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GitLab

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<h3>

Andreas Tille pushed to branch master

at <a href="https://salsa.debian.org/med-team/hhsuite">Debian Med / hhsuite</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/hhsuite/commit/3ed105da775d553528e206156494f730cb3df62a">3ed105da</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-08-21T18:57:58Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge changelog entries

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/hhsuite/commit/f0ab87ffa9410bcea7ab1809cc0f88615c87cf8b">f0ab87ff</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-08-21T19:05:23Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unused quilt patches

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/hhsuite/commit/429db364e5ee19b19254dd76d5bfb7e8965af951">429db364</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-08-21T19:08:43Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not parse d/changelog to obtain version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/hhsuite/commit/e3df8c735a77c9811b569f88ebf07db927a80de7">e3df8c73</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-08-21T19:12:45Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>11 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#c9fe40d82c878b25d3ea7e8f8bafb655f9f80aa1">

<span class="deleted-file">

−

debian/patches/Makefile

</span>

</a>

</li>

<li class="file-stats">

<a href="#9ee1d192bff100bfb580bce0077bd853fb6b8fa2">

<span class="deleted-file">

−

debian/patches/gcc-6.1.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#da05e03307464f7822bc7c4bf5ab542369119a3e">

<span class="deleted-file">

−

debian/patches/gcc-6.1_use_inline.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#9b7a4746a97a8fa6ef5c8ef060dab76b5f983a87">

<span class="deleted-file">

−

debian/patches/help

</span>

</a>

</li>

<li class="file-stats">

<a href="#5e4b0518c13e45ec350228ac0e8a96469f1f5aba">

<span class="deleted-file">

−

debian/patches/paths

</span>

</a>

</li>

<li class="file-stats">

<a href="#1a5c0eea47675e0472187a1e31224d82f2b23a21">

<span class="deleted-file">

−

debian/patches/rest1

</span>

</a>

</li>

<li class="file-stats">

<a href="#76ea3e3af30bd7b6907204399143c3cdea1dee61">

<span class="deleted-file">

−

debian/patches/unnecessary_libz

</span>

</a>

</li>

<li class="file-stats">

<a href="#cbca94541557b81c56257769c221a2c9943a2529">

<span class="deleted-file">

−

debian/patches/unused_variables_warning

</span>

</a>

</li>

<li class="file-stats">

<a href="#e9ec683b043361dc45be4135331a1d2f212a4fda">

<span class="deleted-file">

−

debian/patches/version_bump

</span>

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/hhsuite/compare/7fd79ad6a30a26a425ca9283ca11f552ba5a1166...e3df8c735a77c9811b569f88ebf07db927a80de7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">hhsuite (3.0~beta3+dfsg-2) UNRELEASED; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" 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">

3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">  * Fix Vcs-Browser</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4" 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">

4

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="5" 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">

5

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Tue, 07 Aug 2018 08:11:35 +0200</span>

</pre>

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6

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" 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">

7

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1

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">hhsuite (3.0~beta3+dfsg-1) unstable; urgency=medium</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" 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">

8

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2

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

</pre>

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9

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<td class="diff-line-num new_line old" data-linenumber="3" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">  * Team upload.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" 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">

10

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<td class="diff-line-num new_line old" data-linenumber="3" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="11" 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="diff-line-num new new_line" data-linenumber="3" 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">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  [ Steffen Moeller ]</span>

</pre>

</td>

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<td class="diff-line-num old_line" 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">

11

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<td class="diff-line-num new_line" 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">

4

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">  * New upstream version.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" 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">

12

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<td class="diff-line-num new_line" 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">

5

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">  * debian/upstream/metadata:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" 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">

13

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<td class="diff-line-num new_line" data-linenumber="6" 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">

6

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">    - yamllint cleanliness</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +11,11 @@ hhsuite (3.0~beta3+dfsg-1) unstable; urgency=medium</td>

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18

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<td class="diff-line-num new_line" 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">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">  * Caveat: Does not compile with openmpi libraries discovered.</span>

</pre>

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19

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12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">    See README.source.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" 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">

20

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<td class="diff-line-num new_line" data-linenumber="13" 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">

13

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" 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">

21

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<td class="diff-line-num new_line old" data-linenumber="14" 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="LC21" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org>  Thu, 02 Aug 2018 17:42:28 +0200</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="22" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" 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">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">  [ Andreas Tille ]</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" 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="diff-line-num new new_line" data-linenumber="15" 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">

15

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">  * Fix Vcs-Browser</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" 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="diff-line-num new new_line" data-linenumber="16" 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">

16

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">  * Do not parse d/changelog to obtain version</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" 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="diff-line-num new new_line" data-linenumber="17" 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">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" 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="diff-line-num new new_line" data-linenumber="18" 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">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Tue, 21 Aug 2018 21:09:09 +0200</span>

</pre>

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22

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19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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">

23

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<td class="diff-line-num new_line" data-linenumber="20" 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">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">hhsuite (3.0~beta2+dfsg-3) unstable; urgency=medium</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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21

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>

</pre>

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<br>

</li>

<li id="c9fe40d82c878b25d3ea7e8f8bafb655f9f80aa1">

<a href="https://salsa.debian.org/med-team/hhsuite/compare/7fd79ad6a30a26a425ca9283ca11f552ba5a1166...e3df8c735a77c9811b569f88ebf07db927a80de7#c9fe40d82c878b25d3ea7e8f8bafb655f9f80aa1"><strong>debian/patches/Makefile</strong>

deleted

</a>

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<td class="diff-line-num old old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC1" class="line" lang="make"><span class="nl">Description</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Patch to top level Makefile</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC2" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">Make</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">Makefile</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">DESTDIR-aware.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC3" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">Fix</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">mode</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">of</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">data</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">files.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC4" class="line" lang="make"><span class="nl">Forwarded</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">upstream is aware of these patches</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC5" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">Upstream</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">is</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">Andreas</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">Hauser</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><hauser@genzentrum.lmu.de>.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" 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">

