largescaleprediction study installation issues and errors

[jmbanda]

When installing the package following the instructions on the study page, there are errors related to trying to re-install cyclops as a dependency of BigKnn and PatientLevelPrediction. I was able to work around it by installing Cyclops first then BigKnn with the dependencies = F flag. After that I manually installed all the following dependencies for PatientLevelPrediction - survAUC, xgboost, PythonInR, fuite.logger. After installing said dependencies I was able to install the package.

My full installation script

library(devtools) install_github("ohdsi/OhdsiRTools") install_github("ohdsi/SqlRender") install_github("ohdsi/DatabaseConnector") install_github("ohdsi/Cyclops") install_github("ohdsi/FeatureExtraction") install_github("ohdsi/BigKnn", dependencies = F) install.packages("survAUC") install.packages("xgboost") install.packages("PythonInR") install.packages("futile.logger) install_github("ohdsi/PatientLevelPrediction", dependencies = F)

The last error appears when trying to run:

install_github("ohdsi/StudyProtocolSandbox/LargeScalePrediction")

The error is the following:

install_github("ohdsi/StudyProtocolSandbox/LargeScalePrediction")
Downloading GitHub repo ohdsi/StudyProtocolSandbox@master
from URL https://api.github.com/repos/ohdsi/StudyProtocolSandbox/zipball/master
Error: Does not appear to be an R package (no DESCRIPTION)

While the package project can be acquired from github and locally built, this is far from user friendly and from the installation instructions. Will keep you posted when the package finishes running @jreps and @PRijnbeek

[PRijnbeek]

I have experienced this same issue as well when running on Linux recently and had to build the package locally.

It is still unclear to me why this happens since there is a DESCRIPTION file in the package.

I had no problems under windows and no other issues with this have been reported by the other databases.