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Fitbit Heart Rate Intraday
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<h1 id="frequently-asked-questions">Frequently Asked Questions<a class="headerlink" href="#frequently-asked-questions" title="Permanent link">&para;</a></h1>
<h2 id="cannot-connect-to-your-mysql-server">Cannot connect to your MySQL server<a class="headerlink" href="#cannot-connect-to-your-mysql-server" title="Permanent link">&para;</a></h2>
<details class="failure" open="open"><summary>Problem</summary><div class="highlight"><pre><span></span><code>**Error in .local<span class="o">(</span>drv, <span class="se">\.</span>..<span class="o">)</span> :** **Failed to connect to database: Error:
Can<span class="se">\&#39;</span>t initialize character <span class="nb">set</span> unknown <span class="o">(</span>path: compiled<span class="se">\_</span>in<span class="o">)</span>** :
Calls: dbConnect -&gt; dbConnect -&gt; .local -&gt; .Call
Execution halted
<span class="o">[</span>Tue Mar <span class="m">10</span> <span class="m">19</span>:40:15 <span class="m">2020</span><span class="o">]</span>
Error in rule download_dataset:
jobid: <span class="m">531</span>
output: data/raw/p60/locations_raw.csv
RuleException:
CalledProcessError in line <span class="m">20</span> of /home/ubuntu/rapids/rules/preprocessing.snakefile:
Command <span class="s1">&#39;set -euo pipefail; Rscript --vanilla /home/ubuntu/rapids/.snakemake/scripts/tmp_2jnvqs7.download_dataset.R&#39;</span> returned non-zero <span class="nb">exit</span> status <span class="m">1</span>.
File <span class="s2">&quot;/home/ubuntu/rapids/rules/preprocessing.snakefile&quot;</span>, line <span class="m">20</span>, in __rule_download_dataset
File <span class="s2">&quot;/home/ubuntu/anaconda3/envs/moshi-env/lib/python3.7/concurrent/futures/thread.py&quot;</span>, line <span class="m">57</span>, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above <span class="k">for</span> error message
</code></pre></div>
</details>
<details class="done" open="open"><summary>Solution</summary><p>Please make sure the <code>DATABASE_GROUP</code> in <code>config.yaml</code> matches your DB credentials group in <code>.env</code>.</p>
</details>
<hr />
<h2 id="cannot-start-mysql-in-linux-via-brew-services-start-mysql">Cannot start mysql in linux via <code>brew services start mysql</code><a class="headerlink" href="#cannot-start-mysql-in-linux-via-brew-services-start-mysql" title="Permanent link">&para;</a></h2>
<details class="failure" open="open"><summary>Problem</summary><p>Cannot start mysql in linux via <code>brew services start mysql</code></p>
</details>
<details class="done" open="open"><summary>Solution</summary><p>Use <code>mysql.server start</code></p>
</details>
<hr />
<h2 id="every-time-i-run-force-the-download_dataset-rule-all-rules-are-executed">Every time I run force the download_dataset rule all rules are executed<a class="headerlink" href="#every-time-i-run-force-the-download_dataset-rule-all-rules-are-executed" title="Permanent link">&para;</a></h2>
<details class="failure" open="open"><summary>Problem</summary><p>When running <code>snakemake -j1 -R download_phone_data</code> or <code>./rapids -j1 -R download_phone_data</code> all the rules and files are re-computed</p>
</details>
<details class="done" open="open"><summary>Solution</summary><p>This is expected behavior. The advantage of using <code>snakemake</code> under the hood is that every time a file containing data is modified every rule that depends on that file will be re-executed to update their results. In this case, since <code>download_dataset</code> updates all the raw data, and you are forcing the rule with the flag <code>-R</code> every single rule that depends on those raw files will be executed.</p>
</details>
<hr />
<h2 id="error-table-xxx-doesnt-exist-while-running-the-download_phone_data-or-download_fitbit_data-rule">Error <code>Table XXX doesn't exist</code> while running the <code>download_phone_data</code> or <code>download_fitbit_data</code> rule.<a class="headerlink" href="#error-table-xxx-doesnt-exist-while-running-the-download_phone_data-or-download_fitbit_data-rule" title="Permanent link">&para;</a></h2>
<details class="failure" open="open"><summary>Problem</summary><div class="highlight"><pre><span></span><code>Error in .local<span class="o">(</span>conn, statement, ...<span class="o">)</span> :
could not run statement: Table <span class="s1">&#39;db_name.table_name&#39;</span> doesn<span class="err">&#39;</span>t exist
Calls: colnames ... .local -&gt; dbSendQuery -&gt; dbSendQuery -&gt; .local -&gt; .Call
Execution halted
</code></pre></div>
</details>
<details class="done" open="open"><summary>Solution</summary><p>Please make sure the sensors listed in <code>[PHONE_VALID_SENSED_BINS][PHONE_SENSORS]</code> and the <code>[TABLE]</code> of each sensor you activated in <code>config.yaml</code> match your database tables.</p>
