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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/mecat2">Debian Med / mecat2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mecat2/-/commit/7d355cd59f4aa20a7a96e23f8d903216155a6ef3">7d355cd5</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-06-30T13:51:50+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More files to exclude
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
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<li class="file-stats">
<a href="#2e4d533ed91ff2bdcbdda6e11ae04b4344247f05">
debian/patches/modify_makefiles.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
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<h4>Changes:</h4>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/mecat2/-/commit/7d355cd59f4aa20a7a96e23f8d903216155a6ef3#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,10 +3,11 @@ Upstream-Name: mecat2</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: https://github.com/xiaochuanle/MECAT2</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Files-Excluded: third_party/hdf5-1.10.4.tar.gz</span>
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<td class="diff-line-num new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext"> DEXTRACTOR/*</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> src/ncbi_blast/*</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> src/fsa/*</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">Comment:</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="LC7" class="line" lang="plaintext"> The hdf5-1.10.4.tar.gz file in third_party/ was removed as this </span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> already exists within the debian repository pre-packaged. DEXTRACTOR </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="LC9" class="line" lang="plaintext"> is packaged separately.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> The files listed above were removed as these </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> already exists within the debian repository pre-packaged.</span>
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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">Files: *</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">Copyright: 20xx-20yy <upstream></span>
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<li id="2e4d533ed91ff2bdcbdda6e11ae04b4344247f05">
<a href="https://salsa.debian.org/med-team/mecat2/-/commit/7d355cd59f4aa20a7a96e23f8d903216155a6ef3#2e4d533ed91ff2bdcbdda6e11ae04b4344247f05"><strong>debian/patches/modify_makefiles.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_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="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">@@ -6,18 +6,25 @@ Last-Update: 2020-06-29</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">--- mecat2.orig/Makefile</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mecat2/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -8,47 +8,13 @@</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> BUILD_TOP_DIR := ${PWD}/${OS_TYPE}-${MACHINE_TYPE}</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -1,54 +1,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-PWD := $(shell pwd)</span></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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-OS_TYPE := $(shell echo `uname`)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-MACHINE_TYPE := $(shell echo `uname -m`)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq (${MACHINE_TYPE}, x86_64)</span></span>
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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="diff"><span class="gd" style="color: #000; background-color: #fdd;">- MACHINE_TYPE = amd64</span></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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-BUILD_DIR := ${PWD}/${OS_TYPE}-${MACHINE_TYPE}/bin</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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.PHONY: all clean mecat</span></span>
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12
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-BUILD_TOP_DIR := ${PWD}/${OS_TYPE}-${MACHINE_TYPE}</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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13
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HDF5_VERSION ?= 1.10.4</span></span>
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14
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HDF5_INSTALL = ${BUILD_TOP_DIR}/hdf5</span></span>
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15
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HDF5_SOURCE = ${BUILD_TOP_DIR}/hdf5-${HDF5_VERSION}</span></span>
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16
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HDF5_INCLUDE = ${HDF5_INSTALL}/include</span></span>
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17
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HDF5_LIB = ${HDF5_INSTALL}/lib/libhdf5.a</span></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">
18
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HDF5_TAR_GZ = ${BUILD_TOP_DIR}/hdf5-$(HDF5_VERSION).tar.gz</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.PHONY: all clean mecat</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> </span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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21
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-DEXTRACTOR_BIN_NAME = dexqv dexta dextract undexqv undexta</span></span>
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<td class="diff-line-num old_line" data-linenumber="22" 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">
22
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-DEXTRACTOR_BIN = $(patsubst %, ${BUILD_DIR}/%, $(DEXTRACTOR_BIN_NAME))</span></span>
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23
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<a href="https://salsa.debian.org/med-team/mecat2/-/commit/7d355cd59f4aa20a7a96e23f8d903216155a6ef3#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">@@ -4,15 +4,6 @@</td>
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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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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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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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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># this provides:</span>
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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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<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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<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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<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="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</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">@@ -20,12 +11,3 @@ include /usr/share/dpkg/default.mk</td>
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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"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span></pre>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"># do_stuff_for_testing</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">#endif</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">#get-orig-source:</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"># . debian/get-orig-source</span></pre>
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