6

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC6" class="line" lang="make"><span class="nl">Author</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Laszlo Kajan <lkajan@rostlab.org></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC7" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">---</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">a/Makefile</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" 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">

8

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC8" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+++</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">b/Makefile</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" 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">

9

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-1,5</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+1,5</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" 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">

10

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="make"><span class="nl">-# This can be overridden e.g.</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">make install INSTALL_DIR=...</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="11" 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">

11

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC11" class="line" lang="make"><span class="nv" style="color: teal;">-INSTALL_DIR</span><span class="o" style="font-weight: 600;">?=</span><span class="nv" style="color: teal;">$(PWD)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" 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">

12

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12" class="line" lang="make"><span class="nl">+# This can be overridden e.g.</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">make install PREFIX=...</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13" 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">

13

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC13" class="line" lang="make"><span class="nl">+PREFIX</span><span class="o" style="font-weight: 600;">:</span><span class="nf" style="color: #900; font-weight: 600;">=/usr</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" 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">

14

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="make"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" 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">

15

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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="LC15" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># Guess wether to use lib or lib64</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" 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">

16

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC16" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;">#libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" 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">

17

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-8,19</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+8,17</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span> <span class="nv" style="color: teal;">libdir</span><span class="o" style="font-weight: 600;">=</span>lib</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" 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">

18

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="make"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" 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">

19

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC19" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># Overriding this is currently not fully supported as the code won't know</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" 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">

20

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC20" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># to what this is set then. You can try setting HHLIB.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" 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">

21

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC21" class="line" lang="make"><span class="nv" style="color: teal;">-INSTALL_LIB_DIR</span><span class="o" style="font-weight: 600;">?=</span><span class="nv" style="color: teal;">$(INSTALL_DIR)</span>/<span class="nv" style="color: teal;">$(libdir)</span>/hh</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" 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">

22

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="make"><span class="nv" style="color: teal;">-INSTALL_SCRIPTS_DIR</span><span class="o" style="font-weight: 600;">?=</span><span class="nv" style="color: teal;">$(INSTALL_LIB_DIR)</span>/scripts</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" 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">

23

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="make"><span class="nv" style="color: teal;">-INSTALL_DATA_DIR</span><span class="o" style="font-weight: 600;">?=</span><span class="nv" style="color: teal;">$(INSTALL_LIB_DIR)</span>/data</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" 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">

24

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC24" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span><span class="nv" style="color: teal;">INSTALL_LIB_DIR</span><span class="o" style="font-weight: 600;">?=</span><span class="nv" style="color: teal;">$(PREFIX)</span>/<span class="nv" style="color: teal;">$(libdir)</span>/hhsuite</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="25" 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">

25

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span><span class="nv" style="color: teal;">INSTALL_SCRIPTS_DIR</span><span class="o" style="font-weight: 600;">?=</span><span class="nv" style="color: teal;">$(PREFIX)</span>/share/hhsuite/scripts</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="26" 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">

26

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span><span class="nv" style="color: teal;">INSTALL_DATA_DIR</span><span class="o" style="font-weight: 600;">?=</span><span class="nv" style="color: teal;">$(PREFIX)</span>/share/hhsuite/data</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="27" 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">

27

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span><span class="nv" style="color: teal;">INSTALL_BDATA_DIR</span><span class="o" style="font-weight: 600;">?=</span><span class="nv" style="color: teal;">$(INSTALL_LIB_DIR)</span>/data</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="28" 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">

28

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC28" class="line" lang="make"> <span class="nv" style="color: teal;">INSTALL_LIB_BIN_DIR</span><span class="o" style="font-weight: 600;">?=</span><span class="nv" style="color: teal;">$(INSTALL_LIB_DIR)</span>/bin</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="29" 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">

29

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC29" class="line" lang="make"> </span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="30" 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">

30

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC30" class="line" lang="make"> <span class="nv" style="color: teal;">dist_name</span><span class="o" style="font-weight: 600;">=</span>hhsuite-2.0.16</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="31" 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">

31

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC31" class="line" lang="make"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="32" 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">

32

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC32" class="line" lang="make"><span class="nl">-.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all_static</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="33" 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">

33

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC33" class="line" lang="make"><span class="nl">-all_static</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">ffindex_static</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="34" 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">

34

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC34" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(MAKE)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-C</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">all_static</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="35" 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">

35

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC35" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="36" 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">

36

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC36" class="line" lang="make"> <span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="37" 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">

37

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC37" class="line" lang="make"><span class="nl">-all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">ffindex</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="38" 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">

38

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC38" class="line" lang="make"><span class="nl">+all</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="39" 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">

39

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC39" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(MAKE)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-C</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">data</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">all</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="40" 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">

40

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC40" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(MAKE)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-C</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">all</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="41" 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">

41

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC41" class="line" lang="make"> </span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="42" 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">

42

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC42" class="line" lang="make"> <span class="nl">doc</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="43" 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">

43

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC43" class="line" lang="make"><span class="nl">@@ -40,35 +38,34 @@ ffindex_static</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="44" 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">

44

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC44" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(MAKE)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-C</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">lib/ffindex</span> <span class="nv" style="color: teal;">FFINDEX_STATIC</span><span class="o" style="font-weight: 600;">=</span>1</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="45" 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">

45

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC45" class="line" lang="make">  </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" 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">

