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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/lagan">Debian Med / lagan</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/lagan/commit/61c80a8596e267922515c9d57e747bd9e642ca9f">61c80a85</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-04T08:05:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Hardening and debug symbols also in subdir
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lagan/commit/a2404d1437bc9e2d0983d6c62198f07f88ebd0f6">a2404d14</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-04T08:13:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make sure LDFLAGS will propagate to subdir
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lagan/commit/ffe9c3ccde5968ba1a6f2302641bae7af9fa71a8">ffe9c3cc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-04T08:14:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix permissions
</pre>
</li>
</ul>
<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
debian/patches/hardening.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<a href="https://salsa.debian.org/med-team/lagan/compare/34f05f0f3291c4b5e06b71770a619a26c9fb2601...ffe9c3ccde5968ba1a6f2302641bae7af9fa71a8#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.patch</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">@@ -4,7 +4,7 @@ Last-Update: Tue, 04 Dec 2018 08:36:52 +0100</td>
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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/Makefile</span></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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,<span class="idiff left right">6 +1,6</span> @@</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;">@@ -1,<span class="idiff left right">54 +1,54</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> CC = gcc $(CFLAGS)</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> CPP = g++ $(CFLAGS)</span>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS = -O3 # -Wall -W</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,9 @@ Last-Update: Tue, 04 Dec 2018 08:36:52 +0100</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> TRGT_DIR = ..</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> </span>
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<td class="diff-line-num old_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="diff"> all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay</span>
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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,46 +9,46 @@ clean:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (cd glocal; $(MAKE))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (cd glocal; $(MAKE) LDFLAGS=$(LDFLAGS))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> clean: </span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> rm -f *.o *~ utils/*~ mlagan.purify core</span>
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<td class="diff-line-num new_line" data-linenumber="19" 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="LC19" class="line" lang="diff"> (cd glocal; $(MAKE) clean)</span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> ../anchors: anchors.c skiplist.c</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="81" 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="83" 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">@@ -81,3 +83,22 @@ Last-Update: Tue, 04 Dec 2018 08:36:52 +0100</td>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"> ../utils/dotplot: utils/dotplot.cpp</span>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp</span></span>
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83
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/glocal/Makefile</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/glocal/Makefile</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,6 +1,6 @@</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> CC = g++</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> OPTFLAGS = </span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS = $(OPTFLAGS) -O3</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS += $(OPTFLAGS) -O3</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> CLINKER = g++ </span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> # LIBDIR = -L/usr/local/lib</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> MLIB = -lm</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,7 +10,7 @@ TRGT = glocal</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> </span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> .cpp.o:</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp $(LDFLAGS)</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> $(TRGT): $(OBJECTS)</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/lagan/compare/34f05f0f3291c4b5e06b71770a619a26c9fb2601...ffe9c3ccde5968ba1a6f2302641bae7af9fa71a8#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -11,3 +11,7 @@ override_dh_auto_build:</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> dh_auto_clean</span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> rm -f prolagan</span>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">override_dh_fixperms:</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> dh_fixperms</span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> find debian -name flipchaos.pl -exec chmod +x \{\} \;</span></pre>
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