> On 04 Dec 2015, at 13:16, Dirk Eddelbuettel <e...@debian.org> wrote:
>
>
> 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
>
Ok - (slight embarrassment to follow) I looked at the Environment constructor
and found that it basically just called as.environment, which led my to try
this out in R. This also failed, but for the reason that the requested package
was only loaded, not attached (It’s part of the Import field of my package).
calling library() to attach the package solved the issue…
The obvious follow up question is: Is there no way to use R functions from Rcpp
if they are not part of the users search path (but part of the package
namespace). I generally tend to avoid putting packages in Depends in order to
not pollute the users search path.
Thomas
> | 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
> |
> | _______________________________________________
> | Rcpp-devel mailing list
> | Rcpp-devel@lists.r-forge.r-project.org
> | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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