46

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC46" class="line" lang="make"> <span class="nl">install</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" 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">

47

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC47" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(MAKE)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-C</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">lib/ffindex</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="nv" style="color: teal;">INSTALL_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$(INSTALL_DIR)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" 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">

48

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC48" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DIR)/bin</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" 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">

49

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC49" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/hhblits</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DIR)/bin/hhblits</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="50" 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">

50

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC50" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/hhalign</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DIR)/bin/hhalign</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" 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">

51

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC51" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/hhconsensus</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DIR)/bin/hhconsensus</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="52" 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">

52

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC52" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/hhfilter</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DIR)/bin/hhfilter</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" 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">

53

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC53" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/hhmake</span>      <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DIR)/bin/hhmake</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="54" 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">

54

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC54" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/hhsearch</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DIR)/bin/hhsearch</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="55" 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">

55

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC55" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_LIB_DIR)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="56" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC56" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_LIB_BIN_DIR)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="57" 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">

57

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC57" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/cstranslate</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_LIB_BIN_DIR)/cstranslate</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="58" 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">

58

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC58" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DATA_DIR)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="59" 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">

59

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC59" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-m</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0644</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">data/context_data.lib</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DATA_DIR)/context_data.lib</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="60" 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">

60

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC60" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-m</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0644</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">data/cs219.lib</span>        <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DATA_DIR)/cs219.lib</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="61" 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="LC61" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-m</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0644</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">data/do_not_delete</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DATA_DIR)/do_not_delete</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="62" 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="LC62" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-m</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0644</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">data/do_not_delete.phr</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DATA_DIR)/do_not_delete.phr</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="63" 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="LC63" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-m</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0644</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">data/do_not_delete.pin</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DATA_DIR)/do_not_delete.pin</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" 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="LC64" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-m</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0644</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">data/do_not_delete.psq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_DATA_DIR)/do_not_delete.psq</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="65" 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="LC65" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_SCRIPTS_DIR)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="66" 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="LC66" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-m</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0644</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/Align.pm</span>        <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_SCRIPTS_DIR)/Align.pm</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="67" 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="LC67" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-m</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0644</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/HHPaths.pm</span>      <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_SCRIPTS_DIR)/HHPaths.pm</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/addss.pl</span>        <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_SCRIPTS_DIR)/addss.pl</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/create_profile_from_hhm.pl</span>   <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_SCRIPTS_DIR)/create_profile_from_hhm.pl</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/create_profile_from_hmmer.pl</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_SCRIPTS_DIR)/create_profile_from_hmmer.pl</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/hhmakemodel.pl</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_SCRIPTS_DIR)/hhmakemodel.pl</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/reformat.pl</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_SCRIPTS_DIR)/reformat.pl</span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/splitfasta.pl</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_SCRIPTS_DIR)/splitfasta.pl</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/multithread.pl</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_SCRIPTS_DIR)/multithread.pl</span></span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/hhblitsdb.pl</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="76" 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">

76

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC76" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(PREFIX)/bin</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="77" 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">

77

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC77" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/hhblits</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(PREFIX)/bin/hhblits</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="78" 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">

78

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC78" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/hhalign</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(PREFIX)/bin/hhalign</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="79" 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">

79

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC79" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/hhconsensus</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(PREFIX)/bin/hhconsensus</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="80" 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">

80

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC80" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/hhfilter</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(PREFIX)/bin/hhfilter</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="81" 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">

81

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC81" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/hhmake</span>      <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(PREFIX)/bin/hhmake</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="82" 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">

82

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC82" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/hhsearch</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(PREFIX)/bin/hhsearch</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="83" 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">

83

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC83" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_LIB_DIR)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="84" 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">

84

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC84" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_LIB_BIN_DIR)</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="85" 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">

85

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC85" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src/cstranslate</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_LIB_BIN_DIR)/cstranslate</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="86" 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">

86

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC86" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_DATA_DIR)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_BDATA_DIR)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="87" 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">

87

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC87" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="nv" style="color: teal;">--mode</span><span class="o" style="font-weight: 600;">=</span>0644 data/context_data.lib <span class="nv" style="color: teal;">$(DESTDIR)$(INSTALL_DATA_DIR)</span>/context_data.lib</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="88" 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">

88

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC88" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="nv" style="color: teal;">--mode</span><span class="o" style="font-weight: 600;">=</span>0644 data/cs219.lib        <span class="nv" style="color: teal;">$(DESTDIR)$(INSTALL_DATA_DIR)</span>/cs219.lib</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="89" 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">

89

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC89" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="nv" style="color: teal;">--mode</span><span class="o" style="font-weight: 600;">=</span>0644 data/do_not_delete    <span class="nv" style="color: teal;">$(DESTDIR)$(INSTALL_BDATA_DIR)</span>/do_not_delete</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="90" 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">

90

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC90" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="nv" style="color: teal;">--mode</span><span class="o" style="font-weight: 600;">=</span>0644 data/do_not_delete.phr <span class="nv" style="color: teal;">$(DESTDIR)$(INSTALL_BDATA_DIR)</span>/do_not_delete.phr</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="91" 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">

91

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC91" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="nv" style="color: teal;">--mode</span><span class="o" style="font-weight: 600;">=</span>0644 data/do_not_delete.pin <span class="nv" style="color: teal;">$(DESTDIR)$(INSTALL_BDATA_DIR)</span>/do_not_delete.pin</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="92" 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">

92

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC92" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="nv" style="color: teal;">--mode</span><span class="o" style="font-weight: 600;">=</span>0644 data/do_not_delete.psq <span class="nv" style="color: teal;">$(DESTDIR)$(INSTALL_BDATA_DIR)</span>/do_not_delete.psq</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="93" 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">

