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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/fermi-lite">Debian Med / fermi-lite</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fermi-lite/-/commit/bf6e08b605bf8c968e3a140b1536d84c383cef63">bf6e08b6</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-03-30T10:33:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix sync_instead_of_atomic patch and re-enable it
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fermi-lite/-/commit/c19499e715043ce1a4a7e7da8c8e2275140f9c11">c19499e7</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-03-30T10:49:48+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added a basic test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fermi-lite/-/commit/b4ea6f1de4ad468a421fe67b44e661b6375488b2">b4ea6f1d</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-03-30T10:55:52+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">release 0.1-12
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#7415a76b62777c693ec61a51de4e405a40c7a804">
debian/patches/sync_instead_of_atomic
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#acce358cbc14e13bde1c1d403974d3a9e78e53e0">
<span class="new-file">
+
debian/tests/asm
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/e6ad3623bea78984a8c9013f027d29132008e2e6...b4ea6f1de4ad468a421fe67b44e661b6375488b2#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fermi-lite (0.1-12) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> * debian/patches/sync_instead_of_atomic: fix logic and re-enable (fetch the</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"> previous value, not the new one). Fixes build on mipsel.</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Added a basic package time test & autopkgtest to confirm the patch using</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> fml-asm</span>
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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"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 30 Mar 2020 10:55:37 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">fermi-lite (0.1-11) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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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">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> [ Steve Langasek ]</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/e6ad3623bea78984a8c9013f027d29132008e2e6...b4ea6f1de4ad468a421fe67b44e661b6375488b2#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">@@ -4,4 +4,4 @@ rename_bseq1_t.patch</td>
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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">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">bcf_seqlib.patch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">simde</span>
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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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">ensure-signed-comparison.patch</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><span class="idiff left right"># </span>sync_instead_of_atomic</span></pre>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">sync_instead_of_atomic</span></pre>
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<li id="7415a76b62777c693ec61a51de4e405a40c7a804">
<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/e6ad3623bea78984a8c9013f027d29132008e2e6...b4ea6f1de4ad468a421fe67b44e661b6375488b2#7415a76b62777c693ec61a51de4e405a40c7a804"><strong>debian/patches/sync_instead_of_atomic</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ Subject: fix compatibility on mipsel</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> uint64_t *p = bits + (x>>6);</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> uint64_t z = 1LLU<<(x&0x3f);</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;">- __sync_fetch_and_or(p, z);</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;">+ __atomic_<span class="idiff left right">or_fetch</span>(p, z, __ATOMIC_SEQ_CST);</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;">+ __atomic_<span class="idiff left right">fetch_or</span>(p, z, __ATOMIC_SEQ_CST);</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> static inline void set_bits(uint64_t *bits, const rldintv_t *p)</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@ Subject: fix compatibility on mipsel</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> p[0] = w->visited + (d->z.k[0]>>6); x[0] = 1LLU<<(d->z.k[0]&0x3f);</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> p[1] = w->visited + (d->z.k[1]>>6); x[1] = 1LLU<<(d->z.k[1]&0x3f);</span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ((__sync_fetch_and_or(p[0], x[0])&x[0]) || (__sync_fetch_and_or(p[1], x[1])&x[1])) return;</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ((__atomic_<span class="idiff left right">or_fetch(p[0], x[0], __ATOMIC_SEQ_CST)&x[0]) || (__atomic_or_fetch</span>(p[1], x[1], __ATOMIC_SEQ_CST)&x[1])) return;</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ((__atomic_<span class="idiff left right">fetch_or(p[0], x[0], __ATOMIC_SEQ_CST)&x[0]) || (__atomic_fetch_or</span>(p[1], x[1], __ATOMIC_SEQ_CST)&x[1])) return;</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> d->z.len = d->str.l;</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> if (d->max_l < d->str.m) {</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> d->max_l = d->str.m;</span></pre>
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<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/e6ad3623bea78984a8c9013f027d29132008e2e6...b4ea6f1de4ad468a421fe67b44e661b6375488b2#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,3 +35,9 @@ override_dh_installman:</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> -n 'assemble Illumina short reads in small regions' \</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> -N --no-discard-stderr -h '' ./fml-asm > fml-asm.1</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> dh_installman</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> ./fml-asm test/MT-simu.fq.gz > MT.fq</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> test "$$(wc -l < MT.fq)" = "4"</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">endif</span></pre>
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<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/e6ad3623bea78984a8c9013f027d29132008e2e6...b4ea6f1de4ad468a421fe67b44e661b6375488b2#acce358cbc14e13bde1c1d403974d3a9e78e53e0"><strong>debian/tests/asm</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># autopkgtest check: confirm that fml-asm works</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">INPUT</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">pwd</span><span class="si" style="color: #d14;">)</span>/test/MT-simu.fq.gz</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">test</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>fml-asm <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">INPUT</span><span class="k" style="font-weight: 600;">}</span> | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"4"</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"run: OK"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/e6ad3623bea78984a8c9013f027d29132008e2e6...b4ea6f1de4ad468a421fe67b44e661b6375488b2#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: build-lib</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Depends: @, build-essential</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Tests: asm</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Depends: fml-asm</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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