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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/plink2">Debian Med / plink2</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/5c4d7d84642085afb135dfe023039aec73732e8f">5c4d7d84</a></strong>
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<span>by Andreas Tille</span>
<i>at 2022-02-20T21:24:51+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.00~a3-220218+dfsg</pre>
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<h4>4 changed files:</h4>
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<a href="#5fce52c5aa6c7bce70dfbc7bf69033d4e1b69e50">
include/plink2_base.cc
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<a href="#f2695700d4614304f2acf05f9546dcf4b3608c47">
include/plink2_base.h
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<a href="#e828d66bb2fc597bda91bc643d9d9d5df9c3de2f">
plink2.cc
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<li class="file-stats">
<a href="#5c0ac48ba397674ac28142efc3b29b7de442d076">
plink2_cmdline.cc
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<h4>Changes:</h4>
<li id="5fce52c5aa6c7bce70dfbc7bf69033d4e1b69e50">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/5c4d7d84642085afb135dfe023039aec73732e8f#5fce52c5aa6c7bce70dfbc7bf69033d4e1b69e50"><strong>include/plink2_base.cc</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">@@ -23,7 +23,7 @@ namespace plink2 {</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="24" 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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<td class="new_line diff-line-num" data-linenumber="24" 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="LC24" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">g_failed_alloc_attempt_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if (__GNUC__ <span class="idiff left right"><</span>= 4) && (__GNUC_MINOR__ < 7) && !defined(__APPLE__)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="26" 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="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if <span class="idiff left">((</span>(__GNUC__ <span class="idiff">=</span>= 4) && (__GNUC_MINOR__ < 7)<span class="idiff right">) || (__GNUC__ >= 11))</span> && !defined(__APPLE__)</span></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">pgl_malloc</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pp</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span><span class="p">,</span> <span class="n" style="color: #333;">pp</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">likely</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">S_CAST</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span><span class="p">,</span> <span class="n" style="color: #333;">pp</span><span class="p">)))</span> <span class="p">{</span></span>
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<li id="f2695700d4614304f2acf05f9546dcf4b3608c47">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/5c4d7d84642085afb135dfe023039aec73732e8f#f2695700d4614304f2acf05f9546dcf4b3608c47"><strong>include/plink2_base.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2010" 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="2010" 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">@@ -2010,12 +2010,16 @@ extern uintptr_t g_failed_alloc_attempt_size;</td>
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2010
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2010
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<pre style="margin: 0;"> <span id="LC2010" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// number is printed as well; see e.g.</span></span>
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2011
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2011
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<pre style="margin: 0;"> <span id="LC2011" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// https://stackoverflow.com/questions/15884793/how-to-get-the-name-or-file-and-line-of-caller-method</span></span>
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2012
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2012
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<pre style="margin: 0;"> <span id="LC2012" class="line" lang="cpp"></span>
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2013
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<pre style="margin: 0;">-<span id="LC2013" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if (__GNUC__ == 4) && (__GNUC_MINOR__ < 7) && !defined(__APPLE__)</span></span>
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2013
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<pre style="margin: 0;">+<span id="LC2013" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if <span class="idiff left">((</span>(__GNUC__ == 4) && (__GNUC_MINOR__ < 7)<span class="idiff right">) || (__GNUC__ >= 11))</span> && !defined(__APPLE__)</span></span>
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2014
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2014
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<pre style="margin: 0;"> <span id="LC2014" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// putting this in the header file caused a bunch of gcc 4.4 strict-aliasing</span></span>
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2015
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2015
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<pre style="margin: 0;"> <span id="LC2015" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// warnings, while not doing so seems to inhibit some malloc-related compiler</span></span>
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2016
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2016
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<pre style="margin: 0;"> <span id="LC2016" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// optimizations, bleah</span></span>
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2017
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2017
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<pre style="margin: 0;"> <span id="LC2017" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// compromise: header-inline iff gcc version >= 4.7 (might not be the right</span></span>
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2018
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2018
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<pre style="margin: 0;"> <span id="LC2018" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// cutoff?)</span></span>
