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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