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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