93

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC93" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_SCRIPTS_DIR)</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="94" 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">

94

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC94" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="nv" style="color: teal;">--mode</span><span class="o" style="font-weight: 600;">=</span>0644 scripts/Align.pm        <span class="nv" style="color: teal;">$(DESTDIR)$(INSTALL_SCRIPTS_DIR)</span>/Align.pm</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="95" 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">

95

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC95" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="nv" style="color: teal;">--mode</span><span class="o" style="font-weight: 600;">=</span>0644 scripts/HHPaths.pm      <span class="nv" style="color: teal;">$(DESTDIR)$(INSTALL_SCRIPTS_DIR)</span>/HHPaths.pm</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="96" 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">

96

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC96" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/addss.pl</span>        <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_SCRIPTS_DIR)/addss.pl</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="97" 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">

97

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC97" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/create_profile_from_hhm.pl</span>   <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_SCRIPTS_DIR)/create_profile_from_hhm.pl</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC98" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/create_profile_from_hmmer.pl</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_SCRIPTS_DIR)/create_profile_from_hmmer.pl</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="99" 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">

99

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC99" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>     <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/hhmakemodel.pl</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_SCRIPTS_DIR)/hhmakemodel.pl</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="100" 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">

100

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC100" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/reformat.pl</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_SCRIPTS_DIR)/reformat.pl</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="101" 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">

101

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC101" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/splitfasta.pl</span>  <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_SCRIPTS_DIR)/splitfasta.pl</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="102" 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">

102

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC102" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/multithread.pl</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_SCRIPTS_DIR)/multithread.pl</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="103" 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">

103

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC103" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">install</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">scripts/hhblitsdb.pl</span>   <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DESTDIR)$(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC104" class="line" lang="make"> </span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="105" 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">

105

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC105" class="line" lang="make"> <span class="nl">deinstall</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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="make">         <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(MAKE)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-C</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">lib/ffindex</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">deinstall</span> <span class="nv" style="color: teal;">INSTALL_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$(INSTALL_DIR)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="make"><span class="nl">@@ -89,9 +86,11 @@ deinstall</span><span class="o" style="font-weight: 600;">:</span></span>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="make"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="109" 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="LC109" class="line" lang="make"> <span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean</span></span>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="make"> <span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span></span>

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<td class="diff-line-num old old_line" 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">

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">-</span>    <span class="err" style="color: #a61717; background-color: #e3d2d2;">cd</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">lib/ffindex</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">&&</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(MAKE)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">clean</span></span>

</pre>

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<td class="diff-line-num old old_line" 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">

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="make">         <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(MAKE)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-C</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">src</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">clean</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="make"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="114" 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="LC114" class="line" lang="make"><span class="nl">+.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">distclean</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="make"><span class="nl">+distclean</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC116" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="117" 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="LC117" class="line" lang="make"> <span class="nl">dist/$(dist_name).tar.gz</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="118" 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="LC118" class="line" lang="make">         <span class="err" style="color: #a61717; background-color: #e3d2d2;">make</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">clean</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="make">         <span class="err" style="color: #a61717; background-color: #e3d2d2;">mkdir</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-p</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">dist</span></span></pre>

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<br>

</li>

<li id="9ee1d192bff100bfb580bce0077bd853fb6b8fa2">

<a href="https://salsa.debian.org/med-team/hhsuite/compare/7fd79ad6a30a26a425ca9283ca11f552ba5a1166...e3df8c735a77c9811b569f88ebf07db927a80de7#9ee1d192bff100bfb580bce0077bd853fb6b8fa2"><strong>debian/patches/gcc-6.1.patch</strong>

deleted

</a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: Use system provided log2 and log10 of gcc-6.1</span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/831115</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" 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">

3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>

</pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff">Last-Update: Sat, 13 Aug 2016 07:27:28 +0200</span>

</pre>

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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"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/util.C</span></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/src/util.C</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -55,8 +55,8 @@ inline int iround(double x) {return int(</span></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> inline double fmean(double x, double y, double d) { return pow( (pow(x,d)+pow(y,d))/2 ,1./d);}</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"> // log base 2</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;">-inline float log2(float x)  {return (x<=0? (float)(-100000):1.442695041*log(x));}</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;">-inline float log10(float x) {return (x<=0? (float)(-100000):0.434294481*log(x));}</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;">+//inline float log2(float x)  {return (x<=0? (float)(-100000):1.442695041*log(x));}</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;">+//inline float log10(float x) {return (x<=0? (float)(-100000):0.434294481*log(x));}</span></span>

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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"> </span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> /////////////////////////////////////////////////////////////////////////////////////</span></pre>

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<br>

</li>

<li id="da05e03307464f7822bc7c4bf5ab542369119a3e">

<a href="https://salsa.debian.org/med-team/hhsuite/compare/7fd79ad6a30a26a425ca9283ca11f552ba5a1166...e3df8c735a77c9811b569f88ebf07db927a80de7#da05e03307464f7822bc7c4bf5ab542369119a3e"><strong>debian/patches/gcc-6.1_use_inline.patch</strong>

deleted

</a>

<hr>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: Rename redefined log2 to enable build using gcc-6.1</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> Note: May be its just better to use the system provided log2</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">  ---> While this patch works syntactically the system provided</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff">       log2 and log10 are really used since this patch is</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">       deactivated but left for discussion as alternative to</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">       gcc-6.1</span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/831115</span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" 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="LC9" class="line" lang="diff">Last-Update: Sat, 13 Aug 2016 07:27:28 +0200</span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/util.C</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/util.C</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -55,7 +55,7 @@ inline int iround(double x) {return int(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> inline double fmean(double x, double y, double d) { return pow( (pow(x,d)+pow(y,d))/2 ,1./d);}</span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" 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="LC16" class="line" lang="diff"> // log base 2</span>

