[Debian-med-packaging] [devteam-bioc] BioConductor interactiveDisplayBase can't connect to bioconductor.org

[Dan Tenenbaum]

----- Original Message -----
> From: "maintainer" <maintainer at bioconductor.org>
> To: "Shawn Balcome" <balc0022 at umn.edu>, "maintainer" <maintainer at bioconductor.org>
> Cc: "Debian Med Packaging Team" <debian-med-packaging at lists.alioth.debian.org>, "Debian Science List"
> <debian-science at lists.debian.org>
> Sent: Wednesday, May 11, 2016 11:45:19 PM
> Subject: [devteam-bioc] BioConductor interactiveDisplayBase can't connect to	bioconductor.org

> Hi,
> 
> I intend to package BioConductor interactiveDisplayBase as a new
> dependency for biovizBase version 1.20.0 (of BioConductor 3.3) as a
> Debian package.  The Debian packaging process involves loading the
> package and since the packaging process needs to work on a machine
> disconnected from the internet it results in the following error:
> 
> 
> * installing *source* package ‘interactiveDisplayBase’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Warning in file(filename, "r", encoding = encoding) :
>  unable to connect to 'bioconductor.org' on port 80.
> Error in file(filename, "r", encoding = encoding) :
>  cannot open the connection
> Error : unable to load R code in package ‘interactiveDisplayBase’
> ERROR: lazy loading failed for package ‘interactiveDisplayBase’
> 
> 
> I wonder whether there is any chance to make this error non-critical
> and add a warning to enable passing this step without breaking the
> build on a disconnected box.

I have moved the call to source the remote file into the helper function, so it is not executed when the package is loaded. I verified the package can be installed when offline. This is fixed in release (1.10.2) and devel (1.11.2), available via svn now or biocLite() tomorrow.
Dan


> 
> BTW, even if I try to do this on a box connected to the internet via
> proxy the build ends with the same error which is IMHO a real bug inside
> interactiveDisplayBase since it does not respect the http_proxy variable
> (and possibly whatever means will be done to set the proxy on non-Linux
> systems which I did not verified).
> 




> Kind regards
> 
>        Andreas.
> 
> --
> http://fam-tille.de
> 
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