[Rcpp-devel] Access package installed into user library

[Thomas Lin Pedersen]

Hi

While testing my package on an Amazon cloud instance using the Bioconductor AMI (https://www.bioconductor.org/help/bioconductor-cloud-ami/ <https://www.bioconductor.org/help/bioconductor-cloud-ami/>) I ran into the following problem I had not encountered on my work computer (A Mac OS X).

I have a C++ function that makes use of functionality in the igraph package, so to access this I have the following in my function:

Environment igraph("package:igraph");
Function neighbors = igraph["neighbors”];

This worked fine on my work machine but gave the following error when tried on the Amazon instance:

Error: cannot convert to environment

I was able to reduce the error into trying to get access to a package environment that is installed outside the core package library. The instances created using the Bioconductor AMI have the following package storage structure:

> .libPaths()
[1] "/home/ubuntu/R-libs"      "/usr/local/lib/R/library"

Any package residing in usr/local/lib/R/library will be loaded into the environment fine, while any package in /home/ubuntu/R-libs will throw the error.

Minimal example:

library(Rcpp)

cppFunction('
  void testFail() {
    Environment testEnv("package:boot");
  }
')

cppFunction('
  void testSucces() {
    Environment testEnv("package:stats");
  }
')

testFail() # Will give error
testSucces() # Will work

The session:
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Rcpp_0.12.1          BiocInstaller_1.20.0

loaded via a namespace (and not attached):
[1] tools_3.2.2

Best

Thomas Lin Pedersen

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