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<td class="diff-line-num old old_line" data-linenumber="17" 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="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-inline float log2(float x)  {return (x<=0? (float)(-100000):1.442695041*log(x));}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+inline float log2_i(float x)  {return (x<=0? (float)(-100000):1.442695041*log(x));}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> inline float log10(float x) {return (x<=0? (float)(-100000):0.434294481*log(x));}</span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -63,29 +63,29 @@ inline float log10(float x) {return (x<=</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> // fast log base 2</span>

</pre>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> /////////////////////////////////////////////////////////////////////////////////////</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" 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="LC25" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" 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="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// Fast log2 </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Fast log2_i</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> // ATTENTION: need to compile with g++ -fno-strict-aliasing when using -O2 or -O3!!! </span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> // Maximum deviation: +/- 2.1E-5</span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// Run time: ~1.2E-8s on Intel core2 2.13GHz, log2(): 5.4E-8s</span></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Run time: ~1.2E-8s on Intel core2 2.13GHz, log2_i(): 5.4E-8s</span></span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> // For a negative argument, -128 is returned.</span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> // The function makes use of the representation of 4-byte floating point numbers:</span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> // seee eeee emmm mmmm mmmm mmmm mmmm mmmm</span>

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<td class="diff-line-num old old_line" data-linenumber="35" 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="LC35" class="line" lang="diff"> // s is the sign, eee eee e gives the exponent + 127 (in hex: 0x7f).</span>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> // The following 23 bits give the mantisse, the binary digits after the decimal </span>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"> // point:  x = (-1)^s * 1.mmmmmmmmmmmmmmmmmmmmmmm * 2^(eeeeeeee-127)</span>

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<td class="diff-line-num old old_line" data-linenumber="38" 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="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// Therefore,  log2(x) = eeeeeeee-127 + log2(1.mmmmmm...) </span></span>

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<td class="diff-line-num old old_line" data-linenumber="39" 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="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-//                     = eeeeeeee-127 + log2(1+y),  where y = 0.mmmmmm... </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-//                     ~ eeeeeeee-127 + ((a*y+b)*y+c)*y </span></span>

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<td class="diff-line-num old old_line" data-linenumber="41" 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="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Therefore,  log2_i(x) = eeeeeeee-127 + log2_(1.mmmmmm...) </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//                       = eeeeeeee-127 + log2_(1+y),  where y = 0.mmmmmm... </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//                       ~ eeeeeeee-127 + ((a*y+b)*y+c)*y </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"> // The coefficients a, b  were determined by a least squares fit, and c=1-a-b to get 1 at y=1.</span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> // Lower/higher order polynomials may be used for faster or more precise calculation:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// Order 1: log2(1+y) ~ y                 </span></span>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// Order 2: log2(1+y) = (a*y + 1-a)*y, a=-0.3427                                           </span></span>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Order 1: log2_i(1+y) ~ y                 </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" 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="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Order 2: log2_i(1+y) = (a*y + 1-a)*y, a=-0.3427                                           </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="50" 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="LC50" class="line" lang="diff"> //  => max dev = +/- 8E-3, run time ~ ?</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" 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="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// Order 3: log2(1+y) = ((a*y+b)*y + 1-a-b)*y, a=0.1564, b=-0.5773   </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="52" 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="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Order 3: log2_i(1+y) = ((a*y+b)*y + 1-a-b)*y, a=0.1564, b=-0.5773   </span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"> //  => max dev = +/- 1E-3, run time ~ ?</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="54" 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="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// Order 4: log2(1+y) = (((a*y+b)*y+c)*y + 1-a-b-c)*y, a=-0.0803 b=0.3170 c=-0.6748 </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="55" 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="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Order 4: log2_i(1+y) = (((a*y+b)*y+c)*y + 1-a-b-c)*y, a=-0.0803 b=0.3170 c=-0.6748 </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="56" 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="LC56" class="line" lang="diff"> //  => max dev = +/- 1.4E-4, run time ~ ?</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="57" 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="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// Order 5: log2(1+y) = ((((a*y+b)*y+c)*y+d)*y + 1-a-b-c-d)*y, </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="58" 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="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Order 5: log2_i(1+y) = ((((a*y+b)*y+c)*y+d)*y + 1-a-b-c-d)*y, </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="59" 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="LC59" class="line" lang="diff"> //     a=0.0440047 b=-0.1903190 c=0.4123442 d=-0.7077702 1-a-b-c-d=1.441740</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="60" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC60" class="line" lang="diff"> //  => max dev = +/- 2.1E-5, run time ~ 1.2E-8s</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="61" 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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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC61" class="line" lang="diff"> inline float flog2(float x)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="62" 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="LC62" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -155,7 +155,7 @@ __m128 _mm_flog2_ps(__m128 X)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="63" 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="LC63" class="line" lang="diff">   R = _mm_add_ps(R, CONST32_D);           // R = ((a*X+b)*X+c)*X+d</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" 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="LC64" class="line" lang="diff">   R = _mm_mul_ps(R, X);                   // R = (((a*X+b)*X+c)*X+d)*X</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="65" 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="LC65" class="line" lang="diff">   R = _mm_add_ps(R, CONST32_E);           // R = (((a*X+b)*X+c)*X+d)*X+e</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="66" 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="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  R = _mm_mul_ps(R, X);                   // R = ((((a*X+b)*X+c)*X+d)*X+e)*X ~ log2(1+X) !! </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  R = _mm_mul_ps(R, X);                   // R = ((((a*X+b)*X+c)*X+d)*X+e)*X ~ log2_i(1+X) !! </span></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff">   R = _mm_add_ps(R, _mm_cvtepi32_ps(E));  // convert integer exponent to float and add to mantisse</span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff">   return R;</span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"> }</span>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -172,7 +172,7 @@ __m128 _mm_flog2_ps(__m128 X)</span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"> // In the code, *(int *)&x is an integer which contains the bytes as the </span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"> // floating point variable x is represented in memory. The expression </span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"> //     (((*(int *)&x) & 0x7f800000 ) >>23 )-0x7f is the exponent eeeeeeee, </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;">-// i.e., the largest integer that is smaller than log2(x) (e.g. -1 for 0.9).</span></span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// i.e., the largest integer that is smaller than log2_i(x) (e.g. -1 for 0.9).</span></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"> inline float fast_log2(float x)</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">   static float lg2[1025];         // lg2[i] = log2[1+x/1024]</span></pre>

