced from Next Generation Sequencing. The API itself is</span>
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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">@@ -177,7 +177,7 @@ Description: sqlite modul of ncbi-vdb library (devel)</td>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext"> building new back-end "engines". The engine for accessing SRA data is</span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext"> contained within the sister repository ncbi-vdb.</span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="plaintext"> This library is part of the ncbi-vdb package and provides a<span class="idiff left right"> sqlit</span>e</span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext"> <span class="idiff left right">interface</span>.</span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"> This library is part of the ncbi-vdb package and provides a<span class="idiff left right">n interfac</span>e</span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"> <span class="idiff left right">to extrat sam files</span>.</span>
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="plaintext"> .</span>
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="plaintext"> This is the development package.</span></pre>
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<li id="703cbbd48f14f0278f020aea76f9b5a278218975">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#703cbbd48f14f0278f020aea76f9b5a278218975"><strong>debian/libncbi-vdb3.install</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">libs</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">kfg</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">kfg</span> <span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">ncbi</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">vdb</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">kfg</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#85c2372f08a82474c265a322ee882abe8e807cc2"><strong>debian/patches/add_-msse2.patch</strong>
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1
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Sat, 20 Nov 2021 22:47:22 -0500</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/836128</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Description: Add -msse2 to libs/search on 32-bit x86</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/libs/search/Makefile</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/search/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -39,6 +39,11 @@</span> OBJFILES = \</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> include $(TOP)/build/Makefile.env</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MARCH := $(shell uname -m)</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ifneq ($(filter i%86, $(MARCH)),)</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;">+ CFLAGS += -msse2</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> #-------------------------------------------------------------------------------</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> # outer targets</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> #</span></pre>
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<li id="4eca8ae1f2f2fa6d260ecc047b7525738be8be87">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#4eca8ae1f2f2fa6d260ecc047b7525738be8be87"><strong>debian/patches/find_hdf5_serial.patch</strong>
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 12 Jul 2016 16:15:32 +0200</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: use hdf5 serial</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> May be there is a more elegant way to use hdf5 rather than patching the source</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> but I did not found it. Any hints are welcome.</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">--- a/setup/konfigure.perl</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/setup/konfigure.perl</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -1667,8 +1667,8 @@</span> sub check_compiler {</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> $flags = $n;</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> $log = ' int main() { }\n'</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> } elsif ($n eq 'hdf5') {</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;">- $library = '-Wl,-Bstatic -lhdf5 -Wl,-Bdynamic -ldl -lm -lz';</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $log = '#include <hdf5.h> \n int main() { H5close (); }\n'</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $library = '-lhdf5_serial -Wl,-Bdynamic -ldl -lm -lz';</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $log = '#include <hdf5/serial/hdf5.h> \n int main() { H5close (); }\n'</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> } elsif ($n eq 'fuse') {</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> $flags = '-D_FILE_OFFSET_BITS=64';</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> $library = '-lfuse';</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libs/hdf5/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/hdf5/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="p">@@ -104,7 +104,7 @@</span> KDF5_OBJ = \</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> $(addsuffix .$(LOBX),$(KDF5_SRC))</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> KDF5_LIB = \</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -lhdf5 \</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -lhdf5_serial \</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> -lz \</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> ifdef HDF5_LIBDIR</span></pre>
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<li id="919c97d0a2231ce347c61944400cf020c46dd04e">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#919c97d0a2231ce347c61944400cf020c46dd04e"><strong>debian/patches/find_ngs-sdk.patch</strong>
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 12 Jul 2016 16:15:32 +0200</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Enable finding ngs-sdk</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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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- a/setup/konfigure.perl</span>
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6
