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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/plink2">Debian Med / plink2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/f6c79fd81910146e2417c9bef5887ab9588ce05f">f6c79fd8</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-09-10T10:47:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove debian/patches/crossbuild, applied upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/8b6f0d10ed52e11ed97a57151cb14c8e2236576e">8b6f0d10</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-09-10T10:51:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh debian/patches/Fix_Makefile.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/4e4588eeac1032c8c96d75f9f5fcf40633837ab0">4e4588ee</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-09-10T10:55:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh debian/patches/simde
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/4d245ac2ed1ed8163239503987c404887291ba44">4d245ac2</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-09-10T10:55:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh debian/patches/use_packaged_libdeflate
</pre>
</li>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#e550cadaf6db4389542ef0ecd277e52f0e1197d8">
debian/patches/Fix_Makefile.patch
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</li>
<li class="file-stats">
<a href="#c99edf3687f92ddaeb98b563e4f5489c663bf73c">
<span class="deleted-file">
−
debian/patches/crossbuild
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
debian/patches/simde
</a>
</li>
<li class="file-stats">
<a href="#de4952745e8f1d6e8ce892777bdbb2ff3763cac3">
debian/patches/use_packaged_libdeflate
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="e550cadaf6db4389542ef0ecd277e52f0e1197d8">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/97abfe719aa0dadda2b4e009abb012eed096ea80...4d245ac2ed1ed8163239503987c404887291ba44#e550cadaf6db4389542ef0ecd277e52f0e1197d8"><strong>debian/patches/Fix_Makefile.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">@@ -2,8 +2,8 @@ Author: Dylan Aïssi daissi@debian.org></td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: Fix makefile for Debian packaging.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2019-12-06</span></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="idiff left right">plink2.orig</span>/build_dynamic/Makefile</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;">+++ <span class="idiff left right">plink2</span>/build_dynamic/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">a</span>/build_dynamic/Makefile</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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/build_dynamic/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">@@ -17,13 +17,13 @@</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> # work)</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> # Debug symbols: set DEBUG to -g</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" 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">@@ -20,7 +20,7 @@ Last-Update: 2019-12-06</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> DYNAMIC_MKL =</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> MKLROOT = /home/ubuntu/intel/mkl</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> MKL_IOMP5_DIR = /home/ubuntu/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="p">@@ -6<span class="idiff left right">4,11 +64</span>,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -6<span class="idiff left right">6,11 +66</span>,11 @@</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> CPUCHECK_FLAGS = -O2 -DCPU_CHECK_AVX2 ${CXXWARN2}</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> endif</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="34" 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">@@ -34,23 +34,22 @@ Last-Update: 2019-12-06</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> # zstd appears to be seriously targeted at -O3; see 26 Jul 2016 entry at</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> # cbloom.com/rants.html</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> ifdef ZSTD_O2</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="p">@@ -14<span class="idiff left right">6,14 +146</span>,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="p">@@ -14<span class="idiff left right">8,14 +148</span>,14 @@</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> all: plink2 pgen_compress</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> plink2: $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <span class="idiff left right">gcc</span> $(CFLAGS) $(CSRC2) -c</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right">gcc</span> $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <span class="idiff left right">$(CC)</span> $(CFLAGS) $(CSRC2) -c</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right">$(CC)</span> $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> $(SKIP_STATIC_ZSTD) gcc $(ZCFLAGS) $(ZCSRC2) -c</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- g++ $(CXXFLAGS) $(CCSRC2) -c</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- g++ $(CPUCHECK_FLAGS) ../plink2_cpu.cc -c</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- g++ $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS)</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ g++ $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ g++ $(CPUCHECK_FLAGS) $(CXXFLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ g++ $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS) $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CXXFLAGS) $(CCSRC2) -c</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CPUCHECK_FLAGS) ../plink2_cpu.cc -c</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPUCHECK_FLAGS) $(CXXFLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> $(CXX) $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS)</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> pgen_compress: $(PGCSRC2)</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <span class="idiff left right">g++</span> $(CXXFLAGS) $(PGCSRC2) -o pgen_compress</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right">g++</span> $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <span class="idiff left right">$(CXX)</span> $(CXXFLAGS) $(PGCSRC2) -o pgen_compress</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right">$(CXX)</span> $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> .PHONY: clean</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> clean:</span></pre>
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<li id="c99edf3687f92ddaeb98b563e4f5489c663bf73c">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/97abfe719aa0dadda2b4e009abb012eed096ea80...4d245ac2ed1ed8163239503987c404887291ba44#c99edf3687f92ddaeb98b563e4f5489c663bf73c"><strong>debian/patches/crossbuild</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Subject: enable cross building</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/chrchang/plink-ng/pull/145</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- plink2.orig/build_dynamic/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ plink2/build_dynamic/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">@@ -29,6 +29,8 @@</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> MKL_IOMP5_DIR = /home/ubuntu/intel/compilers_and_libraries_2017.2.174/linux/compiler/lib/intel64</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> FORCE_32BIT =</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> DEBUG =</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CC ?= gcc</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CXX ?= g++</span></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"> BASEFLAGS=-DZSTD_MULTITHREAD</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> # ***** end configuration *****</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="p">@@ -146,14 +148,14 @@</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> all: plink2$(SFX) pgen_compress$(SFX)</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> plink2$(SFX): $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc</span>