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<br>

</li>

<li id="9b7a4746a97a8fa6ef5c8ef060dab76b5f983a87">

<a href="https://salsa.debian.org/med-team/hhsuite/compare/7fd79ad6a30a26a425ca9283ca11f552ba5a1166...e3df8c735a77c9811b569f88ebf07db927a80de7#9b7a4746a97a8fa6ef5c8ef060dab76b5f983a87"><strong>debian/patches/help</strong>

deleted

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: fix paths in help pages</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> Fix issues where the path in help pages is taken from the build-time location of the executables.</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Forwarded: not-needed</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff">Author: Laszlo Kajan <lkajan@rostlab.org></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/hhblits.C</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/hhblits.C</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -411,7 +411,12 @@ void help(char all=0)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="8" 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">

8

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">   printf("An extended list of options can be obtained by calling 'hhblits -help'\n");</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="9" 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">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">   }</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="10" 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">

10

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff">   printf("\n");</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="11" 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">

11

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  printf("Example: %s -i query.fas -oa3m query.a3m -n 1  \n",program_name);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="12" 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">

12

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  printf("Examples:\n");</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="13" 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">

13

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  printf("%s -i query.fas -o query.hhr -d ./uniprot20\n",program_name);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="14" 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">

14

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  printf("\n");</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="15" 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">

15

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  printf("%s -i query.fas -o query.hhr -oa3m query.a3m -n 1 -d ./uniprot20\n",program_name);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="16" 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">

16

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  printf("\n");</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="17" 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">

17

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  printf("Download databases from <ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/databases/>.\n");</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="18" 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">

18

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff">   cout<<endl;</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="19" 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">

19

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> }</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="20" 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">

20

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="21" 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">

21

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<td class="diff-line-num new_line old" data-linenumber="0" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/hhsearch.C</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="22" 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">

22

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/hhsearch.C</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="23" 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">

23

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -48,6 +48,7 @@</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="24" 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">

24

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> #include <float.h>    // FLT_MIN</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="25" 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">

25

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> #include <ctype.h>    // islower, isdigit etc</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="26" 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">

26

</td>

<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> #include <time.h>     // clock_gettime etc. (in realtime library (-lrt compiler option))</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="27" 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">

27

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<td class="diff-line-num new_line old" data-linenumber="0" 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">

</td>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <unistd.h></span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="28" 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="LC28" class="line" lang="diff"> #include <errno.h>    // perror()</span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> #include <cassert></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> #include <stdexcept></span></pre>

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<br>

</li>

<li id="5e4b0518c13e45ec350228ac0e8a96469f1f5aba">

<a href="https://salsa.debian.org/med-team/hhsuite/compare/7fd79ad6a30a26a425ca9283ca11f552ba5a1166...e3df8c735a77c9811b569f88ebf07db927a80de7#5e4b0518c13e45ec350228ac0e8a96469f1f5aba"><strong>debian/patches/paths</strong>

deleted

</a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: Set hhsuite paths.</span>

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<td class="diff-line-num old old_line" data-linenumber="2" 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="LC2" class="line" lang="diff"> Set paths to hhsuite components - as installed on Debian - correctly in absence of the (now superflouos) HHLIB environment variable.</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Forwarded: not-needed</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff">Author: Laszlo Kajan <lkajan@rostlab.org></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/HHPaths.pm</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/HHPaths.pm</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -31,6 +31,7 @@ use Exporter;</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> our $VERSION = "version 2.0.16 (January 2013)";</span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> our @ISA     = qw(Exporter);</span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> our @EXPORT  = qw($VERSION $hhlib $hhdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib $v);</span>

</pre>

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11

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+push @EXPORT, qw($hhshare $hhbdata);</span></span>

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12

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> ##############################################################################################</span>

</pre>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> # PLEASE COMPLETE THE PATHS ... TO PSIPRED AND OLD-STYLE BLAST (NOT BLAST+) (NEEDED FOR PSIPRED) </span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -54,11 +55,13 @@ our $dssp    =  "/cluster/databases/dssp</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> # The lines below probably do not need to be changed</span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> # Setting paths for hh-suite perl scripts</span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-our $hhlib    = $ENV{"HHLIB"};     # main hh-suite directory</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;">-our $hhdata   = $hhlib."/data";    # path to data directory for hhblits, example files</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;">+our $hhlib    = $ENV{"HHLIB"} || "/usr/lib/hhsuite";     # main hh-suite directory</span></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+our $hhshare  = $ENV{"HHLIB"} || "/usr/share/hhsuite";   # main hh-suite directory</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;">+our $hhdata   = $hhshare."/data";  # path to arch indep data directory for hhblits, example files</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;">+our $hhbdata  = $hhlib."/data";    # path to arch dep data directory for hhblits, example files</span></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> our $hhbin    = $hhlib."/bin";     # path to cstranslate (path to hhsearch, hhblits etc. should be in environment variable PATH)</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;">-our $hhscripts= $hhlib."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)</span></span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-our $dummydb  = $hhdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb)</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;">+our $hhscripts= $hhshare."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)</span></span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+our $dummydb  = $hhbdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb)</span></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> # HHblits data files</span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> our $cs_lib = "$hhdata/cs219.lib";</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;">--- a/src/hhdecl.C</span></span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/hhdecl.C</span></span>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -285,7 +285,7 @@ void Parameters::SetDefaultPaths(char *p</span></span>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff">   if(getenv("HHLIB"))</span>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff">     strcpy(hhlib, getenv("HHLIB"));</span>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff">   else</span>

