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 `[CONTAINER]` of each sensor you activated in `config.yaml` match your database tables or files.
## 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:
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:
- In the same file(s) replace `dbEngine <- dbConnect(MariaDB(), default.file = "./.env", group = group)` with `dbEngine <- dbConnect(MySQL(), default.file = "./.env", group = group)`
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`
This is because R timezone library is not set. Please add `Sys.setenv(“TZDIR” = file.path(R.home(), “share”, “zoneinfo”))` to the file active.R in renv folder to set the timezone library. For further details on how to test if `TZDIR` is properly set, please refer to `https://github.com/tidyverse/lubridate/issues/928#issuecomment-720059233`.
You get the following error when downloading Fitbit data:
```bash
Error: Unimplemented MAX_NO_FIELD_TYPES
Execution halted
```
???+ done "Solution"
At the moment RMariaDB [cannot handle](https://github.com/r-dbi/RMariaDB/issues/127) MySQL columns of JSON type. Change the type of your Fitbit data column to `longtext` (note that the content will not change and will still be a JSON object just interpreted as a string).
As of Feb 2020 in M1 macs, R needs to be installed via brew under Rosetta (x86 arch) due to some incompatibility with selected R libraries. To do this, run your terminal [via Rosetta](https://www.youtube.com/watch?v=nv2ylxro7rM&t=138s), then proceed with the usual brew installation command. x86 homebrew should be installed in `/usr/local/bin/brew `, you can check which brew you are using by typing `which brew`. Then use x86 homebrew to install R and restore RAPIDS packages (`renv_restore`).
