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<h2id="cannot-connect-to-your-mysql-server">Cannot connect to your MySQL server<aclass="headerlink"href="#cannot-connect-to-your-mysql-server"title="Permanent link">¶</a></h2>
<detailsclass="failure"open="open"><summary>Problem</summary><divclass="highlight"><pre><span></span><code>**Error in .local<spanclass="o">(</span>drv, <spanclass="se">\.</span>..<spanclass="o">)</span> :** **Failed to connect to database: Error:
Can<spanclass="se">\'</span>t initialize character <spanclass="nb">set</span> unknown <spanclass="o">(</span>path: compiled<spanclass="se">\_</span>in<spanclass="o">)</span>** :
<spanclass="o">[</span>Tue Mar <spanclass="m">10</span><spanclass="m">19</span>:40:15 <spanclass="m">2020</span><spanclass="o">]</span>
Error in rule download_dataset:
jobid: <spanclass="m">531</span>
output: data/raw/p60/locations_raw.csv
RuleException:
CalledProcessError in line <spanclass="m">20</span> of /home/ubuntu/rapids/rules/preprocessing.snakefile:
Command <spanclass="s1">'set -euo pipefail; Rscript --vanilla /home/ubuntu/rapids/.snakemake/scripts/tmp_2jnvqs7.download_dataset.R'</span> returned non-zero <spanclass="nb">exit</span> status <spanclass="m">1</span>.
File <spanclass="s2">"/home/ubuntu/rapids/rules/preprocessing.snakefile"</span>, line <spanclass="m">20</span>, in __rule_download_dataset
File <spanclass="s2">"/home/ubuntu/anaconda3/envs/moshi-env/lib/python3.7/concurrent/futures/thread.py"</span>, line <spanclass="m">57</span>, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above <spanclass="k">for</span> error message
</code></pre></div>
</details>
<detailsclass="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/>
<h2id="cannot-start-mysql-in-linux-via-brew-services-start-mysql">Cannot start mysql in linux via <code>brew services start mysql</code><aclass="headerlink"href="#cannot-start-mysql-in-linux-via-brew-services-start-mysql"title="Permanent link">¶</a></h2>
<detailsclass="failure"open="open"><summary>Problem</summary><p>Cannot start mysql in linux via <code>brew services start mysql</code></p>
<h2id="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<aclass="headerlink"href="#every-time-i-run-force-the-download_dataset-rule-all-rules-are-executed"title="Permanent link">¶</a></h2>
<detailsclass="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>
<detailsclass="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/>
<h2id="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.<aclass="headerlink"href="#error-table-xxx-doesnt-exist-while-running-the-download_phone_data-or-download_fitbit_data-rule"title="Permanent link">¶</a></h2>
<detailsclass="failure"open="open"><summary>Problem</summary><divclass="highlight"><pre><span></span><code>Error in .local<spanclass="o">(</span>conn, statement, ...<spanclass="o">)</span> :
could not run statement: Table <spanclass="s1">'db_name.table_name'</span> doesn<spanclass="err">'</span>t exist
<detailsclass="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/>
<h2id="how-do-i-install-rapids-on-ubuntu-1604">How do I install RAPIDS on Ubuntu 16.04<aclass="headerlink"href="#how-do-i-install-rapids-on-ubuntu-1604"title="Permanent link">¶</a></h2>
<li>Install <ahref="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 <ahref="https://github.com/Homebrew/linuxbrew-core/issues/17812">bug</a>)</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/>
<h2id="mysqlh-cannot-be-found"><code>mysql.h</code> cannot be found<aclass="headerlink"href="#mysqlh-cannot-be-found"title="Permanent link">¶</a></h2>
<h2id="configuration-failed-because-openssl-was-not-found">Configuration failed because <code>openssl</code> was not found.<aclass="headerlink"href="#configuration-failed-because-openssl-was-not-found"title="Permanent link">¶</a></h2>
<detailsclass="failure"open="open"><summary>Problem</summary><p><code>openssl</code> cannot be found</p>
<h2id="configuration-failed-because-libxml-20-was-not-found">Configuration failed because <code>libxml-2.0</code> was not found<aclass="headerlink"href="#configuration-failed-because-libxml-20-was-not-found"title="Permanent link">¶</a></h2>
<detailsclass="failure"open="open"><summary>Problem</summary><p><code>libxml-2.0</code> cannot be found</p>
<h2id="ssl-connection-error-when-running-rapids">SSL connection error when running RAPIDS<aclass="headerlink"href="#ssl-connection-error-when-running-rapids"title="Permanent link">¶</a></h2>
<detailsclass="failure"open="open"><summary>Problem</summary><p>You are getting the following error message when running RAPIDS:
<divclass="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>
<detailsclass="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 <ahref="https://bugs.launchpad.net/ubuntu/+source/mysql-8.0/+bug/1872541">here</a></p>
</details>
<hr/>
<h2id="db_tables-key-not-found"><code>DB_TABLES</code> key not found<aclass="headerlink"href="#db_tables-key-not-found"title="Permanent link">¶</a></h2>
<detailsclass="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>
<detailsclass="done"open="open"><summary>Solution</summary><p>You need to add or remove any leading whitespaces as needed on that line.</p>
<spanclass="nt">COMPUTE</span><spanclass="p">:</span><spanclass="l l-Scalar l-Scalar-Plain">False</span><spanclass="c1"># This flag is automatically ignored (set to True) if you are extracting PHONE_VALID_SENSED_DAYS or screen or Barnett's location features</span>
<spanclass="nt">BIN_SIZE</span><spanclass="p">:</span><spanclass="nl">&bin_size</span><spanclass="l l-Scalar l-Scalar-Plain">5</span><spanclass="c1"># (in minutes)</span>
<h2id="error-while-updating-your-conda-environment-in-ubuntu">Error while updating your conda environment in Ubuntu<aclass="headerlink"href="#error-while-updating-your-conda-environment-in-ubuntu"title="Permanent link">¶</a></h2>
<detailsclass="failure"open="open"><summary>Problem</summary><p>You get the following error:
<divclass="highlight"><pre><span></span><code>CondaMultiError: CondaVerificationError: The package <spanclass="k">for</span> tk located at /home/ubuntu/miniconda2/pkgs/tk-8.6.9-hed695b0_1003
appears to be corrupted. The path <spanclass="s1">'include/mysqlStubs.h'</span>
specified in the package manifest cannot be found.
ClobberError: This transaction has incompatible packages due to a shared path.
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