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