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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/quicktree">Debian Med / quicktree</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/quicktree/-/commit/cb1c621205130ca61996228c6949198615c4e26b">cb1c6212</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-07T16:37:05+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/quicktree/-/commit/157b67367156b72570b72e91b0fd03f5005ac477">157b6736</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-07T16:37:25+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install relevant examples
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/quicktree/-/commit/f341e75896107d2b49991561c78446d09e71a46d">f341e758</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-07T16:37:48+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spellings
</pre>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
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debian/examples
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#14fea0078728545f6a156de7c63df9f8ed927ef8">
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+
debian/tests/README
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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debian/tests/control
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<li class="file-stats">
<a href="#25298b08f143628514b3b8b96330842a14a292e5">
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debian/tests/data/cysprot.stockholm
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
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debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<a href="https://salsa.debian.org/med-team/quicktree/-/compare/b809b19533a9b9947b23ff8a4a434010984d3563...f341e75896107d2b49991561c78446d09e71a46d#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">debian/tests/data/cysprot.stockholm</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/quicktree/-/compare/b809b19533a9b9947b23ff8a4a434010984d3563...f341e75896107d2b49991561c78446d09e71a46d#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,6 +8,8 @@ export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed</td>
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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">
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh $@</span>
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<td class="diff-line-num new_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="LC9" class="line" lang="plaintext"></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">override_dh_auto_build:</span>
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<td class="diff-line-num new new_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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> sed -i 's/expexted/expected/' src/tree.c</span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"> sed -i 's/optio\\n/option/' src/quicktree.c </span>
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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="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"> dh_auto_build</span>
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> help2man -i debian/quicktree.htm --no-discard-stderr ./quicktree > quicktree.1</span>
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<li id="14fea0078728545f6a156de7c63df9f8ed927ef8">
<a href="https://salsa.debian.org/med-team/quicktree/-/compare/b809b19533a9b9947b23ff8a4a434010984d3563...f341e75896107d2b49991561c78446d09e71a46d#14fea0078728545f6a156de7c63df9f8ed927ef8"><strong>debian/tests/README</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests for quicktree</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"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">The data for tests has been referenced from:</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> https://salsa.debian.org/med-team/bioperl-run/-/blob/master/t/data/cysprot.stockholm</span></pre>
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<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/quicktree/-/compare/b809b19533a9b9947b23ff8a4a434010984d3563...f341e75896107d2b49991561c78446d09e71a46d#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span></pre>
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<li id="25298b08f143628514b3b8b96330842a14a292e5">
<a href="https://salsa.debian.org/med-team/quicktree/-/compare/b809b19533a9b9947b23ff8a4a434010984d3563...f341e75896107d2b49991561c78446d09e71a46d#25298b08f143628514b3b8b96330842a14a292e5"><strong>debian/tests/data/cysprot.stockholm</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># STOCKHOLM 1.0</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">#=GF ID NoName</span>
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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">CATH_HUMAN/1-335 ....MWATLPLLCAGAWLLGVPVCGAAELSVN..........................SLEKFHFKSWMSKHRKTYS.TEEYHHRLQTFASNWRKINAHN....NGNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSATKS..NYLRGTG..PYPPSVDWRKKGNFVSPVKNQGACGSCWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDF........NNYGCQGGLPSQAFEYILYNKGIMGEDTYPYQGKDGY.CKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVT.QDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNG.....IPYWIVKNSWGPQWGMNGYFLIERGK....NMCGLAACASYPIPLV</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">CATH_RAT/1-333 ....MWTALPLLCAGAWLLSAGAT..AELTVN..........................AIEKFHFTSWMKQHQKTYS.SREYSHRLQVFANNWRKIQAHN....QRNHTFKMGLNQFSDMSFAEIKHKYLWSEPQNCSATKS..NYLRGTG..PYPSSMDWRKKGNVVSPVKNQGACGSCWTFSTTGALESAVAIASGKMMTLAEQQLVDCAQNF........NNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGKNGQ.CKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVT.EDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYGEQNG.....LLYWIVKNSWGSNWGNNGYFLIERGK....NMCGLAACASYPIPQV</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">ALEU_HORVU/1-362 ....MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTN....RKGLPYRLGINRFSDMSWEEFQATRLG.AAQTCSATLAGNHLMRDAA..ALPETKDWREDG.IVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGF........NNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGV.CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVI.DGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENG.....VPYWLIKNSWGADWGDNGYFKMEMGK....NMCAIATCASYPVVAA</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">PAPA_CARPA/1-345 MAMIPSISKLLFVAICLFVYMGLSFGDFSIVG.................YSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETN....KKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKG.AVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDR..........RSYGCNGGYPWSALQLVAQYG.IHYRNTYPYEGVQRY.CRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVG....PCGNKVDHAVAAVGYGPN.........YILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">CATL_HUMAN/1-333 ......MNPTLILAAFCLGIASATLTFDHSLE..............................AQWTKWKAMHNRLYG.MNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQ....NRKPRKGKVFQEPLFYEAPRSVDWREKG.YVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGP....QG....NEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEES.CKYNPKYSVANDTGFVDIPK.QEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPD..CSSEDMDHGVLVVGYGFESTESDNNK.YWLVKNSWGEEWGMGGYVKMAKDRR...NHCGIASAASYPTV..</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">CATL_RAT/1-334 ......MTPLLLLAVLCLGTALATPKFDQTFN..............................AQWHQWKSTHRRLYG.TNEEEWRRAVWEKNMRMIQLHNGEYSNGKHGFTMEMNAFGDMTNEEFRQIVNGYR....HQKHKKGRLFQEPLMLQIPKTVDWREKG.CVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVDCSHD....QG....NQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGS.CKYRAEYAVANDTGFVDIPQ.QEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPN..CSSKDLDHGVLVVGYGYEGTDSNKDK.YWLVKNSWGKEWGMDGYIKIAKDRN...NHCGLATAASYPIVN.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">CYS1_DICDI/1-343 ......MKVILLFVLAVFTVFVSSRGIPPEEQ..............................SQFLEFQDKFNKKYS.HEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG.AVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPK.NETVMAGYIVSTGPLAIAADA..VEWQFYIGGVFDIP...CNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK....NTCGVSNFVSTSII..</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">//</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/quicktree/-/compare/b809b19533a9b9947b23ff8a4a434010984d3563...f341e75896107d2b49991561c78446d09e71a46d#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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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/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" 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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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>quicktree</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test Basic functionality'</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">quicktree <span class="nt" style="color: #000080;">-upgma</span> <span class="nt" style="color: #000080;">-boot</span> 0 cysprot.stockholm </span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"></span></pre>
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