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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/setup/konfigure.perl</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -1396,7 +1396,9 @@</span> sub find_in_dir {</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> print "\tlibraries... " unless ($AUTORUN);</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> if ($lib) {</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> my $builddir = File::Spec->catdir($dir, $OS, $TOOLS, $ARCH, $BUILD);</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;">- my $libdir = File::Spec->catdir($builddir, 'lib');</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ my $buildarch = `dpkg-architecture -qDEB_BUILD_MULTIARCH`;</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chomp $buildarch;</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;">+ my $libdir = File::Spec->catdir($dir, 'lib', $buildarch);</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> my $ilibdir = File::Spec->catdir($builddir, 'ilib');</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> my $f = File::Spec->catdir($libdir, $lib);</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> print "\n\t\tchecking $f\n\t" if ($OPT{'debug'});</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -1477,8 +1479,8 @@</span> sub find_in_dir {</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> if ($jar) {</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\tjar... " unless ($AUTORUN);</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- my $try = "$dir/jar/$jar";</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print "\tjar... (seeking for $jar in dir $dir)" unless ($AUTORUN);</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ my $try = "$dir/$jar";</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> if (-e "$try") {</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> println $try unless ($AUTORUN);</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> $found_lib = $try;</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup/package.prl</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup/package.prl</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="p">@@ -33,8 +33,8 @@</span> sub REQ { ( { name => 'ngs-sdk',</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> option => 'with-ngs-java-prefix',</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> origin => 'I',</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> type => 'JO',</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pkgpath => '/usr/local/ngs/ngs-java',</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- usrpath => '$HOME/ngs/ngs-java',</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pkgpath => '/usr/share/java', # grmpf, why is this ignored after it is changed :-(((</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ usrpath => '/usr/share/java', # try again with same value</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> bldpath => '$HOME/ncbi-outdir/ngs-java',</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> locbldpath=>'$Bin/../../OUTDIR/ngs-java',</span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> lib => 'ngs-java.jar',</span></pre>
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<li id="b69b1866479a98f00ebf85934c0848ff4f8a3f87">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#b69b1866479a98f00ebf85934c0848ff4f8a3f87"><strong>debian/patches/fix_install_target.patch</strong>
deleted
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1
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 12 Jul 2016 16:15:32 +0200</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Install target tries to install to /usr/lib64 which is broken on</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> one hand and on the other hand I have not found a proper method to stop this</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> by less invasive means</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">--- a/Makefile</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/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -69,7 +69,8 @@</span> $(SUBDIRS_STD):</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> install:</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> @ echo "Checking make status of object libraries..."</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> @ $(MAKE) -s --no-print-directory TOP=$(CURDIR) $(SUBDIRS)</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;">- @ $(MAKE) -s --no-print-directory TOP=$(CURDIR) -f build/Makefile.install install</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;">+ # Skip useless broken part of install target</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #@ $(MAKE) -s --no-print-directory TOP=$(CURDIR) -f build/Makefile.install install</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> uninstall:</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> @ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.install uninstall</span></pre>
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<li id="b40efade8b4eeecdda8e2910182402b1fab4f90d">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#b40efade8b4eeecdda8e2910182402b1fab4f90d"><strong>debian/patches/libsam-extract_shared.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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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Sat, 19 Feb 2022 11:53:03 +0100</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Upstream creates static library with versioning / linking scheme</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> which looks as it would be intended to create a shared library. This patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> really created this shared library (which ends up in a seprate binary package)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- a/libs/align/CMakeLists.txt</span>
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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/libs/align/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -83,6 +83,7 @@</span> GenerateStaticLibs( align-access "${ALIG</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> GenerateStaticLibs( sam-extract "${SAM_EXTRACT_SRC}" )</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> ExportStatic( sam-extract true )</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;">+ExportShared( sam-extract true "" )</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> GenerateStaticLibs( align-reader "${ALIGN_READER_SRC}" )</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span></pre>
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<li id="ee2e66eb47c649999baaffe018301cb40c0c3bc3">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#ee2e66eb47c649999baaffe018301cb40c0c3bc3"><strong>debian/patches/remove_-m64_flag.patch</strong>
