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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/gff2aplot">Debian Med / gff2aplot</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/43d849a817dc027fbf09c3c30cfd8fb492a905c0">43d849a8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-10T06:38:51Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">README files in examples are actually scripts - fix PATH to gff2aplot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/4e5053f5eb9629902a2a3944689d6cecac9b4fe8">4e5053f5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-10T06:44:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/574d9f434b8ebab4d5853b72baa0f3208adab1a5">574d9f43</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-10T06:51:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix issue with Perl 5.28
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/b727e01b1d247b5b138d944343551225505a2344">b727e01b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-10T08:09:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">avoid useless install step to /usr/local/bin
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/9d46dc60ba97f8ffaca5bf888f1eb221b691f6f5">9d46dc60</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-10T08:11:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix definition of CP in upstream makefile; Make sure sprint buffers have proper size
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/9fb1e11db0fd9afcb75907f3434de01c16d3b748">9fb1e11d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-10T08:23:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add comment about not fully working patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/e377e8db864c41846edf76d38708190219fe0b28">e377e8db</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-10T08:24:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Properly install examples
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gff2aplot/commit/4e7aefe1271969e6b27353bf32d3827c7483f589">4e7aefe1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-10T08:39:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make sure .pl files will be renamed
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#f858b44a6868a44c99740387bb3697091f0fba60">
<span class="new-file">
+
debian/patches/enhance_sprintf_buffer.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#80cf7b1a5df94c95e4b656a55c91b3fcfa237036">
<span class="new-file">
+
debian/patches/fix_install_ali2gff.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#1059c3645d4481142e798e809fdde14d8eed783a">
<span class="new-file">
+
debian/patches/perl_5.28.patch
</span>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
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</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/gff2aplot/compare/0dd91f60236262da22b5927f5421e363e1ab52bc...4e7aefe1271969e6b27353bf32d3827c7483f589#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gff2aplot (2.0-11) UNRELEASED; 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"> * README files in examples are actually scripts - fix PATH to gff2aplot</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"> * Add autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #890789</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"> * Fix issue with Perl 5.28</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Fix definition of CP in upstream makefile</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Make sure sprint buffers have proper size</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 10 Dec 2018 07:36:57 +0100</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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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">gff2aplot (2.0-10) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * debhelper 11</span>
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<li id="f858b44a6868a44c99740387bb3697091f0fba60">
<a href="https://salsa.debian.org/med-team/gff2aplot/compare/0dd91f60236262da22b5927f5421e363e1ab52bc...4e7aefe1271969e6b27353bf32d3827c7483f589#f858b44a6868a44c99740387bb3697091f0fba60"><strong>debian/patches/enhance_sprintf_buffer.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Mon, 10 Dec 2018 07:36:57 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Enhance print buffer to avoid:</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 36 and 3418 bytes into a destination of size 1000</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> Finally this patch is not fully working since the enhanced buffers</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> make sprint assume that even larger buffers are needed.</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 class="gd" style="color: #000; background-color: #fdd;">--- a/src/ali2gff/ali2gff.c</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/ali2gff/ali2gff.c</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -234,7 +234,7 @@ void processGFFfile() {</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> unsigned long int yseqLen_4 = LONG_MAX;</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"> float score;</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;">- char scores[MAXSTRING];</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;">+ char scores[2*MAXSTRING];</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"> char strand1;</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> char strand2;</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -426,8 +426,8 @@ void processMumfile() {</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> time_t now;</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> char nowString[100];</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char nextMUM[MAXSTRING] = "";</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char nextGAP[MAXSTRING] = "";</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char nextMUM[5*MAXSTRING] = "";</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char nextGAP[3*MAXSTRING] = "";</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> char seq1[MAX_SEQUENCE_LENGTH];</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -974,7 +974,7 @@ void processSimfile() {</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> FILE *simfile;</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> char line[MAXSTRING]; /*----- read line -----*/</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char seqboundsline[MAXSTRING];</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char seqboundsline[2*MAXSTRING];</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> char *ptr; /*----- pointer to line -----*/</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> char waste[MAXSTRING];</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1000,7 +1000,7 @@ void processSimfile() {</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> unsigned long int yrev; /* start position + end position of y sequence --- this term is used to calculate positions of rev. compl. fragments on forward strand */ </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> unsigned short int aliPrinted = 0;</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char aliPrintString[MAXSTRING];</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char aliPrintString[4*MAXSTRING];</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> /*----- open alignment file -----*/</span></pre>
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<li id="80cf7b1a5df94c95e4b656a55c91b3fcfa237036">
