Dependencies of Imports not attached?

Encountered an error in scripting, which can be reproduced using Rscript as
follows:

$ Rscript -e "library(httr); handle('http://cran.r-project.org')"

Error in getCurlHandle(cookiefile = cookie_path, .defaults = list()) :
 could not find function "getClass"
Calls: handle -> getCurlHandle

or by starting R without the methods package attached:

$ R_DEFAULT_PACKAGES=base R
[snip]

library(httr)
handle('http://cran.fhcrc.org/')

Error in getCurlHandle(cookiefile = cookie_path, .defaults = list()) :
 could not find function "getClass"

As far as I can tell the error occurs when getCurlHandle .Calls a C
function which then calls SET_CLASS, which (I guess) requires
methods::setClass to be in the search path.

Now 'httr' Imports 'RCurl' which Depends on 'methods'. So I think
`library(httr)` should end up attaching 'methods' to the search path, but
it seems 'methods' is just imported to RCurl's namespace.

I think this is a problem since the Depends line is indicating that
'methods' must be attached for RCurl to work, whether or not RCurl itself
is being attached.

On May 7, 2013, at 11:35 PM, Peter Meilstrup wrote:

Encountered an error in scripting, which can be reproduced using Rscript as
follows:

$ Rscript -e "library(httr); handle('http://cran.r-project.org')"

Error in getCurlHandle(cookiefile = cookie_path, .defaults = list()) :
  could not find function "getClass"
Calls: handle -> getCurlHandle

or by starting R without the methods package attached:

$ R_DEFAULT_PACKAGES=base R
[snip]

library(httr)
handle('http://cran.fhcrc.org/')

Error in getCurlHandle(cookiefile = cookie_path, .defaults = list()) :
  could not find function "getClass"

As far as I can tell the error occurs when getCurlHandle .Calls a C
function which then calls SET_CLASS, which (I guess) requires
methods::setClass to be in the search path.

Now 'httr' Imports 'RCurl' which Depends on 'methods'. So I think
`library(httr)` should end up attaching 'methods' to the search path, but
it seems 'methods' is just imported to RCurl's namespace.

I think this is a problem since the Depends line is indicating that
'methods' must be attached for RCurl to work, whether or not RCurl itself
is being attached.

For the record, I see the same problem with other packages that use S4 - very often it trips packages that don't use S4 but import a package that does. The analysis is correct - if a package B just imports a function from another package A which in turn relies on something in Depends, it breaks, because A is not on the search path and thus A doesn't have access to the dependencies it needs. I don't know that was the intended design. I see two way to fix this
1) make sure Depends: are always put on the search path even if the package is not attached
2) automatically generate imports for all packages in Depends:

The main problem is that B is helpless - only a change in A can make it work. Fix for A is to explicitly add import(methods) even though it's already in Depends:. Note that R CMD check doesn't detect this.

Cheers,
Simon

On 05/08/2013 10:25 AM, Simon Urbanek wrote:

On May 7, 2013, at 11:35 PM, Peter Meilstrup wrote:

Encountered an error in scripting, which can be reproduced using Rscript as
follows:

$ Rscript -e "library(httr); handle('http://cran.r-project.org')"

Error in getCurlHandle(cookiefile = cookie_path, .defaults = list()) :
 could not find function "getClass"
Calls: handle -> getCurlHandle

or by starting R without the methods package attached:

$ R_DEFAULT_PACKAGES=base R
[snip]

library(httr)
handle('http://cran.fhcrc.org/')

Error in getCurlHandle(cookiefile = cookie_path, .defaults = list()) :
 could not find function "getClass"

As far as I can tell the error occurs when getCurlHandle .Calls a C
function which then calls SET_CLASS, which (I guess) requires
methods::setClass to be in the search path.

Now 'httr' Imports 'RCurl' which Depends on 'methods'. So I think
`library(httr)` should end up attaching 'methods' to the search path, but
it seems 'methods' is just imported to RCurl's namespace.

I think this is a problem since the Depends line is indicating that
'methods' must be attached for RCurl to work, whether or not RCurl itself
is being attached.

For the record, I see the same problem with other packages that use S4 - very often it trips packages that don't use S4 but import a package that does. The analysis is correct - if a package B just imports a function from another package A which in turn relies on something in Depends, it breaks, because A is not on the search path and thus A doesn't have access to the dependencies it needs. I don't know that was the intended design. I see two way to fix this
1) make sure Depends: are always put on the search path even if the package is not attached
2) automatically generate imports for all packages in Depends:

The main problem is that B is helpless - only a change in A can make it work. Fix for A is to explicitly add import(methods) even though it's already in Depends:. Note that R CMD check doesn't detect this.

As described, this is a 'package maintainer' problem -- fix package A. Also, this isn't unique to methods, other packages routinely Depend: on something that should instead be Import:'ed.

But I think Peter's case is different, because the C implementations of

   SEXP R_do_MAKE_CLASS(const char *what);
   SEXP R_getClassDef  (const char *what);

need to be called from inside the package environment, but there is no way to pass the package environment through the interface above.

Maybe the partial patch (attached) points to a solution? It changes the interface (though would only break a couple of Bioconductor packages in a minor way) (I think there's a missing PROTECT in there too.)

Cheers,
Simon

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