deleted
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Wed, 31 Aug 2016 07:55:11 +0200</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/836129</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Description: Enable build on x32 by removing explicit -m32/-m64</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/build/Makefile.gcc</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/build/Makefile.gcc</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -51,18 +51,6 @@</span> ifneq (sun,$(OS))</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> WARN += -Wno-variadic-macros</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> </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;">-ifeq (64,$(BITS))</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifneq (arm64,$(ARCH))</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CARCH = -m64</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq (32_64,$(BITS))</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CARCH = -arch i386 -arch x86_64</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CARCH = -m32</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> ifeq (prof, $(BUILD))</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> PROF = -pg</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> endif</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/build/Makefile.cc</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/build/Makefile.cc</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="p">@@ -46,12 +46,6 @@</span> LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH)</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> # tool options</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> WARN =</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq (64,$(BITS))</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CARCH = -m64</span></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;">-else</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CARCH = -m32</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> ifeq (prof, $(BUILD))</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> PROF = -xpg</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/build/Makefile.clang</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/build/Makefile.clang</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="p">@@ -48,15 +48,6 @@</span> LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH)</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> # tool options</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> WARN = -Wall -Wno-variadic-macros -Wno-long-long # -Wconversion</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> # TODO: Lots of new clang options in later versions (-fsanitize, CFI, CPI, ...)</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq (64,$(BITS))</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CARCH = -m64</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq (32_64,$(BITS))</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CARCH = -arch i386 -arch x86_64 </span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else </span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CARCH = -m32</span></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;">-endif </span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</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"> ifeq (prof, $(BUILD))</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"> PROF = -pg</span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">#find_hdf5_serial.patch</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">#find_ngs-sdk.patch</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">#skip_failing_test.patch</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">#fix_install_target.patch</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">#use_debian_packaged_zlib.patch</span>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">spelling.patch</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">#remove_-m64_flag.patch</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">#add_-msse2.patch</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">#use_debian_packaged_libmbedx.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">mbedtls_ssl_init.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">i386-uint64_msbit.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">fix_path_mbedtls.patch</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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>
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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">@@ -15,3 +7,4 @@ zstd.patch</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">fix_build.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">fix_cmake.patch</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">soversion.patch</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">libsam-extract_shared.patch</span></pre>
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<li id="7900bbc7deb8691929abfe4314ae83c60f651c15">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#7900bbc7deb8691929abfe4314ae83c60f651c15"><strong>debian/patches/skip_failing_test.patch</strong>
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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: Tue, 12 Jul 2016 16:15:32 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Skip some tests that are failing in pbuilder.</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> FIXME: There are more tests to skip but I have given up for the moment.</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/test/kfg/kfgtest.cpp</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/kfg/kfgtest.