</pre>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    strcpy(hhlib, "/usr/lib/hh");</span></span>

</pre>

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40

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    strcpy(hhlib, "/usr/lib/hhsuite");</span></span>

</pre>

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41

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff">   strcat(strcpy(hhdata, hhlib), "/data");</span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff">   strcat(strcpy(clusterfile, hhdata), "/context_data.lib");</span>

</pre>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -300,7 +300,7 @@ void Parameters::SetDefaultPaths(char *p</span></span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff">       /* we did not find HHLIB, if called with full path or in dist dir, we can try relative to program path */</span>

</pre>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff">       if(program_path != NULL)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff">  {</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;">-   strcat(strcpy(hhlib, program_path), "../lib/hh");</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+   strcat(strcpy(hhlib, program_path), "../lib/hhsuite");</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff">    strcat(strcpy(hhdata, hhlib), "/data");</span>

</pre>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff">    strcat(strcpy(clusterfile, hhdata), "/context_data.lib");</span>

</pre>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff">    strcat(strcpy(cs_library, hhdata), "/cs219.lib");</span></pre>

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<br>

</li>

<li id="1a5c0eea47675e0472187a1e31224d82f2b23a21">

<a href="https://salsa.debian.org/med-team/hhsuite/compare/7fd79ad6a30a26a425ca9283ca11f552ba5a1166...e3df8c735a77c9811b569f88ebf07db927a80de7#1a5c0eea47675e0472187a1e31224d82f2b23a21"><strong>debian/patches/rest1</strong>

deleted

</a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: Assorted patches</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">  * Set paths to hhsuite components for Perl scripts.</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">  * Add a Makefile to generate data/do_not_delete.phr,do_not_delete.pin,do_not_delete.psq .</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff">Author: Laszlo Kajan <lkajan@rostlab.org></span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Makefile</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -14,13 +14,13 @@ endif</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> ifdef ICC</span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff">   CXX = env LANG=C icc</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;">-  CXXFLAGS = -fast -Wall -fno-strict-aliasing -finline-functions -funroll-loops -fp-model fast=2 -fast-transcendentals -wd981 -wd383 -wd2259 -wd1572 -D HH_SSE3 -I$(CS_DIR) -I$(FFINDEX_DIR)</span></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;">+  CXXFLAGS += -fast -Wall -fno-strict-aliasing -finline-functions -funroll-loops -fp-model fast=2 -fast-transcendentals -wd981 -wd383 -wd2259 -wd1572 -D HH_SSE3 -I$(CS_DIR)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC13" class="line" lang="diff">   HHSEARCH_LIBS = -lpthread -lrt</span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff">   HHBLITS_LIBS = -lpthread -lrt -openmp</span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff">   OBJECT_LIBS = -openmp</span>

</pre>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> else # ifndef ICC</span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff">   CXX = g++</span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -I$(FFINDEX_DIR) -fopenmp</span></span>

</pre>

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19

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  CXXFLAGS += -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff">   HHSEARCH_LIBS = -lpthread</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC21" class="line" lang="diff">   HHBLITS_LIBS = -lpthread -fopenmp</span>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff">   HHALIGN_LIBS = </span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -51,7 +51,7 @@ else # ifndef ICC</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff">   endif</span>

</pre>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> endif # ifndef ICC</span>

</pre>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CPP = $(CXX) $(CXXFLAGS)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CPP = $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS)</span></span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> CPP_VALGRIND = $(CXX) -g $(CXXFLAGS)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -92,7 +92,7 @@ hhsearch_valgrind: hhsearch.C $(SOURCES)</span></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff">    $(CPP_VALGRIND) hhsearch.C -o hhsearch_valgrind $(CS_OBJECTS) $(HHSEARCH_LIBS)</span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="35" 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="LC35" class="line" lang="diff"> hhblits: hhblits.C $(SOURCES) $(HEADERS) $(CS_OBJECTS)</span>

</pre>

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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;">-  $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a</span></span>

</pre>

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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;">+  $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) -lffindex</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" 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="LC39" class="line" lang="diff"> hhblits_static: hhblits.C $(SOURCES) $(HEADERS)$(CS_OBJECTS)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff">   $(CPP) -static hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a</span></pre>

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<br>

</li>

<li id="76ea3e3af30bd7b6907204399143c3cdea1dee61">

<a href="https://salsa.debian.org/med-team/hhsuite/compare/7fd79ad6a30a26a425ca9283ca11f552ba5a1166...e3df8c735a77c9811b569f88ebf07db927a80de7#76ea3e3af30bd7b6907204399143c3cdea1dee61"><strong>debian/patches/unnecessary_libz</strong>

deleted

</a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: remove unnecessary libz link</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Forwarded: yes</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Author: Laszlo Kajan <lkajan@rostlab.org></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Makefile</span></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -46,7 +46,7 @@ else # ifndef ICC</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">     HHSEARCH_LIBS = -lpthread -lrt</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">     HHBLITS_LIBS+=-lrt</span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">     ifndef NO_PNG</span>