<a href="https://salsa.debian.org/med-team/gff2aplot/compare/0dd91f60236262da22b5927f5421e363e1ab52bc...4e7aefe1271969e6b27353bf32d3827c7483f589#80cf7b1a5df94c95e4b656a55c91b3fcfa237036"><strong>debian/patches/fix_install_ali2gff.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Mon, 10 Dec 2018 07:36:57 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Make sure target dir exists when performing parallel builds</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> Somehow CP is resolved to "cp 1" - no idea why, just force proper copy statement</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</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/Makefile</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;">@@ -84,7 +84,7 @@</span></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"> RM = $(firstword $(shell which rm )) $(V)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> RD = $(firstword $(shell which rmdir)) $(V)</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;">- CP = $(firstword $(shell which cp )) $(V)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CP = cp -v</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> MV = $(firstword $(shell which mv )) $(V)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> LN = $(firstword $(shell which ln )) $(V)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> MD = $(firstword $(shell which mkdir)) $(V)</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -145,7 +145,8 @@ installbin : $(BINCODE)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> ### FINISHING CODE</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> $(addprefix $(BIN)/, $(ALI2GFF)) : $(addprefix $(ALI2GFFD)/, $(ALI2GFF))</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @${CP} $(addprefix $(ALI2GFFD)/, $(ALI2GFF)) \</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;">+ mkdir -p $(BIN)</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;">+ cp $(addprefix $(ALI2GFFD)/, $(ALI2GFF)) \</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> $(addprefix $(BIN)/, $(ALI2GFF))</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> $(addprefix $(ALI2GFFD)/, $(ALI2GFF)) : $(addprefix $(addprefix $(ALI2GFFD)/, $(ALI2GFF)), .h .c)</span></pre>
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<li id="1059c3645d4481142e798e809fdde14d8eed783a">
<a href="https://salsa.debian.org/med-team/gff2aplot/compare/0dd91f60236262da22b5927f5421e363e1ab52bc...4e7aefe1271969e6b27353bf32d3827c7483f589#1059c3645d4481142e798e809fdde14d8eed783a"><strong>debian/patches/perl_5.28.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Mon, 10 Dec 2018 07:36:57 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/bin/gff2aplot line 1737.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></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/gff2aplot.pl</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/gff2aplot.pl</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;">@@ -1733,7 +1733,7 @@ sub varscheck() {</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> || return $F;</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> $flag && do {</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> my @tmpary = ();</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- defined( @{ $varec->{$class}{ $$rec[1] } } ) || do {</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @{ $varec->{$class}{ $$rec[1] } } || do {</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> @{ $varec->{$class}{ $$rec[1] } } = ();</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> };</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> @tmpary = &find_regexp( $$rec[0] );</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/gff2aplot/compare/0dd91f60236262da22b5927f5421e363e1ab52bc...4e7aefe1271969e6b27353bf32d3827c7483f589#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -3,3 +3,6 @@</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">use-dpkg-buildflags.patch</span>
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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">mayhem.patch</span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">fis-privacy-breach.patch</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">perl_5.28.patch</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">fix_install_ali2gff.patch</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">enhance_sprintf_buffer.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/gff2aplot/compare/0dd91f60236262da22b5927f5421e363e1ab52bc...4e7aefe1271969e6b27353bf32d3827c7483f589#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">@@ -10,6 +10,10 @@</td>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">override_dh_auto_clean:</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> rm -f src/ali2gff/ali2gff bin/ali2gff</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># We need to rename some *.pl files</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"># We need to rename some *.pl files<span class="idiff left right"> (done in dh_auto_install to avoid useless install step to /usr/local/bin)</span></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">override_dh_auto_install:</span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> for script in `find bin -name "*.pl"` ; do mv $$script bin/`basename $$script .pl` ; done</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">override_dh_installexamples:</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> dh_installexamples</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> find debian/*/usr/share/doc/*/examples -name README -exec sed -i 's?^$$BIN/gff2aplot.pl?gff2aplot?' \{\} \;</span></pre>
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<a href="https://salsa.debian.org/med-team/gff2aplot/compare/0dd91f60236262da22b5927f5421e363e1ab52bc...4e7aefe1271969e6b27353bf32d3827c7483f589#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/gff2aplot/compare/0dd91f60236262da22b5927f5421e363e1ab52bc...4e7aefe1271969e6b27353bf32d3827c7483f589#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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/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: navy;">-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: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span>gff2aplot</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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6
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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="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</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;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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14
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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: navy;">-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="k" style="font-weight: 600;">for </span>script <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span>find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-name</span> README<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cd</span> <span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: teal;">$script</span><span class="k" style="font-weight: 600;">)</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> sh README</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> ..</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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