**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
```
???+ done "Solution"
Please make sure the `DATABASE_GROUP` in `config.yaml` matches your DB credentials group in `.env`.
---
## Cannot start mysql in linux via `brew services start mysql`
???+ failure "Problem"
Cannot start mysql in linux via `brew services start mysql`
???+ done "Solution"
Use `mysql.server start`
---
## Every time I run force the download_dataset rule all rules are executed
???+ failure "Problem"
When running `snakemake -j1 -R download_phone_data` or `./rapids -j1 -R download_phone_data` all the rules and files are re-computed
???+ done "Solution"
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.
---
## Error `Table XXX doesn't exist` while running the `download_phone_data` or `download_fitbit_data` rule.
???+ failure "Problem"
```bash
Error in .local(conn, statement, ...) :
could not run statement: Table 'db_name.table_name' doesn't exist
Please make sure the sensors listed in `[PHONE_VALID_SENSED_BINS][PHONE_SENSORS]` and the `[TABLE]` of each sensor you activated in `config.yaml` match your database tables.
---
## How do I install RAPIDS on Ubuntu 16.04
???+ done "Solution"
1. Install dependencies (Homebrew - if not installed):
## Configuration failed because `openssl` was not found.
???+ failure "Problem"
`openssl` cannot be found
???+ done "Solution"
Install `openssl`
```bash
sudo apt install libssl-dev
```
---
## Configuration failed because `libxml-2.0` was not found
???+ failure "Problem"
`libxml-2.0` cannot be found
???+ done "Solution"
Install `libxml-2.0`
```bash
sudo apt install libxml2-dev
```
---
## SSL connection error when running RAPIDS
???+ failure "Problem"
You are getting the following error message when running RAPIDS:
```bash
Error: Failed to connect: SSL connection error: error:1425F102:SSL routines:ssl_choose_client_version:unsupported protocol.
```
???+ done "Solution"
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 `--ssl-mode=DISABLED` but we can\'t do this from the R connector.
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 `mysql-client` and `libmysqlclient-dev` with `mariadb-client` and `libmariadbclient-dev` and reinstall renv. More info about this issue [here](https://bugs.launchpad.net/ubuntu/+source/mysql-8.0/+bug/1872541)
---
## `DB_TABLES` key not found
???+ failure "Problem"
If you get the following error `KeyError in line 43 of preprocessing.smk: 'PHONE_SENSORS'`, it means that the indentation of the key `[PHONE_SENSORS]` is not matching the other child elements of `PHONE_VALID_SENSED_BINS`
???+ done "Solution"
You need to add or remove any leading whitespaces as needed on that line.
```yaml
PHONE_VALID_SENSED_BINS:
COMPUTE: False # This flag is automatically ignored (set to True) if you are extracting PHONE_VALID_SENSED_DAYS or screen or Barnett's location features
BIN_SIZE: &bin_size 5 # (in minutes)
PHONE_SENSORS: []
```
---
## Error while updating your conda environment in Ubuntu
???+ failure "Problem"
You get the following error:
```bash
CondaMultiError: CondaVerificationError: The package for tk located at /home/ubuntu/miniconda2/pkgs/tk-8.6.9-hed695b0_1003
appears to be corrupted. The path 'include/mysqlStubs.h'
specified in the package manifest cannot be found.
ClobberError: This transaction has incompatible packages due to a shared path.
You get the following error when downloading sensor data:
```bash
Error in result_fetch(res@ptr, n = n) :
embedded nul in string:
```
???+ done "Solution"
This problem is due to the way `RMariaDB` handles a mismatch between data types in R and MySQL (see [this issue](https://github.com/r-dbi/RMariaDB/issues/121)). Since it seems this problem won't be handled by `RMariaDB`, you have two options:
1. If it's only a few rows that are causing this problem, remove the the null character from the conflictive table cell.
2. If it's not feasible to modify your data you can try swapping `RMariaDB` with `RMySQL`. Just have in mind you might have problems connecting to modern MySQL servers running in Linux:
- Go to `src/data/download_phone_data.R` or `src/data/download_fitbit_data.R` and replace `library(RMariaDB)` with `library(RMySQL)`
- In the same file replace `dbEngine <- dbConnect(MariaDB(), default.file = "./.env", group = group)` with `dbEngine <- dbConnect(MySQL(), default.file = "./.env", group = group)`
## There is no package called `RMariaDB`
???+ failure "Problem"
You get the following error when executing RAPIDS:
```bash
Error in library(RMariaDB) : there is no package called 'RMariaDB'
Execution halted
```
???+ done "Solution"
In RAPIDS v0.1.0 we replaced `RMySQL` R package with `RMariaDB`, this error means your R virtual environment is out of date, to update it run `snakemake -j1 renv_restore`
