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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/genomethreader">Debian Med / genomethreader</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/genomethreader/commit/b40f68245525e6335fc6107559609f583a2b5c1e">b40f6824</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-23T13:37:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">skip fastdp tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/genomethreader/commit/d430b803eac80f066aa078311bcdfd1a3da5f1eb">d430b803</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-23T13:46:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">do not include CFLAGS in binary for improved reproducibility
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/genomethreader/commit/732141a7903644e9e946c5f1aa8e7448b3e87320">732141a7</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-23T13:46:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add patch header
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#e906cffef2b1481d274f6952b2f6310812bbab6a">
<span class="new-file">
+
debian/patches/disable-fastdp-tests.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#76258ff6f1526200cf3fda90e9f37fd9ee4b4364">
debian/patches/reproducible.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/ac099ddcc02a829013f5116d740240b48ba1ac76...732141a7903644e9e946c5f1aa8e7448b3e87320#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">genomethreader (1.7.3+dfsg-4) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Skip fastdp tests on i386 (see</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/genometools/genomethreader/issues/14)</span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext"> * Do not include CFLAGS in binary for improved reproducibility.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Sascha Steinbiss <satta@debian.org> Thu, 23 Jan 2020 13:32:02 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">genomethreader (1.7.3+dfsg-3) unstable; urgency=medium</span>
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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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"> * Use defined LANG when building to avoid breaking the Built-Using</span>
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<li id="e906cffef2b1481d274f6952b2f6310812bbab6a">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/ac099ddcc02a829013f5116d740240b48ba1ac76...732141a7903644e9e946c5f1aa8e7448b3e87320#e906cffef2b1481d274f6952b2f6310812bbab6a"><strong>debian/patches/disable-fastdp-tests.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: disable some tests on i386</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Bug: https://github.com/genometools/genomethreader/issues/14</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-01-23</span></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/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/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -163,6 +163,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> STEST_FLAGS += -memcheck</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ifeq ($(nofastdp),yes)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ STEST_FLAGS += -keywords not fastdp</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> RNV_DIR:=src/external/rnv-1.7.10</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> LIBRNV_SRC:=$(RNV_DIR)/rn.c $(RNV_DIR)/rnc.c $(RNV_DIR)/rnd.c $(RNV_DIR)/rnl.c \</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> $(RNV_DIR)/rnv.c $(RNV_DIR)/rnx.c $(RNV_DIR)/drv.c \</span></pre>
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<li id="76258ff6f1526200cf3fda90e9f37fd9ee4b4364">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/ac099ddcc02a829013f5116d740240b48ba1ac76...732141a7903644e9e946c5f1aa8e7448b3e87320#76258ff6f1526200cf3fda90e9f37fd9ee4b4364"><strong>debian/patches/reproducible.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: improve reproducibility</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></span>
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1
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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/Makefile</span></span>
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2
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4
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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/Makefile</span></span>
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3
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">@@ -184,7 +184,7 @@</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -9,3 +11,16 @@</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> LIBGENOMETHREADER_OBJ:=$(LIBGENOMETHREADER_SRC:%.c=obj/%.o)</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> LIBGENOMETHREADER_DEP:=$(LIBGENOMETHREADER_SRC:%.c=obj/%.d)</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/libgenomethreader/gthversionfunc.c</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;">+++ b/src/libgenomethreader/gthversionfunc.c</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -25,8 +25,10 @@</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> printf("Copyright (c) 2013-2016 Wikena GmbH\n\n");</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> printf("Email: gordon@gremme.org\n\n");</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/* removed due to reproducibility issues</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> printf("Used compiler: %s\n", GTH_CC);</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> printf("Compile flags: %s\n", GTH_CFLAGS);</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+*/</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> #ifndef NOLICENSEMANAGER</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> if (lm_license) {</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> putchar('\n');</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/ac099ddcc02a829013f5116d740240b48ba1ac76...732141a7903644e9e946c5f1aa8e7448b3e87320#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,3 +4,4 @@ hardening.patch</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">search-paths.patch</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">m32-m64-ignore.patch</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">reproducible.patch</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">disable-fastdp-tests.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/genomethreader/compare/ac099ddcc02a829013f5116d740240b48ba1ac76...732141a7903644e9e946c5f1aa8e7448b3e87320#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,6 +17,11 @@ ifeq ($(BITS),64)</td>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">else</span>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> 64BIT:=no</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">ifeq ($(DARCH),i386)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> EXTRATESTOPT:=nofastdp=yes</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,7 +42,7 @@ override_dh_auto_install:</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> make licensemanager=no 64bit=$(64BIT) test</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> make licensemanager=no 64bit=$(64BIT) <span class="idiff left right">$(EXTRATESTOPT) </span>test</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">override_dh_installman:</span>
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