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       <h1>Debugging strategies</h1>


       <small class="dont-index">Source: <a href="https://github.com/apache/arrow/blob/main/r/vignettes/developers/debugging.Rmd" class="external-link"><code>vignettes/developers/debugging.Rmd</code></a></small>
       <div class="d-none name"><code>debugging.Rmd</code></div>
     </div>


 <p>If you are a developer working with Arrow code, the package’s use of
 tidy eval and C++ necessitates a solid debugging strategy. In this
 article, we recommend a few approaches.</p>
 <div class="section level2">
 <h2 id="debugging-r-code">Debugging R code<a class="anchor" aria-label="anchor" href="#debugging-r-code"></a>
 </h2>
 <p>In general, we have found that using interactive debugging
 (e.g. calls to <code><a href="https://rdrr.io/r/base/browser.html" class="external-link">browser()</a></code>), where you can inspect objects in
 a particular environment, is more efficient than simpler techniques such
 as <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code> statements.</p>
 </div>
 <div class="section level2">
 <h2 id="getting-more-descriptive-c-error-messages-after-a-segfault">Getting more descriptive C++ error messages after a segfault<a class="anchor" aria-label="anchor" href="#getting-more-descriptive-c-error-messages-after-a-segfault"></a>
 </h2>
 <p>If you are working in the RStudio IDE, your R session will be aborted
 if there is a segfault. If you re-run your code in a command-line R
 session, the session isn’t automatically aborted and so it will be
 possible to copy the error message accompanying the segfault. Here is an
 example from a bug which existed at time of writing.</p>
 <pre class="shell"><code>&gt; S3FileSystem$create()

  *** caught segfault ***
 address 0x1a0, cause 'memory not mapped'

 Traceback:
  1: (function (anonymous, access_key, secret_key, session_token,     role_arn, session_name, external_id, load_frequency, region,     endpoint_override, scheme, background_writes) {    .Call(`_arrow_fs___S3FileSystem__create`, anonymous, access_key,         secret_key, session_token, role_arn, session_name, external_id,         load_frequency, region, endpoint_override, scheme, background_writes)})(access_key = "", secret_key = "", session_token = "", role_arn = "",     session_name = "", external_id = "", load_frequency = 900L,     region = "", endpoint_override = "", scheme = "", background_writes = TRUE,     anonymous = FALSE)
  2: exec(fs___S3FileSystem__create, !!!args)
  3: S3FileSystem$create()</code></pre>
 <p>This output provides the R traceback; however, it doesn’t provide any
 information about the exact line of C++ code from which the segfault
 originated. For this, you will need to run R with the C++ debugger
 attached.</p>
 <div class="section level3">
 <h3 id="running-r-code-with-the-c-debugger-attached">Running R code with the C++ debugger attached<a class="anchor" aria-label="anchor" href="#running-r-code-with-the-c-debugger-attached"></a>
 </h3>
 <p>As Arrow has C++ code at its core, debugging code can sometimes be
 tricky when errors originate in the C++ rather than the R layer. If you
 are adding new code which triggers a C++ bug (or find one in existing
 code), this can result in a segfault. If you are working in RStudio, the
 session is aborted, and you may not be able to retrieve the error
 messaging needed to diagnose and/or report the bug. One way around this
 is to find the code that causes the error, and run R with a C++
 debugger.</p>
 <p>If you are using macOS and have installed R using the Apple
 installer, you will not be able to run R with a debugger attached;
 please see <a href="https://mac.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R" class="external-link">the
 instructions here for details on causes of this and workarounds.</a></p>
 <p>Firstly, load R with your debugger. The most common debuggers are
 <code>gdb</code> (typically found on Linux, sometimes on macOS, or
 Windows via MinGW or Cygwin) and <code>lldb</code> (the default macOS
 debugger).</p>
 <p>In my case it’s <code>gdb</code>, but if you’re using the
 <code>lldb</code> debugger (for example, if you’re on a Mac), just swap
 in that command here.</p>
 <pre class="shell"><code>R -d gdb</code></pre>
 <p>Next, run R.</p>
 <pre class="shell"><code><span><span class="va">run</span></span></code></pre>
 <p>You should now be in an R session with the C++ debugger attached.
 This will look similar to a normal R session, but with extra output.</p>
 <p>Now, run your code - either directly in the session or by sourcing it
 from a file. If the code results in a segfault, you will have extra
 output that you can use to diagnose the problem or attach to an issue as
 extra information.</p>
 <p>Here is debugger output from the segfault shown in the previous
 example. You can see here that the exact line which triggers the
 segfault is included in the output.</p>
 <pre class="shell"><code>&gt; S3FileSystem$create()

