failed to install ‘FeatureExtraction’ ‘CohortMethod’ about databaseconnector

[schuemie]

Hi @leeanhu789 ,

Did you install RTools? Both FeatureExtraction and CohortMethod contain C++ code that requires RTools to compile.

Cheers,
Martijn

[leeanhu789]

Hi Martijn,
Thanks so much for all the help. I did install RTools on both the home and work computer, but somehow on both computers, I failed to install these two packages. Would the version of the R or version of the RTools matter? I think I installed the newest version of RTools (Rtools34.exe) on home computer, and Rtools33.exe on work computer.
By the way, is there any data set that we can use to run all the R codes in KeppraAngioedema project?

Thank you!
Lian

[schuemie]

Hi Lian,

Digging a bit deeper, it seems there's a problem installing the packages on the latest version of R (>=3.3.0)! I can easily reproduce it on my machine. I'm looping in @msuchard , since he knows most about drat, which seems to be causing the problems.

In the mean time, you can use devtools to install the packages instead:

install.packages("devtools", "Cyclops", "SqlRender")
library(devtools)
install_github("ohdsi/OhdsiRTools", args = "--no-multiarch") 
install_github("ohdsi/DatabaseConnector", args = "--no-multiarch")
install_github("ohdsi/FeatureExtraction", args = "--no-multiarch") 
install_github("ohdsi/CohortMethod", args = "--no-multiarch")
install_github("ohdsi/OhdsiSharing", args = "--no-multiarch")

# You may want to skip this one for now:
install.packages("aws.s3", repos = "http://cloudyr.github.io/drat")

install_github("ohdsi/StudyProtocols/KeppraAngioedema", args = "--no-multiarch")

One dataset you can use just to run the code is the Synpuf dataset in CDM format created by Lee Evans. You would need to load the dataset into a database.

Cheers,
Martijn

[leeanhu789]

Hi Martijn,
Awesome. Thanks for your help. All are installed fine now, in both R 3.2.4 32bit (work computer) and R 3.3.1. 64 bits (home computer). I wonder whether the problem was that I had not install OhdsiRTools as instructed here in your note. Instead, I had only installed RTools in the root directory as instructed on OSDHI wiki regarding R environment set up (http://www.ohdsi.org/web/wiki/doku.php?id=documentation:r_setup).

Thank you so much!

Lian