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Achilles R Package Installation Requirements Clarification


#1

Hello all. I am working through the instructions listed here: https://github.com/OHDSI/Achilles. I am new to Achilles.

I am new to R, but more familiar with Python so I installed R studio from the Anaconda distribution. When I attempted to run this devtools:: install_github("OHDSI/Achilles"), it through errors saying I needed to install packages DatabaseConnectorJars, DatabaseConnector, and DBI. I was able to install the 1st and 3rd ones, but for DatabaseConnector it through this error:

* installing *source* package 'DatabaseConnector' ...
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'UsingDatabaseConnector.Rmd' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (DatabaseConnector)
In R CMD INSTALL
"C:/ANACON~1/envs/env3.5/lib/R/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD  \
  INSTALL "C:/Users/myusername/AppData/Local/Temp/RtmpqKtkUO/devtools1b641f4e55fd/OHDSI-Achilles-222b091"  \
  --library="C:/Anaconda2/envs/env3.5/lib/R/library" --install-tests 

ERROR: dependency 'ParallelLogger' is not available for package 'Achilles'
* removing 'C:/Anaconda2/envs/env3.5/lib/R/library/Achilles'
In R CMD INSTALL
Installation failed: Command failed (1)
> devtools::install("ParallelLogger")
Error: Can't find 'C:\Users\myusername\ParallelLogger'.
> devtools::install("ParallelLogger")
Error: Can't find 'C:\Users\myusername\ParallelLogger'.

Is there specific wiki documentation out there for the prerequisites/required packages for the master branch or anything else that is required like the appropriate java version for master branch to be installed without error? Maybe it is located somewhere else and I am not finding it. I mentioned I installed R studio from the Anaconda distribution for windows 64 bit (windows 10) in a virtual environment with python 3.5. The R studio version is 1.1.456.

Any clarification is appreciated thank you.


(Ajit Londhe) #2

Use devtools::install_github("OHDSI/ParallelLogger")

We’ll add it to the README, good idea :slight_smile:


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