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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;">- gcc $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c</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;">- $(SKIP_STATIC_ZSTD) gcc $(ZCFLAGS) $(ZCSRC2) -c</span></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;">- g++ $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c</span></span>
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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;">- g++ $(CPUCHECK_FLAGS) $(CXXFLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c</span></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;">- g++ $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2$(SFX) $(BLASFLAGS) $(LINKFLAGS) $(LDFLAGS)</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c</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;">+ $(SKIP_STATIC_ZSTD) $(CC) $(ZCFLAGS) $(ZCSRC2) -c</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;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c</span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPUCHECK_FLAGS) $(CXXFLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2$(SFX) $(BLASFLAGS) $(LINKFLAGS) $(LDFLAGS)</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> pgen_compress$(SFX): $(PGCSRC2)</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- g++ $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress$(SFX)</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress$(SFX)</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> </span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> .PHONY: clean</span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> clean:</span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/97abfe719aa0dadda2b4e009abb012eed096ea80...4d245ac2ed1ed8163239503987c404887291ba44#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Fix_Makefile.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">simde</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">use_packaged_libdeflate</span></pre>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">crossbuild</span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/97abfe719aa0dadda2b4e009abb012eed096ea80...4d245ac2ed1ed8163239503987c404887291ba44#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: Enable buidling on non-AMD64</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/chrchang/plink-ng/pull/146</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">plink2.orig</span>/include/plink2_base.h</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">plink2</span>/include/plink2_base.h</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/include/plink2_base.h</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/include/plink2_base.h</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -134,14 +134,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;"> <span id="LC8" 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">@@ -20,8 +20,8 @@ Forwarded: https://github.com/chrchang/plink-ng/pull/146</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> # ifdef __SSE4_2__</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> # define USE_SSE42</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> # include <smmintrin.h></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;">--- <span class="idiff left right">plink2.orig</span>/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">plink2</span>/Makefile</span></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;">--- <span class="idiff left right">a</span>/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"><span class="p">@@ -6,7 +6,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> # Does not currently support -DCPU_CHECK_...</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">@@ -31,8 +31,8 @@ Forwarded: https://github.com/chrchang/plink-ng/pull/146</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> # BASEFLAGS=-g -msse4.2 -DZSTD_MULTITHREAD</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> # BASEFLAGS=-g -DZSTD_MULTITHREAD</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> </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;">--- <span class="idiff left right">plink2.orig</span>/include/SFMT.h</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;">+++ <span class="idiff left right">plink2</span>/include/SFMT.h</span></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;">--- <span class="idiff left right">a</span>/include/SFMT.h</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;">+++ <span class="idiff left right">b</span>/include/SFMT.h</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"><span class="p">@@ -129,7 +129,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> 128-bit SIMD like data type for standard C</span>
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<pre style="margin: 0;"> <span id="LC38" 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">@@ -43,9 +43,9 @@ Forwarded: https://github.com/chrchang/plink-ng/pull/146</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> /** 128-bit data structure */</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> union W128_T {</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">plink2.orig</span>/plink2.cc</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">plink2</span>/plink2.cc</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">067,7 +3067</span>,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/plink2.cc</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/plink2.cc</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">113,7 +3113</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> #ifdef __APPLE__</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> fesetenv(FE_DFL_DISABLE_SSE_DENORMS_ENV);</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> #else</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">@@ -54,9 +54,9 @@ Forwarded: https://github.com/chrchang/plink-ng/pull/146</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> _MM_SET_FLUSH_ZERO_MODE(_MM_FLUSH_ZERO_ON);</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> # endif</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">plink2.orig</span>/build_dynamic/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">plink2</span>/build_dynamic/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="p">@@ -14<span class="idiff left right">3,17 +143</span>,19 @@</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/build_dynamic/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/build_dynamic/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -14<span class="idiff left right">5,17 +145</span>,19 @@</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> CXXFLAGS += -Wno-sign-compare</span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> endif</span>
