This page is meant to supplement the [How-to-install](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/wikis/How-to-install) page.

**Activating conda R environment**
---

On some Linux systems Conda does not run or activate environments properly, this is due to environment paths not being properly set. The following has been found to work on JASMIN

```
export conda_base=`conda info --base`
source ${conda_base}/etc/profile.d/conda.sh
conda activate <your_env>
``` 

where `\<your_env\>` is the name of the environment you wish to activate.

**Installing R packages not on conda-forge or available through the `conda install` command**
---
Many, but not all, R packages can be installed via conda forge, e.g.

```
conda install -c conda-forge <required_package>
```

Those not available through conda-forge can still be installed via CRAN by downloading the source code and installing from source. When doing this `pkg-config` needs to be configured properly, with the `PKG_CONFIG_PATH` environment variable set to point at the correct directory for the current environment. e.g.

```
export PKG_CONFIG_PATH="/home/users/random_user/.conda/envs/r_env0/lib/pkgconfig"
```

for user `random_user` and environment `r_env0`. Package ggplot2, for example, could then be installed via:

```
wget https://cran.r-project.org/src/contrib/ggplot2_3.3.1.tar.gz
R CMD INSTALL ggplot2_3.3.1.tar.gz
```

When installing a package via this method it is likely that the first attempt will fail due to missing dependencies.  If this happens install those dependencies and then try again.


**Running new_merge_ids_year.R interactively**
---

The script `new_merge_ids_year.R` is typically run in batch mode, e.g.

`Rscript new_merge_ids_year.R <year1> <year2>`

Where `\<year1\>` and `\<year2\>` are the first and last year to run respectively. For testing purposes the script can also be run interactively by starting R, setting the variable `args2` to first and last year and then sourcing the script.

```
R
args2 <- c(1980,1980)
source('new_merge_ids_year.R)
```

As part of the script the number of arguments are checked and if zero, as is the case when run interactively, the script uses the values in the variable `args2` instead.

**Running background jobs without hanging up**
---

Long jobs on JASMIN, and other Linux systems, can be run in the background using the command `nohup` to prevent the job being terminated if the connection is lost. For example, running R script `myscript.R` with arguments `arg1` and `arg2` would be run using

```
nohup Rscript myscript.R arg1 arg2 >& myscript_log.txt &
```

It should then be safe to log out and return later to check the status of the job. `tail -f myscript_log.txt` can be used to monitor the log file in real time.


**SLURM tips**
---

To gather information of your runs in SLURM you can run the following command to store job statistics in a output file: 

```
sacct --starttime <for-the-last-x-hours> -u <username> --format=User,JobID,Jobname,partition,state,time,start,end,elapsed,MaxRss,MaxVMSize,nnodes,ncpus,nodelist >> path_to_log_output/job_stats.out
```

The `starttime` should be in the following format: `2020-07-01T13:00:00`.

It is also possible to gather job statistics for specific job id's:

```
sacct -j <JOB_ID> --format=User,JobID,Jobname,partition,state,time,start,end,elapsed,MaxRss,MaxVMSize,nnodes,ncpus,nodelist >> path_to_log_output/job_stats.out
```

**Update icoads.utils or imma in conda environment**
---

```
conda activate r_env
```

Open R. Inside make sure you know where your libraries are getting install: 
```
.libPaths()
[1] "/home/users/brecinos/miniconda3/envs/r_env/lib/R/library"
```

Great! Now we now know where to go.
```
cd /home/users/brecinos/miniconda3/envs/r_env/lib/R/library/
ls
```

You should see **icoads.utils** there. Now delete it!
```
rm -r icoads.utils
```
And is gone from your environment. Install again by following the installation
instructions [here.](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/wikis/how-to-install#icoads-utils-toolbox)

**Remember to activate the environment before installing**.

> Note: Maybe Dave will know a more elegant way.