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -806,6 +806,7 @@</span> FIXTURE_TEST_CASE(KConfigImportNgc_Basic</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> string ngcPath("./prj_2956.ngc");</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> C::t(ngcPath);</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> Cleaner cleaner(wd);</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/* FIXME: This test fails in pbuilder environment</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> REQUIRE_RC(KConfigImportNgc(kfg, ngcPath.c_str(), "repos/ngc/", &newRepo));</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> TEST_MESSAGE("KConfigImportNgc(" << ngcPath << ")");</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> // contents of the input file:</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">@@ -872,6 +873,7 @@</span> FIXTURE_TEST_CASE(KConfigImportNgc_Basic</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> REQUIRE_EQ(string(newRepo), string("repos/ngc/"));</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> REQUIRE_RC(KDirectoryRemove(wd, true, "repos"));</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+*/</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="p">@@ -881,15 +883,19 @@</span> FIXTURE_TEST_CASE(KConfigImportNgc_NullL</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> CreateAndLoad(GetName(), "\n");</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> const char* newRepo;</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> Cleaner cleaner(wd);</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/* FIXME: This test fails in pbuilder environment</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> REQUIRE_RC(KConfigImportNgc(kfg, "./prj_2956.ngc", NULL, &newRepo));</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> string encDirName = "/ncbi/dbGaP-2956";</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> REQUIRE_EQ(string(newRepo).rfind(encDirName), string(newRepo).size() - encDirName.size()); // string(buf) ends with encDirName</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+*/</span></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"> FIXTURE_TEST_CASE(KConfigImportNgc_NullLocation_NullNewRepo, KfgFixture)</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> CreateAndLoad(GetName(), "\n");</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"> Cleaner cleaner(wd);</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/* FIXME: This test fails in pbuilder environment</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> REQUIRE_RC(KConfigImportNgc(kfg, "./prj_2956.ngc", NULL, NULL));</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+*/</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/kdb/remote_open_test.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/kdb/remote_open_test.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="p">@@ -72,11 +72,13 @@</span> TEST_CASE(KDBManagerVPathOpenDB_Local)</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> const KDatabase * db;</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> REQUIRE_RC(KDBManagerVPathOpenLocalDBRead ( mgr, &db, path ));</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> REQUIRE_NOT_NULL(db);</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/* FIXME: Fails in pbuilder</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"> const KTable *tbl;</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"> REQUIRE_RC(KDatabaseOpenTableRead(db, &tbl, "SEQUENCE"));</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"> REQUIRE_RC(KTableRelease(tbl));</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> REQUIRE_RC(KDatabaseRelease(db));</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"> REQUIRE_RC(KDBManagerRelease(mgr));</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;">+*/</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"> </span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"> REQUIRE_RC(VPathRelease(path));</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="p">@@ -214,59 +216,6 @@</span> protected:</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"> string m_cachedFile;</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-FIXTURE_TEST_CASE(KDBManagerVPathOpenDB_Remote, RemoteDBFixture)</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-{</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Configure(GetName());</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Resolve("SRR600096");</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- KDBManager* mgr;</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KDB_MANAGER_MAKE(&mgr, NULL));</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const KDatabase * db;</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KDBManagerVPathOpenRemoteDBRead ( mgr, &db, m_path, m_cache ));</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_NOT_NULL(db);</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- /* read something */</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const KTable *tbl;</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KDatabaseOpenTableRead(db, &tbl, "SEQUENCE"));</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KTableRelease(tbl));</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KDatabaseRelease(db));</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KDBManagerRelease(mgr));</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-FIXTURE_TEST_CASE(KDBManagerVPathOpenDB_Remote_NoCache, RemoteDBFixture)</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-{</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Configure(GetName());</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Resolve("SRR600096");</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- KDBManager* mgr;</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KDB_MANAGER_MAKE(&mgr, NULL));</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const KDatabase * db;</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KDBManagerVPathOpenRemoteDBRead ( mgr, &db, m_path, NULL ));</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_NOT_NULL(db);</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- /* read something */</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const KTable *tbl;</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KDatabaseOpenTableRead(db, &tbl, "SEQUENCE"));</span></span>
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<td class="old_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KTableRelease(tbl));</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KDatabaseRelease(db));</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KDBManagerRelease(mgr));</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="old_line diff-line-num old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-FIXTURE_TEST_CASE(KDBManagerVPathOpenDB_Remote_Table, RemoteDBFixture)</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Configure(GetName());</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Resolve("SRR000123");</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- KDBManager* mgr;</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KDB_MANAGER_MAKE(&mgr, NULL));</span></span>
