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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/f288d354bc98f36308ab69089e4b831de6cdac69">f288d354</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-11-11T10:57:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/37076545b687af49947904b460eeca5fd3e05c83">37076545</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-11-12T11:13:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove d/p/simde, upstream applied
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/bce6865ff8b3375f07b2fc4cf233eea182ea43eb">bce6865f</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-11-12T11:16:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patch
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#e550cadaf6db4389542ef0ecd277e52f0e1197d8">
debian/patches/Fix_Makefile.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
<span class="deleted-file">
−
debian/patches/simde
</span>
</a>
</li>
<li class="file-stats">
<a href="#ebfd2c3cfb38e2d9369281f7f7f48f34e374970a">
debian/patches/use_packaged_libdeflate
→
debian/patches/use_packaged_libdeflate.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="e550cadaf6db4389542ef0ecd277e52f0e1197d8">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/fee4d5fc88ccc5267185c977396a359d5f52b602...bce6865ff8b3375f07b2fc4cf233eea182ea43eb#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">@@ -34,22 +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">@@ -1<span class="idiff left right">48,14 +148</span>,14 @@</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"> all: plink2<span class="idiff left right"> pgen_compress</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left right">50,14 +150</span>,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> all: plink2<span class="idiff left right">$(SFX) pgen_compress$(SFX)</span></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) $(CCSRC2) ../plink2_cpu.cc</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> plink2<span class="idiff left right">$(SFX)</span>: $(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;">- $(CC) $(CFLAGS) $(CSRC2) -c</span></span>
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<td class="diff-line-num old_line" data-linenumber="42" 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="LC42" 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="LC43" class="line" lang="diff"> $(SKIP_STATIC_ZSTD) <span class="idiff left right">gcc</span> $(ZCFLAGS) $(ZCSRC2) -c</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> $(SKIP_STATIC_ZSTD) <span class="idiff left right">$(CC)</span> $(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;">- $(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) $(C<span class="idiff left right">XXFLAGS) $(C</span>PPFLAGS) ../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 <span class="idiff left right">plink2</span> $(BLASFLAGS) $(LINKFLAGS)</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) $(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 $(ARCH32) -o <span class="idiff left right">$@</span> $(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="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CXXFLAGS) $(PGCSRC2) -o <span class="idiff left right">pgen_compress</span></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;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(<span class="idiff left right">LDFLAGS) $(PGCSRC2) -o pgen_compress</span></span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> pgen_compress<span class="idiff left right">$(SFX)</span>: $(PGCSRC2)</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;">- $(CXX) $(CXXFLAGS) $(PGCSRC2) -o <span class="idiff left right">$@</span></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;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(<span class="idiff left right">PGCSRC2) -o $@</span></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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<a href="https://salsa.debian.org/med-team/plink2/-/compare/fee4d5fc88ccc5267185c977396a359d5f52b602...bce6865ff8b3375f07b2fc4cf233eea182ea43eb#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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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">simde</span>
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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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">use_packaged_libdeflate.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/-/compare/fee4d5fc88ccc5267185c977396a359d5f52b602...bce6865ff8b3375f07b2fc4cf233eea182ea43eb#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong>
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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: Enable buidling on non-AMD64</span></span>
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3
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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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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/include/plink2_base.h</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/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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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> #ifdef __LP64__</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;">-# ifndef __SSE2__</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// possible todo: remove this requirement, the 32-bit VecW-using code does most</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// of what we need. But little point in doing this before we have e.g. an</span></span>
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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;">-// ARM-based machine to test with that scientists would plausibly want to run</span></span>
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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;">-// plink2 on.</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# error "64-bit builds currently require SSE2. Try producing a 32-bit build instead."</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;">-# endif</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# include <emmintrin.h></span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# define SIMDE_ENABLE_NATIVE_ALIASES</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# include <simde/x86/sse2.h></span></span>
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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;">--- a/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;">+++ b/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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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-BASEFLAGS=-g -mavx2 -mbmi -mbmi2 -mlzcnt -DZSTD_MULTITHREAD</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;">+BASEFLAGS=-g -DZSTD_MULTITHREAD</span></span>
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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;">--- a/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;">+++ b/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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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> #ifdef __LP64__</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;">- #include <emmintrin.h></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;">+ #define SIMDE_ENABLE_NATIVE_ALIASES</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;">+ #include <simde/x86/sse2.h></span></span>
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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;">--- a/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;">+++ b/plink2.cc</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="p">@@ -3113,7 +3113,7 @@</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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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# ifdef __LP64__</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;">+# if defined __LP64__ && defined __x86_64__</span></span>
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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;">--- a/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;">+++ b/build_dynamic/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="p">@@ -145,17 +145,19 @@</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 old old_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-all: plink2 pgen_compress</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SFX ?= ""</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-plink2: $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc</span></span>
