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OHDSI / StudyProtocolSandbox

This repository is for developing study packages for OHDSI studies. Once completed, they can be moved to the StudyProtocols repository.
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largescaleprediction study installation issues and errors #4

Open jmbanda opened 7 years ago

jmbanda commented 7 years ago

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 commented 7 years ago

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.