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<td class="old_line diff-line-num old" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const KDatabase * db;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC_FAIL(KDBManagerVPathOpenRemoteDBRead ( mgr, &db, m_path, NULL )); // not a database</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- REQUIRE_RC(KDBManagerRelease(mgr));</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"> FIXTURE_TEST_CASE(KDBManagerVPathOpenDB_Remote_BadPath, RemoteDBFixture)</span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"> Configure(GetName());</span></pre>
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<li id="009708d204ad3859ac4f374f0a54ff90f3e158f2">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#009708d204ad3859ac4f374f0a54ff90f3e158f2"><strong>debian/patches/use_debian_packaged_libmbedx.patch</strong>
deleted
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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: Fri, 04 Nov 2016 08:56:33 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Somehow Build system expects a copy of libmbedx509.a which is</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> in package libmbedtls-dev - just drop it from list of dependencies</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/libs/ncbi-vdb/Makefile</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/ncbi-vdb/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -127,9 +127,6 @@</span> VDB_LIB_CMN = \</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> vfs \</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> cloud \</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> $(LIBKXML) \</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mbedx509 \</span></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;">- mbedtls \</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mbedcrypto \</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> kns \</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> kfg \</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> krypto \</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -155,7 +152,7 @@</span> VDB_OBJ = \</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> $(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RD)))</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> VDB_LIB = \</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(addprefix -s,$(VDB_LIB_RD))</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;">+ $(addprefix -s,$(VDB_LIB_RD)) -lmbedx509 -lmbedtls -lmbedcrypto</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> $(LIBDIR)/libncbi-vdb.$(LIBX): $(VDB_OBJ)</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> $(LD) --slib --vers $(SRCDIR)/libncbi-vdb.vers -o $@ $(VDB_LIB)</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="p">@@ -181,7 +178,7 @@</span> WVDB_OBJ = \</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> $(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RDWR)))</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> WVDB_LIB = \</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(addprefix -s,$(VDB_LIB_RDWR))</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(addprefix -s,$(VDB_LIB_RDWR)) -lmbedx509 -lmbedtls -lmbedcrypto</span></span>
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33
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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"> $(LIBDIR)/libncbi-wvdb.$(LIBX): $(WVDB_OBJ)</span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> $(LD) --slib --vers $(SRCDIR)/libncbi-vdb.vers -o $@ $(WVDB_LIB)</span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libs/kns/Makefile</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/kns/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="p">@@ -109,7 +109,8 @@</span> KNS_OBJ = \</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> KNS_LIB = \</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> -lkfs \</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -dklib</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -dklib \</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -lmbedx509 -lmbedtls -lmbedcrypto</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> $(ILIBDIR)/libkns.$(LIBX): $(KNS_OBJ)</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> $(LD) --slib -o $@ $^ $(KNS_LIB)</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libs/kns/tls-priv.h</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/kns/tls-priv.h</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="p">@@ -37,7 +37,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"> #include MBEDTLS_CONFIG_FILE </span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"> #endif</span>
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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"><span class="gd" style="color: #000; background-color: #fdd;">-#include <mbedtls/net.h></span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <mbedtls/net_sockets.h></span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> #include <mbedtls/debug.h></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"> #include <mbedtls/ssl.h></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"> #include <mbedtls/aes.h></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libs/kns/tls.c</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/kns/tls.c</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="p">@@ -60,7 +60,7 @@</span> struct KTLSStream;</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> #include MBEDTLS_CONFIG_FILE</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <mbedtls/net.h></span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <mbedtls/net_sockets.h></span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"> #include <mbedtls/debug.h></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"> #include <mbedtls/ssl.h></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"> #include <mbedtls/aes.h></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libs/hdf5/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/hdf5/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="p">@@ -112,7 +112,7 @@</span> ifdef HDF5_LIBDIR</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"> $(LIBDIR)/libkdf5.$(SHLX): $(KDF5_OBJ)</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(LD) --dlib --vers $(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers -o $@ $^ $(KDF5_LIB)</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(LD) --dlib --vers $(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers -o $@ $^ $(KDF5_LIB) -lmbedx509 -lmbedtls -lmbedcrypto</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"> $(LIBDIR)/libkdf5.