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<td class="diff-line-num old old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+all: plink2$(SFX) pgen_compress$(SFX)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num old old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+plink2$(SFX): $(CSRC2) $(ZCSRC2) $(CCSRC2) ../plink2_cpu.cc</span></span>
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<td class="diff-line-num old old_line" data-linenumber="70" 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">
70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"> $(CC) $(CPPFLAGS) $(CFLAGS) $(CSRC2) -c</span>
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<td class="diff-line-num old old_line" data-linenumber="71" 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">
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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<td class="diff-line-num old old_line" data-linenumber="72" 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">
72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"> $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CCSRC2) -c</span>
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<td class="diff-line-num old old_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"> $(CXX) $(CPUCHECK_FLAGS) $(CXXFLAGS) $(CPPFLAGS) ../plink2_cpu.cc -c</span>
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<td class="diff-line-num old old_line" data-linenumber="74" 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">
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;">- $(CXX) $(OBJ2) plink2_cpu.o $(ARCH32) -o plink2 $(BLASFLAGS) $(LINKFLAGS)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="75" 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">
75
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC75" 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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<td class="diff-line-num old old_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="77" 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">
77
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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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<td class="diff-line-num old old_line" data-linenumber="78" 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">
78
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+pgen_compress$(SFX): $(PGCSRC2)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="80" 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">
80
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(PGCSRC2) -o pgen_compress$(SFX)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"> .PHONY: clean</span>
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<td class="diff-line-num old old_line" data-linenumber="83" 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">
83
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC83" class="line" lang="diff"> clean:</span>
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<td class="diff-line-num old old_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/plink2_glm.cc</span></span>
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<td class="diff-line-num old old_line" data-linenumber="85" 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">
85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/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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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <simde/x86/sse2.h></span></span>
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<pre style="margin: 0;">-<span id="LC92" 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="LC93" class="line" lang="diff"> #ifdef __cplusplus</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"> namespace plink2 {</span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"> #endif</span></pre>
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<li id="ebfd2c3cfb38e2d9369281f7f7f48f34e374970a">
<a href="https://salsa.debian.org/med-team/plink2/-/compare/fee4d5fc88ccc5267185c977396a359d5f52b602...bce6865ff8b3375f07b2fc4cf233eea182ea43eb#ebfd2c3cfb38e2d9369281f7f7f48f34e374970a"><strong>debian/patches/use_packaged_libdeflate</strong>
→
<strong>debian/patches/use_packaged_libdeflate.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>
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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">@@ -6,7 +6,7 @@ Description: Use the Debian packaged version of libdeflate</td>
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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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> </span>
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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/<span class="idiff left right">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/</span>cpu_features.c</span></span>
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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/<span class="idiff left right">crc32.c libdeflate/lib/deflate_compress.c libdeflate/lib/deflate_decompress.c libdeflate/lib/gzip_compress.c libdeflate/lib/gzip_decompress.c libdeflate/lib/utils.c libdeflate/lib/zlib_compress.c libdeflate/lib/zlib_decompress.c libdeflate/lib/arm/arm_cpu_features.c libdeflate/lib/x86/x86_</span>cpu_features.c</span></span>
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10
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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/zstd_compress_superblock.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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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="15" 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">@@ -15,18 +15,18 @@ Description: Use the Debian packaged version of libdeflate</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> OBJ3 = $(CSRC2:.c=.o) $(ZCSRC2:.c=.o) $(CCSRC2:.cc=.o)</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"><span class="gd" style="color: #000; background-color: #fdd;">-CINCLUDE = -Ilibdeflate -Ilibdeflate/common</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CINCLUDE2 = -I../libdeflate -I../libdeflate/common</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#CINCLUDE = -Ilibdeflate -Ilibdeflate/common</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#CINCLUDE2 = -I../libdeflate -I../libdeflate/common</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CINCLUDE = -Ilibdeflate -Ilibdeflate/common -Isimde</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CINCLUDE2 = -I../libdeflate -I../libdeflate/common -I../simde</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#CINCLUDE = -Ilibdeflate -Ilibdeflate/common -Isimde</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#CINCLUDE2 = -I../libdeflate -I../libdeflate/common -I../simde</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> CXXINCLUDE = -Isimde</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> CXXINCLUDE2 = -I../simde</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> ZSTD_INCLUDE = -Izstd/lib -Izstd/lib/common</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> ZSTD_INCLUDE2 = -I../zstd/lib -I../zstd/lib/common</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="p">@@ -30,5 +30,5 @@</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> PGCOBJ = $(PGCSRC:.c=.o)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -32,5 +32,5 @@</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> PGCOBJ = $(PGCSRC:.cc=.o)</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> PGCSRC2 = $(foreach fname,$(PGCSRC),../$(fname))</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> </span>
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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="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CLEAN = *.o include/*.o libdeflate/lib/*.o libdeflate/lib/<span class="idiff left right">arm/*.o libdeflate/lib/</span>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;">--- a/include/plink2_bgzf.h</span></span>
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