</details>
<hr />
<h2 id="how-do-i-install-rapids-on-ubuntu-1604">How do I install RAPIDS on Ubuntu 16.04<a class="headerlink" href="#how-do-i-install-rapids-on-ubuntu-1604" title="Permanent link">&para;</a></h2>
<details class="done" open="open"><summary>Solution</summary><ol>
<li>
<p>Install dependencies (Homebrew - if not installed):</p>
<ul>
<li><code>sudo apt-get install libmariadb-client-lgpl-dev libxml2-dev libssl-dev</code></li>
<li>Install <a href="https://docs.brew.sh/Homebrew-on-Linux">brew</a> for linux and add the following line to <code>~/.bashrc</code>: <code>export PATH=$HOME/.linuxbrew/bin:$PATH</code></li>
<li><code>source ~/.bashrc</code></li>
</ul>
</li>
<li>
<p>Install MySQL</p>
<ul>
<li><code>brew install mysql</code></li>
<li><code>brew services start mysql</code></li>
</ul>
</li>
<li>
<p>Install R, pandoc and rmarkdown:</p>
<ul>
<li><code>brew install r</code></li>
<li><code>brew install gcc@6</code> (needed due to this <a href="https://github.com/Homebrew/linuxbrew-core/issues/17812">bug</a>)</li>
<li><code>HOMEBREW_CC=gcc-6 brew install pandoc</code></li>
</ul>
</li>
<li>
<p>Install miniconda using these <a href="https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html">instructions</a></p>
</li>
<li>
<p>Clone our repo:</p>
<ul>
<li><code>git clone https://github.com/carissalow/rapids</code></li>
</ul>
</li>
<li>
<p>Create a python virtual environment:</p>
<ul>
<li><code>cd rapids</code></li>
<li><code>conda env create -f environment.yml -n MY_ENV_NAME</code></li>
<li><code>conda activate MY_ENV_NAME</code></li>
</ul>
</li>
<li>
<p>Install R packages and virtual environment:</p>
<ul>
<li><code>snakemake renv_install</code></li>
<li><code>snakemake renv_init</code></li>
<li><code>snakemake renv_restore</code></li>
</ul>
<p>This step could take several minutes to complete. Please be patient and let it run until completion.</p>
</li>
</ol>
</details>
<hr />
<h2 id="mysqlh-cannot-be-found"><code>mysql.h</code> cannot be found<a class="headerlink" href="#mysqlh-cannot-be-found" title="Permanent link">&para;</a></h2>
<details class="failure" open="open"><summary>Problem</summary><div class="highlight"><pre><span></span><code>--------------------------<span class="o">[</span> ERROR MESSAGE <span class="o">]</span>----------------------------
&lt;stdin&gt;:1:10: fatal error: mysql.h: No such file or directory
compilation terminated.
-----------------------------------------------------------------------
ERROR: configuration failed <span class="k">for</span> package <span class="s1">&#39;RMySQL&#39;</span>
</code></pre></div>
</details>
<details class="done" open="open"><summary>Solution</summary><div class="highlight"><pre><span></span><code>sudo apt install libmariadbclient-dev
</code></pre></div>
</details>
<hr />
<h2 id="no-package-libcurl-found">No package <code>libcurl</code> found<a class="headerlink" href="#no-package-libcurl-found" title="Permanent link">&para;</a></h2>
<details class="failure" open="open"><summary>Problem</summary><p><code>libcurl</code> cannot be found</p>
</details>
<details class="done" open="open"><summary>Solution</summary><p>Install <code>libcurl</code>
<div class="highlight"><pre><span></span><code>sudo apt install libcurl4-openssl-dev
</code></pre></div></p>
</details>
<hr />
<h2 id="configuration-failed-because-openssl-was-not-found">Configuration failed because <code>openssl</code> was not found.<a class="headerlink" href="#configuration-failed-because-openssl-was-not-found" title="Permanent link">&para;</a></h2>
<details class="failure" open="open"><summary>Problem</summary><p><code>openssl</code> cannot be found</p>
</details>
<details class="done" open="open"><summary>Solution</summary><p>Install <code>openssl</code>
<div class="highlight"><pre><span></span><code>sudo apt install libssl-dev
</code></pre></div></p>
</details>
<hr />
<h2 id="configuration-failed-because-libxml-20-was-not-found">Configuration failed because <code>libxml-2.0</code> was not found<a class="headerlink" href="#configuration-failed-because-libxml-20-was-not-found" title="Permanent link">&para;</a></h2>
<details class="failure" open="open"><summary>Problem</summary><p><code>libxml-2.0</code> cannot be found</p>
</details>
<details class="done" open="open"><summary>Solution</summary><p>Install <code>libxml-2.0</code>
<div class="highlight"><pre><span></span><code>sudo apt install libxml2-dev
</code></pre></div></p>
</details>
<hr />
<h2 id="ssl-connection-error-when-running-rapids">SSL connection error when running RAPIDS<a class="headerlink" href="#ssl-connection-error-when-running-rapids" title="Permanent link">&para;</a></h2>
<details class="failure" open="open"><summary>Problem</summary><p>You are getting the following error message when running RAPIDS:
<div class="highlight"><pre><span></span><code>Error: Failed to connect: SSL connection error: error:1425F102:SSL routines:ssl_choose_client_version:unsupported protocol.
