On 4 December 2015 at 12:31, Thomas Lin Pedersen wrote:
| Hi
|
| While testing my package on an Amazon cloud instance using the Bioconductor
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.
So maybe don't install into /home/ubuntu/R-libs ?
There are no hardcoded path in Rcpp. This strikes me as a run-time config
(and hence not an Rcpp question for this list).
Dirk
| 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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| Rcpp-devel@lists.r-forge.r-project.org
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--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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