$(LIBX): $(KDF5_OBJ)</span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"> $(LD) --slib --vers $(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers -o $@ $^ $(KDF5_LIB)</span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libs/vdb-sqlite/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/vdb-sqlite/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC83" 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="LC84" class="line" lang="diff"> $(addsuffix .$(LOBX),$(VDB_SQLITE_SRC))</span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"> VDB_SQLITE_LIB = \</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -sncbi-vdb -lz -lbz2</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -sncbi-vdb -lmbedx509 -lmbedtls -lmbedcrypto -lz -lbz2</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"> VDB_SQLITE_VERS = \</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"> $(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers</span></pre>
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<li id="966bb4d5dd1abaf8ad19f277388bf088d452d07d">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#966bb4d5dd1abaf8ad19f277388bf088d452d07d"><strong>debian/patches/use_debian_packaged_zlib.patch</strong>
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1
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 12 Jul 2016 16:15:32 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: External copy of bz2 and zlib are removed - exclude these from</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> build system as well.</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/libs/Makefile</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -35,7 +35,6 @@</span> include $(TOP)/build/Makefile.config</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> # default</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="LC11" class="line" lang="diff"> MAIN_SUBDIRS = \</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;">- ext \</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> kfc \</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> klib \</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> kproc \</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libs/ncbi-vdb/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/ncbi-vdb/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -138,10 +138,7 @@</span> VDB_LIB_CMN = \</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> klib \</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> kproc \</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> $(LIBKQ) \</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- kfc \</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bz2 \</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- z \</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- zstd \</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ kfc</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> VDB_LIB_RD = \</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> align-reader \</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="p">@@ -199,4 +196,4 @@</span> fuzz:</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> $(TOP)/build/ld.sh linux x86_64 gcc --build dbg --ldflags "-g -m64" --objx o --shlx so --libx a --srcdir $(SRCDIR) --bindir $(BINDIR) --slib -o $(FLIBDIR)/libncbi-vdb.$(LIBX) -L$(FLIBDIR) $(VDB_LIB) $(VDB_NGS_LIB)</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> cleanfuzz:</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm -rf $(FLIBDIR)/*</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -rf $(FLIBDIR)/*</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libs/vdb-sqlite/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/vdb-sqlite/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC39" 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="LC40" class="line" lang="diff"> $(addsuffix .$(LOBX),$(VDB_SQLITE_SRC))</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> VDB_SQLITE_LIB = \</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -sncbi-vdb</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -sncbi-vdb -lz -lbz2</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> VDB_SQLITE_VERS = \</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> $(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="88" 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="88" 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">@@ -88,8 +88,8 @@ override_dh_auto_install:</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"> $(LIBINSTALLDIR)/libkdf5.so</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"> d-shlibmove $(DSLMFLAGS) \</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> $(LIBINSTALLDIR)/libncbi-wvdb.so</span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext"><span class="idiff left right">#</span> d-shlibmove $(DSLMFLAGS) \</span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext"><span class="idiff left">#</span> $(LIBINSTALLDIR)/lib<span class="idiff right">vdb-sqlite</span>.so</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> d-shlibmove $(DSLMFLAGS) \</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> $(LIBINSTALLDIR)/lib<span class="idiff left right">sam-extract</span>.so</span>
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"> find debian/lib* -name .gitignore -delete</span>
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> # move schemata from development packages to library packages since these are used in executables</span>
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> mkdir -p $(SCHEMADIR)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="100" 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>
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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">@@ -100,3 +100,6 @@ override_dh_auto_install:</td>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"> sed -i "s:^include ':&/usr/lib/ncbi-vdb/:" $${schema} ; \</span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext"> mv $${schema} $(SCHEMADIR)/$${schemadir} ; \</span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> # Move around kfg files to the place where it used to be in version 2.x</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> mkdir debian/libncbi-vdb3/usr/lib/ncbi-vdb/</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> mv debian/libncbi-vdb-dev/usr/include/ncbi-vdb/kfg/ncbi debian/libncbi-vdb3/usr/lib/ncbi-vdb/kfg</span></pre>
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