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10

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      HHALIGN_LIBS = -DNO_FREETYPE -DHH_PNG -lpng -lz</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      HHALIGN_LIBS = -DNO_FREETYPE -DHH_PNG -lpng</span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff">     endif</span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff">   endif</span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> endif # ifndef ICC</span></pre>

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<br>

</li>

<li id="cbca94541557b81c56257769c221a2c9943a2529">

<a href="https://salsa.debian.org/med-team/hhsuite/compare/7fd79ad6a30a26a425ca9283ca11f552ba5a1166...e3df8c735a77c9811b569f88ebf07db927a80de7#cbca94541557b81c56257769c221a2c9943a2529"><strong>debian/patches/unused_variables_warning</strong>

deleted

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: fix unused variables warning</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Forwarded: yes</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Author: Laszlo Kajan <lkajan@rostlab.org></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/pngwriter.cc</span></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/pngwriter.cc</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -3343,13 +3343,13 @@ void pngwriter::scale_wh(int finalwidth,</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">      {</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">   std::cerr << " PNGwriter::scale_wh - ERROR **: Negative or zero final width or height not allowed." << std::endl;</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"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">-<span id="LC11" 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="LC12" class="line" lang="diff">    double kx;</span>

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<td class="diff-line-num old old_line" data-linenumber="13" 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">

13

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff">    double ky;</span>

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<td class="diff-line-num old old_line" data-linenumber="14" 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">

14

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> </span>

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<td class="diff-line-num old old_line" data-linenumber="15" 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">

15

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff">    kx = ((double)finalwidth)/((double)width_);</span>

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<td class="diff-line-num old old_line" data-linenumber="16" 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="LC16" class="line" lang="diff">    ky = ((double)finalheight)/((double)height_);</span>

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<td class="diff-line-num old old_line" data-linenumber="17" 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">

17

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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18

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+*/</span></span>

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19

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff">    pngwriter temp(finalwidth, finalheight, 0, "temp");</span>

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20

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> </span>

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21

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff">    int red, green, blue;</span></pre>

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<br>

</li>

<li id="e9ec683b043361dc45be4135331a1d2f212a4fda">

<a href="https://salsa.debian.org/med-team/hhsuite/compare/7fd79ad6a30a26a425ca9283ca11f552ba5a1166...e3df8c735a77c9811b569f88ebf07db927a80de7#e9ec683b043361dc45be4135331a1d2f212a4fda"><strong>debian/patches/version_bump</strong>

deleted

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<hr>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: fix version where it is not up to date</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Author: Laszlo Kajan <lkajan@rostlab.org></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/hhdecl.C</span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/hhdecl.C</span></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,7 +10,7 @@</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> //// Constants</span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> /////////////////////////////////////////////////////////////////////////////////////</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-EXTERN const char VERSION_AND_DATE[]="version 2.0.15 (June 2012)";</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+EXTERN const char VERSION_AND_DATE[]="version 2.0.16 (January 2013)";</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> EXTERN const char REFERENCE[]="Remmert M, Biegert A, Hauser A, and Soding J.\nHHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.\nNat. Methods 9:173-175 (2011).\n";</span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> EXTERN const char COPYRIGHT[]="(C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser\n";</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC13" class="line" lang="diff"> EXTERN const int MAXSEQ=65535; //max number of sequences in input alignment (must be <~30000 on cluster nodes??)</span></pre>

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<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/hhsuite/compare/7fd79ad6a30a26a425ca9283ca11f552ba5a1166...e3df8c735a77c9811b569f88ebf07db927a80de7#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

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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">@@ -5,7 +5,8 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"># Uncomment this to turn on verbose mode.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">#export DH_VERBOSE=1</span>

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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>

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<td class="diff-line-num new_line old" data-linenumber="8" 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="LC8" class="line" lang="plaintext">VERSION=$(shell dpkg-parsechangelog -SVersion | cut -f1 -d+)</span>

</pre>

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<td class="diff-line-num new new_line" 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">include /usr/share/dpkg/default.mk</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="9" 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="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" 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="LC10" class="line" lang="plaintext">TIMESTAMP=$(shell dpkg-parsechangelog -STimestamp)</span>

</pre>

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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" 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">DATE=$(shell date --date=@$(TIMESTAMP) '+%d %B %Y')</span>

</pre>

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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,7 +26,7 @@ override_dh_installman: $(HHMANPAGES)</td>

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<td class="diff-line-num old_line" data-linenumber="25" 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="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">     dh_installman</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="27" 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="LC27" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" 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="diff-line-num new_line" data-linenumber="28" 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="LC28" class="line" lang="plaintext">$(HHMANPAGES): %.1 : debian/tmp/usr/bin/%</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" 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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<td class="diff-line-num new_line old" data-linenumber="29" 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="LC28" class="line" lang="plaintext">     unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string $(<span class="idiff left right">VERSION</span>) -n "$$n_$*" '$<' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > '$@'</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="29" 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="diff-line-num new new_line" data-linenumber="29" 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="LC29" class="line" lang="plaintext">     unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string $(<span class="idiff left right">DEB_VERSION_UPSTREAM</span>) -n "$$n_$*" '$<' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > '$@'</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" 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="LC30" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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="diff-line-num new_line" data-linenumber="31" 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="LC31" class="line" lang="plaintext">override_dh_auto_clean:</span>

</pre>

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31

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32

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">     dh_auto_clean</span>

</pre>

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