 Thread 1 "R" received signal SIGSEGV, Segmentation fault.
 0x00007ffff0128369 in std::__atomic_base&lt;long&gt;::operator++ (this=0x178) at /usr/include/c++/9/bits/atomic_base.h:318
 318       operator++() noexcept</code></pre>
 <div class="section level4">
 <h4 id="getting-debugger-output-if-your-session-hangs">Getting debugger output if your session hangs<a class="anchor" aria-label="anchor" href="#getting-debugger-output-if-your-session-hangs"></a>
 </h4>
 <p>The instructions above can provide valuable additional context when a
 segfault occurs. However, there are occasionally circumstances in which
 a bug could cause your session to hang indefinitely without segfaulting.
 In this case, it may be diagnostically useful to interrupt the debugger
 and generate backtraces from all running threads.</p>
 <p>To do this, firstly, press Ctrl/Cmd and C to interrupt the debugger,
 and then run:</p>
 <pre class="shell"><code>thread apply all bt</code></pre>
 <p>This will generate a large amount of output, but this information is
 useful when identifying the cause of the issue.</p>
 </div>
 </div>
 </div>
 <div class="section level2">
 <h2 id="further-reading">Further reading<a class="anchor" aria-label="anchor" href="#further-reading"></a>
 </h2>
 <p>The following resources provide detailed guides to debugging R
 code:</p>
 <ul>
 <li><a href="https://adv-r.hadley.nz/debugging.html" class="external-link">The chapter on
 debugging in ‘Advanced R’ by Hadley Wickham</a></li>
 <li><a href="https://support.rstudio.com/hc/en-us/articles/205612627-Debugging-with-RStudio" class="external-link">The
 RStudio debugging documentation</a></li>
 </ul>
 <p>For an excellent in-depth guide to using the C++ debugger in R, see
 <a href="https://blog.davisvaughan.com/2019/04/05/debug-r-package-with-cpp/" class="external-link">this
 blog post by David Vaughan.</a></p>
 <p>You can find a list of equivalent <a href="https://lldb.llvm.org/use/map.html" class="external-link">gdb and lldb commands on the
 LLDB website.</a></p>
 </div>
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	<main id="main" class="col-md-9"><div class="page-header">

	<h1>Debugging strategies</h1>


	<small class="dont-index">Source: <a href="https://github.com/apache/arrow/blob/main/r/vignettes/developers/debugging.Rmd" class="external-link"><code>vignettes/developers/debugging.Rmd</code></a></small>
	<div class="d-none name"><code>debugging.Rmd</code></div>
	</div>



	<p>If you are a developer working with Arrow code, the package’s use of
	tidy eval and C++ necessitates a solid debugging strategy. In this
	article, we recommend a few approaches.</p>
	<div class="section level2">
	<h2 id="debugging-r-code">Debugging R code<a class="anchor" aria-label="anchor" href="#debugging-r-code"></a>
	</h2>
	<p>In general, we have found that using interactive debugging
	(e.g. calls to <code><a href="https://rdrr.io/r/base/browser.html" class="external-link">browser()</a></code>), where you can inspect objects in
	a particular environment, is more efficient than simpler techniques such
	as <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code> statements.</p>
	</div>
	<div class="section level2">
	<h2 id="getting-more-descriptive-c-error-messages-after-a-segfault">Getting more descriptive C++ error messages after a segfault<a class="anchor" aria-label="anchor" href="#getting-more-descriptive-c-error-messages-after-a-segfault"></a>
	</h2>
	<p>If you are working in the RStudio IDE, your R session will be aborted
	if there is a segfault. If you re-run your code in a command-line R
	session, the session isn’t automatically aborted and so it will be
	possible to copy the error message accompanying the segfault. Here is an
	example from a bug which existed at time of writing.</p>
	<pre class="shell"><code>> S3FileSystem$create()

	* caught segfault *
	address 0x1a0, cause 'memory not mapped'

