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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/tiddit">Debian Med / tiddit</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/367c6e78664672861465841c91b892965575b101">367c6e78</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-27T10:48:11+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix build
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#ee54dc79014b3def963898e50c98877d46c6b27e">
debian/patches/use_debian_packaged_libs.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/tiddit/-/commit/367c6e78664672861465841c91b892965575b101#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,8 +6,9 @@ Priority: optional</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> cmake,</span>
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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-python,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python3,</span>
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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC10" class="line" lang="plaintext"> libbamtools-dev,</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">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> cython3,</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">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python3-dev,</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"> libbamtools-dev (>= 2.5.1+dfsg-6),</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> zlib1g-dev</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">Standards-Version: 4.5.0</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">Vcs-Browser: https://salsa.debian.org/med-team/tiddit</span>
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<li id="ee54dc79014b3def963898e50c98877d46c6b27e">
<a href="https://salsa.debian.org/med-team/tiddit/-/commit/367c6e78664672861465841c91b892965575b101#ee54dc79014b3def963898e50c98877d46c6b27e"><strong>debian/patches/use_debian_packaged_libs.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 25 May 2020 11:58:02 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Use Debian packaged bamtools</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> Note: Tiddit source came with a patched BamTools. The Debian packaged bamtools</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="diff"> has taken it over in</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> https://salsa.debian.org/med-team/bamtools/-/blob/master/debian/patches/tiddit.patch</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">--- a/CMakeLists.txt</span>
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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/CMakeLists.txt</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">@@ -14,8 +14,8 @@</span> set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOU</span>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +18,7 @@</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> </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"> # source code</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">@@ -28,<span class="idiff left right">8 +28,15</span> @@</span> file(GLOB TIDDIT_FILES</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -28,<span class="idiff left right">10 +28,17</span> @@</span> file(GLOB TIDDIT_FILES</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>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> </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">@@ -29,3 +36,6 @@</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> # TIDDIT executable</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> add_executable(TIDDIT ${TIDDIT_FILES})</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> target_link_libraries(TIDDIT ${ZLIB_LIBRARIES})</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-target_link_libraries(TIDDIT BamTools)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+target_link_libraries(TIDDIT bamtools)</span></span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/tiddit/-/commit/367c6e78664672861465841c91b892965575b101#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">@@ -3,25 +3,23 @@</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</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">export LC_ALL=C.UTF-8</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># this provides:</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># DEB_SOURCE: the source package name</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM: the package's upstream version</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"># SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"># specified by <https://reproducible-builds.org/specs/source-date-epoch/></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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18
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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9
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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="LC21" class="line" lang="plaintext"> dh $@ --buildsystem=cmake</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> dh $@ --<span class="idiff left right">with python3 --</span>buildsystem=cmake</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">override_dh_auto_configure:</span>
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24
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> dh_auto_configure -- -DCMAKE_BUILD_TYPE=RelWithDebInfo</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> dh_auto_configure --sourcedirectory=src --buildsystem=pybuild</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> dh_auto_build --sourcedirectory=src --buildsystem=pybuild</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> dh_auto_install</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> dh_auto_install --sourcedirectory=src --buildsystem=pybuild</span>
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25
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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27
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">#override_dh_auto_test:</span>
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