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<pre style="margin: 0;">+<span id="LC2019" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// update (18 Feb 2022): looks like inlined pgl_malloc is not compiled as</span></span>
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<pre style="margin: 0;">+<span id="LC2020" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// intended by gcc 11, due to new ipa-modref pass? Open to suggestions on how</span></span>
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<pre style="margin: 0;">+<span id="LC2021" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// to fix this; maybe it's now necessary to define type-specific malloc</span></span>
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<pre style="margin: 0;">+<span id="LC2022" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// wrappers, ugh...</span></span>
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2023
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<pre style="margin: 0;"> <span id="LC2023" class="line" lang="cpp"><span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">pgl_malloc</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uintptr_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2024" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;"> <span id="LC2025" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Unfortunately, defining the second parameter to be of type void** doesn't do</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/5c4d7d84642085afb135dfe023039aec73732e8f#e828d66bb2fc597bda91bc643d9d9d5df9c3de2f"><strong>plink2.cc</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">@@ -71,7 +71,7 @@ static const char ver_str[] = "PLINK v2.00a3"</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="">#ifdef USE_MKL</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang=""> " Intel"</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="">#endif</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang=""> " (1<span class="idiff left right">7</span> Feb 2022)";</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang=""> " (1<span class="idiff left right">8</span> Feb 2022)";</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="">static const char ver_str2[] =</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang=""> // include leading space if day < 10, so character length stays the same</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang=""> ""</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">@@ -10944,13 +10944,7 @@ int main(int argc, char** argv) {</td>
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<pre style="margin: 0;"> <span id="LC10944" class="line" lang=""> reterr = kPglRetWriteFail;</span>
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10945
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<pre style="margin: 0;"> <span id="LC10945" class="line" lang=""> }</span>
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<pre style="margin: 0;"> <span id="LC10946" class="line" lang=""> if (bigstack_ua) {</span>
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10947
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<pre style="margin: 0;">-<span id="LC10947" class="line" lang=""> if (g_debug_on) {</span>
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10948
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<pre style="margin: 0;">-<span id="LC10948" class="line" lang=""> fputs("--debug: Trying to free bigstack_ua.\n", stdout);</span>
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<pre style="margin: 0;">-<span id="LC10949" class="line" lang=""> }</span>
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<pre style="margin: 0;"> <span id="LC10947" class="line" lang=""> free(bigstack_ua);</span>
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<pre style="margin: 0;"> <span id="LC10948" class="line" lang=""> }</span>
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<pre style="margin: 0;">-<span id="LC10952" class="line" lang=""> if (g_debug_on) {</span>
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<pre style="margin: 0;">-<span id="LC10953" class="line" lang=""> fputs("--debug: Exiting.\n", stdout);</span>
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<pre style="margin: 0;">-<span id="LC10954" class="line" lang=""> }</span>
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<pre style="margin: 0;"> <span id="LC10949" class="line" lang=""> return S_CAST(int32_t, reterr);</span>
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<pre style="margin: 0;"> <span id="LC10950" class="line" lang="">}</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">@@ -526,15 +526,9 @@ BoolErr CleanupLogfile(uint32_t print_end_time) {</td>
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="cpp"> <span class="p">}</span></span>
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="cpp"> <span class="n" style="color: #333;">BoolErr</span> <span class="n" style="color: #333;">ret_boolerr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g_logfile</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g_debug_on</span><span class="p">)</span> <span class="p">{</span></span>
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530
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"--debug: g_log_failed = %u.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">g_log_failed</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">g_log_failed</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="cpp"> <span class="n" style="color: #333;">logputs_silent</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="cpp"> <span class="n" style="color: #333;">logputs_silent</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g_debug_on</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="cpp"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">"--debug: Trying to close log.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unlikely</span><span class="p">(</span><span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">g_logfile</span><span class="p">)))</span> <span class="p">{</span></span>
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539
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp"> <span class="n" style="color: #333;">fflush</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>
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534
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error: Failed to finish writing to log: %s.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">strerror</span><span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">));</span></span>
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