	Traceback:
	1: (function (anonymous, access_key, secret_key, session_token, role_arn, session_name, external_id, load_frequency, region, endpoint_override, scheme, background_writes) { .Call(`_arrow_fs___S3FileSystem__create`, anonymous, access_key, secret_key, session_token, role_arn, session_name, external_id, load_frequency, region, endpoint_override, scheme, background_writes)})(access_key = "", secret_key = "", session_token = "", role_arn = "", session_name = "", external_id = "", load_frequency = 900L, region = "", endpoint_override = "", scheme = "", background_writes = TRUE, anonymous = FALSE)
	2: exec(fs___S3FileSystem__create, !!!args)
	3: S3FileSystem$create()</code></pre>
	<p>This output provides the R traceback; however, it doesn’t provide any
	information about the exact line of C++ code from which the segfault
	originated. For this, you will need to run R with the C++ debugger
	attached.</p>
	<div class="section level3">
	<h3 id="running-r-code-with-the-c-debugger-attached">Running R code with the C++ debugger attached<a class="anchor" aria-label="anchor" href="#running-r-code-with-the-c-debugger-attached"></a>
	</h3>
	<p>As Arrow has C++ code at its core, debugging code can sometimes be
	tricky when errors originate in the C++ rather than the R layer. If you
	are adding new code which triggers a C++ bug (or find one in existing
	code), this can result in a segfault. If you are working in RStudio, the
	session is aborted, and you may not be able to retrieve the error
	messaging needed to diagnose and/or report the bug. One way around this
	is to find the code that causes the error, and run R with a C++
	debugger.</p>
	<p>If you are using macOS and have installed R using the Apple
	installer, you will not be able to run R with a debugger attached;
	please see <a href="https://mac.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R" class="external-link">the
	instructions here for details on causes of this and workarounds.</a></p>
	<p>Firstly, load R with your debugger. The most common debuggers are
	<code>gdb</code> (typically found on Linux, sometimes on macOS, or
	Windows via MinGW or Cygwin) and <code>lldb</code> (the default macOS
	debugger).</p>
	<p>In my case it’s <code>gdb</code>, but if you’re using the
	<code>lldb</code> debugger (for example, if you’re on a Mac), just swap
	in that command here.</p>
	<pre class="shell"><code>R -d gdb</code></pre>
	<p>Next, run R.</p>
	<pre class="shell"><code><span><span class="va">run</span></span></code></pre>
	<p>You should now be in an R session with the C++ debugger attached.
	This will look similar to a normal R session, but with extra output.</p>
	<p>Now, run your code - either directly in the session or by sourcing it
	from a file. If the code results in a segfault, you will have extra
	output that you can use to diagnose the problem or attach to an issue as
	extra information.</p>
	<p>Here is debugger output from the segfault shown in the previous
	example. You can see here that the exact line which triggers the
	segfault is included in the output.</p>
	<pre class="shell"><code>> S3FileSystem$create()

	Thread 1 "R" received signal SIGSEGV, Segmentation fault.
	0x00007ffff0128369 in std::__atomic_base<long>::operator++ (this=0x178) at /usr/include/c++/9/bits/atomic_base.h:318
	318 operator++() noexcept</code></pre>
	<div class="section level4">
	<h4 id="getting-debugger-output-if-your-session-hangs">Getting debugger output if your session hangs<a class="anchor" aria-label="anchor" href="#getting-debugger-output-if-your-session-hangs"></a>
	</h4>
	<p>The instructions above can provide valuable additional context when a
	segfault occurs. However, there are occasionally circumstances in which
	a bug could cause your session to hang indefinitely without segfaulting.
	In this case, it may be diagnostically useful to interrupt the debugger
	and generate backtraces from all running threads.</p>
	<p>To do this, firstly, press Ctrl/Cmd and C to interrupt the debugger,
	and then run:</p>
	<pre class="shell"><code>thread apply all bt</code></pre>
	<p>This will generate a large amount of output, but this information is
	useful when identifying the cause of the issue.</p>
	</div>
	</div>
	</div>
	<div class="section level2">
	<h2 id="further-reading">Further reading<a class="anchor" aria-label="anchor" href="#further-reading"></a>
	</h2>
	<p>The following resources provide detailed guides to debugging R
	code:</p>
	<ul>
	<li><a href="https://adv-r.hadley.nz/debugging.html" class="external-link">The chapter on
	debugging in ‘Advanced R’ by Hadley Wickham</a></li>
	<li><a href="https://support.rstudio.com/hc/en-us/articles/205612627-Debugging-with-RStudio" class="external-link">The
	RStudio debugging documentation</a></li>
	</ul>
	<p>For an excellent in-depth guide to using the C++ debugger in R, see
	<a href="https://blog.davisvaughan.com/2019/04/05/debug-r-package-with-cpp/" class="external-link">this
	blog post by David Vaughan.</a></p>
	<p>You can find a list of equivalent <a href="https://lldb.llvm.org/use/map.html" class="external-link">gdb and lldb commands on the
	LLDB website.</a></p>
	</div>
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