rapids/docs/usage/faq.rst

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Frequently Asked Questions
============================
1. Cannot connect to the MySQL server
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**Error in .local(drv, ...) :**
**Failed to connect to database: Error: Can't initialize character set unknown (path: compiled_in)**
::
Calls: dbConnect -> dbConnect -> .local -> .Call
Execution halted
[Tue Mar 10 19:40:15 2020]
Error in rule download_dataset:
jobid: 531
output: data/raw/p60/locations_raw.csv
RuleException:
CalledProcessError in line 20 of /home/ubuntu/rapids/rules/preprocessing.snakefile:
Command 'set -euo pipefail; Rscript --vanilla /home/ubuntu/rapids/.snakemake/scripts/tmp_2jnvqs7.download_dataset.R' returned non-zero exit status 1.
File "/home/ubuntu/rapids/rules/preprocessing.snakefile", line 20, in __rule_download_dataset
File "/home/ubuntu/anaconda3/envs/moshi-env/lib/python3.7/concurrent/futures/thread.py", line 57, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
**Solution:**
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Please make sure the ``MY_GROUP`` in ``config.yaml`` and ``.env`` match.
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2. Cannot start mysql in linux via ``brew services start mysql``
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use the following command instead:
``mysql.server start``
3. Every time I run ``snakemake -R download_dataset`` all rules are executed
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This is expected behavior. The advantage of using ``snakemake`` 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 ``download_dataset`` updates all the raw data, and you are forcing the rule with the flag ``-R`` every single rule that depends on those raw files will be executed.
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4. Got an error ``Table XXX doesn't exist`` while running the download_dataset rule.
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::
Error in .local(conn, statement, ...) :
could not run statement: Table 'db_name.table_name' doesn't exist
Calls: colnames ... .local -> dbSendQuery -> dbSendQuery -> .local -> .Call
Execution halted
**Solution:**
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Please make sure the sensors listed in SENSORS in ``config.yaml`` match your database tables.
5. How do I install on Ubuntu 16.04
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#. Install dependencies (Homebrew - if not installed):
- ``sudo apt-get install libmariadb-client-lgpl-dev libxml2-dev libssl-dev``
- Install brew_ for linux and add the following line to ~/.bashrc: ``export PATH=$HOME/.linuxbrew/bin:$PATH``
- ``source ~/.bashrc``
#. Install MySQL
- ``brew install mysql``
- ``brew services start mysql``
#. Install R, pandoc and rmarkdown:
- ``brew install r``
- ``brew install gcc@6`` (needed due to this bug_)
- ``HOMEBREW_CC=gcc-6 brew install pandoc``
#. Install miniconda using these instructions_
#. Clone our repo:
- ``git clone https://github.com/carissalow/rapids``
#. Create a python virtual environment:
- ``cd rapids``
- ``conda env create -f environment.yml -n MY_ENV_NAME``
- ``conda activate MY_ENV_NAME``
#. Install R packages and virtual environment:
- ``snakemake renv_install``
- ``snakemake renv_init``
- ``snakemake renv_restore``
- This step could take several minutes to complete. Please be patient and let it run until completion.
#. See :ref:`Usage section <usage-section>`.
6. Configuration failed for package ``RMySQL``
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::
--------------------------[ ERROR MESSAGE ]----------------------------
<stdin>:1:10: fatal error: mysql.h: No such file or directory
compilation terminated.
-----------------------------------------------------------------------
ERROR: configuration failed for package 'RMySQL'
sudo apt install libmariadbclient-dev
7. No package ``libcurl`` found
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The ``libcurl`` needs to installed using the following command
``sudo apt install libcurl4-openssl-dev``
8. Configuration failed because ``openssl`` was not found.
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Install the ``openssl`` library using the following command
``sudo apt install libssl-dev``
9. Configuration failed because ``libxml-2.0`` was not found
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Install the ``xml`` library using the following command
``sudo apt install libxml2-dev``
.. ------------------------ Links --------------------------- ..
.. _bug: https://github.com/Homebrew/linuxbrew-core/issues/17812
.. _instructions: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
.. _brew: https://docs.brew.sh/Homebrew-on-Linux