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="67" 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="67" 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">@@ -67,22 +67,22 @@ Forwarded: https://github.com/chrchang/plink-ng/pull/146</td>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+all: plink2$(SFX) pgen_compress$(SFX)</span></span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+plink2$(SFX): $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"> <span class="idiff left right">gcc</span> $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> <span class="idiff left right">$(CC)</span> $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c</span>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> $(SKIP_STATIC_ZSTD) gcc $(ZCFLAGS) $(ZCSRC2) -c</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"> <span class="idiff left right">g++</span> $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c</span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"> <span class="idiff left right">g++</span> $(CPUCHECK_FLAGS) $(CXXFLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <span class="idiff left right">g++ $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS) $(LD</span>FLAGS)</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right">g++</span> $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2$(SFX) $(BLASFLAGS) $(LINKFLAGS) $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> <span class="idiff left right">$(CXX)</span> $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> <span class="idiff left right">$(CXX)</span> $(CPUCHECK_FLAGS) $(CXXFLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <span class="idiff left right">$(CXX) $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINK</span>FLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right">$(CXX)</span> $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2$(SFX) $(BLASFLAGS) $(LINKFLAGS) $(LDFLAGS)</span></span>
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-pgen_compress: $(PGCSRC2)</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <span class="idiff left right">g++</span> $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <span class="idiff left right">$(CXX)</span> $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+pgen_compress$(SFX): $(PGCSRC2)</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right">g++</span> $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress$(SFX)</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right">$(CXX)</span> $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress$(SFX)</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"> .PHONY: clean</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">plink2.orig</span>/plink2_glm.cc</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">plink2</span>/plink2_glm.cc</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/plink2_glm.cc</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/plink2_glm.cc</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"><span class="p">@@ -19,6 +19,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"> #include "plink2_glm.h"</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"> #include "plink2_matrix.h"</span>
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<li id="de4952745e8f1d6e8ce892777bdbb2ff3763cac3">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/97abfe719aa0dadda2b4e009abb012eed096ea80...4d245ac2ed1ed8163239503987c404887291ba44#de4952745e8f1d6e8ce892777bdbb2ff3763cac3"><strong>debian/patches/use_packaged_libdeflate</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: Use the Debian packaged version of libdeflate</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">plink2.orig</span>/Makefile.src</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">plink2</span>/Makefile.src</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/Makefile.src</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/Makefile.src</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">@@ -5,7 +5,7 @@</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> CWARN2 = -Wall -Wextra -Wshadow -Wformat-security</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> CXXWARN2 = ${CWARN2} -Wold-style-cast</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -9,7 +9,7 @@ Description: Use the Debian packaged version of libdeflate</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CSRC = include/SFMT.c libdeflate/lib/adler32.c libdeflate/lib/aligned_malloc.c libdeflate/lib/crc32.c libdeflate/lib/deflate_compress.c libdeflate/lib/deflate_decompress.c libdeflate/lib/gzip_compress.c libdeflate/lib/gzip_decompress.c libdeflate/lib/zlib_compress.c libdeflate/lib/zlib_decompress.c libdeflate/lib/x86/cpu_features.c</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CSRC = include/SFMT.c</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> ZCSRC = zstd/lib/common/debug.c zstd/lib/common/entropy_common.c zstd/lib/common/zstd_common.c zstd/lib/common/error_private.c zstd/lib/common/xxhash.c zstd/lib/common/fse_decompress.c zstd/lib/common/pool.c zstd/lib/common/threading.c zstd/lib/compress/fse_compress.c zstd/lib/compress/hist.c zstd/lib/compress/huf_compress.c zstd/lib/compress/zstd_double_fast.c zstd/lib/compress/zstd_fast.c zstd/lib/compress/zstd_lazy.c zstd/lib/compress/zstd_ldm.c zstd/lib/compress/zstd_opt.c zstd/lib/compress/zstd_compress.c zstd/lib/compress/zstd_compress_literals.c zstd/lib/compress/zstd_compress_sequences.c zstd/lib/compress/zstdmt_compress.c zstd/lib/decompress/huf_decompress.c zstd/lib/decompress/zstd_decompress.c zstd/lib/decompress/zstd_ddict.c zstd/lib/decompress/zstd_decompress_block.c</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> ZCSRC = zstd/lib/common/debug.c zstd/lib/common/entropy_common.c zstd/lib/common/zstd_common.c zstd/lib/common/error_private.c zstd/lib/common/xxhash.c zstd/lib/common/fse_decompress.c zstd/lib/common/pool.c zstd/lib/common/threading.c zstd/lib/compress/fse_compress.c zstd/lib/compress/hist.c zstd/lib/compress/huf_compress.c zstd/lib/compress/zstd_double_fast.c zstd/lib/compress/zstd_fast.c zstd/lib/compress/zstd_lazy.c zstd/lib/compress/zstd_ldm.c zstd/lib/compress/zstd_opt.c zstd/lib/compress/zstd_compress.c zstd/lib/compress/zstd_compress_literals.c zstd/lib/compress/zstd_compress_sequences.c zstd/lib/compress/zstd<span class="idiff left right">_compress_superblock.c zstd/lib/compress/zstd</span>mt_compress.c zstd/lib/decompress/huf_decompress.c zstd/lib/decompress/zstd_decompress.c zstd/lib/decompress/zstd_ddict.c zstd/lib/decompress/zstd_decompress_block.c</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="p">@@ -21,8 +21,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" 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="29" 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">@@ -29,8 +29,8 @@ Description: Use the Debian packaged version of libdeflate</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CLEAN = *.o include/*.o libdeflate/lib/*.o libdeflate/lib/x86/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CLEAN = *.o include/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> CLEAN3 = $(foreach expr,$(CLEAN),../$(expr))</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">plink2.orig</span>/include/plink2_bgzf.h</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">plink2</span>/include/plink2_bgzf.h</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/include/plink2_bgzf.h</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/include/plink2_bgzf.h</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"><span class="p">@@ -35,7 +35,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> #include "plink2_string.h"</span>
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