</code></pre></div></p>
</details>
<details class="done" open="open"><summary>Solution</summary><p>This is a bug in Ubuntu 20.04 when trying to connect to an old MySQL server with MySQL client 8.0. You should get the same error message if you try to connect from the command line. There you can add the option <code>--ssl-mode=DISABLED</code> but we can't do this from the R connector.</p>
<p>If you can't update your server, the quickest solution would be to import your database to another server or to a local environment. Alternatively, you could replace <code>mysql-client</code> and <code>libmysqlclient-dev</code> with <code>mariadb-client</code> and <code>libmariadbclient-dev</code> and reinstall renv. More info about this issue <a href="https://bugs.launchpad.net/ubuntu/+source/mysql-8.0/+bug/1872541">here</a></p>
</details>
<hr />
<h2 id="db_tables-key-not-found"><code>DB_TABLES</code> key not found<a class="headerlink" href="#db_tables-key-not-found" title="Permanent link">&para;</a></h2>
<details class="failure" open="open"><summary>Problem</summary><p>If you get the following error <code>KeyError in line 43 of preprocessing.smk: 'PHONE_SENSORS'</code>, it means that the indentation of the key <code>[PHONE_SENSORS]</code> is not matching the other child elements of <code>PHONE_VALID_SENSED_BINS</code></p>
</details>
<details class="done" open="open"><summary>Solution</summary><p>You need to add or remove any leading whitespaces as needed on that line.</p>
<div class="highlight"><pre><span></span><code><span class="nt">PHONE_VALID_SENSED_BINS</span><span class="p">:</span>
<span class="nt">COMPUTE</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span> <span class="c1"># This flag is automatically ignored (set to True) if you are extracting PHONE_VALID_SENSED_DAYS or screen or Barnett&#39;s location features</span>
<span class="nt">BIN_SIZE</span><span class="p">:</span> <span class="nl">&amp;bin_size</span> <span class="l l-Scalar l-Scalar-Plain">5</span> <span class="c1"># (in minutes)</span>
<span class="nt">PHONE_SENSORS</span><span class="p">:</span> <span class="p p-Indicator">[]</span>
</code></pre></div>
</details>
<hr />
<h2 id="error-while-updating-your-conda-environment-in-ubuntu">Error while updating your conda environment in Ubuntu<a class="headerlink" href="#error-while-updating-your-conda-environment-in-ubuntu" title="Permanent link">&para;</a></h2>
<details class="failure" open="open"><summary>Problem</summary><p>You get the following error:
<div class="highlight"><pre><span></span><code>CondaMultiError: CondaVerificationError: The package <span class="k">for</span> tk located at /home/ubuntu/miniconda2/pkgs/tk-8.6.9-hed695b0_1003
appears to be corrupted. The path <span class="s1">&#39;include/mysqlStubs.h&#39;</span>
specified in the package manifest cannot be found.
ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0, anaconda/linux-64::intel-openmp-2019.4-243
path: <span class="s1">&#39;lib/libiomp5.so&#39;</span>
</code></pre></div></p>
</details>
<details class="done" open="open"><summary>Solution</summary><p>Reinstall conda</p>
</details>
<h2 id="embedded-nul-in-string">Embedded nul in string<a class="headerlink" href="#embedded-nul-in-string" title="Permanent link">&para;</a></h2>
<details class="failure" open="open"><summary>Problem</summary><p>You get the following error when downloading sensor data:
<div class="highlight"><pre><span></span><code>Error in result_fetch<span class="o">(</span>res@ptr, <span class="nv">n</span> <span class="o">=</span> n<span class="o">)</span> :
embedded nul in string:
</code></pre></div></p>
</details>
<details class="done" open="open"><summary>Solution</summary><p>This problem is due to the way <code>RMariaDB</code> handles a mismatch between data types in R and MySQL (see <a href="https://github.com/r-dbi/RMariaDB/issues/121">this issue</a>). Since it seems this problem won&rsquo;t be handled by <code>RMariaDB</code>, you have two options:</p>
<ol>
<li>If it&rsquo;s only a few rows that are causing this problem, remove the the null character from the conflictive table cell.</li>
<li>If it&rsquo;s not feasible to modify your data you can try swapping <code>RMariaDB</code> with <code>RMySQL</code>. Just have in mind you might have problems connecting to modern MySQL servers running in Liunx:<ul>
<li>Add <code>RMySQL</code> to the renv environment by running the following command in a terminal open on RAPIDS root folder
<div class="highlight"><pre><span></span><code>R -e <span class="s1">&#39;renv::install(&quot;RMySQL&quot;)&#39;</span>
</code></pre></div></li>
<li>Go to <code>src/data/download_phone_data.R</code> and replace <code>library(RMariaDB)</code> with <code>library(RMySQL)</code></li>
<li>In the same file replace <code>dbEngine &lt;- dbConnect(MariaDB(), default.file = "./.env", group = group)</code> with <code>dbEngine &lt;- dbConnect(MySQL(), default.file = "./.env", group = group)</code></li>
</ul>
</li>
</ol>
</details>
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