From mtmorgan at fhcrc.org  Thu Apr 11 07:29:05 2013
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Wed, 10 Apr 2013 22:29:05 -0700
Subject: [Rd] question re: error message --- package error:
 "functionName" not resolved from current namespace
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Message-ID: <51664A21.8020508@fhcrc.org>

For what it's worth, the package loads many DLLs in its NAMESPACE via repeated 
calls to useDynLib. antsImageRead is not in the first DLL loaded, and from 
NEWS.Rd, the problem comes from

     o   A foreign function call (.C() etc) in a package without a PACKAGE
	argument will only look in the first DLL specified in the NAMESPACE
	file of the package rather than searching all loaded DLLs.  A few
	packages needed PACKAGE arguments added.

 From ?.Call, 'PACKAGE' is I believe meant to name the DLL (libRantsImageRead in 
this case) rather than the R package.

Some archaeology below.

Martin

On 04/10/2013 02:35 PM, brian avants wrote:
> Thank you for the advice - the function formed like this:
>
> antsImageRead <- function( filename , dimension , pixeltype = "float" )
> {
>       rval <- (.Call("antsImageRead", filename, pixeltype, dimension))
>       return(rval)
> }
>
> worked up to R 2.15.x  but fails in R 3.0.x
>
> if i include the PACKAGE = 'whatever' , in the .Call above, as here:
>
> antsImageRead <- function( filename , dimension , pixeltype = "float" )
> {
>       rval <- (.Call("antsImageRead", filename, pixeltype, dimension,
> PACKAGE="ANTsR"))
>       return(rval)
> }
>
> then it fails in both 2.15.x and 3.0.x ....

When .Call has a PACKAGE argument, or when R tries to guess the DLL from the 
fact that .Call is from within a NAMESPACE, only one DLL is found (from 
R_FindNativeSymbolFromDLL in main/dotcode.c:1331, which calls getCallingDLLe). 
the function "antsImageRead" is not in the DLL returned by getCallingDLLe, so 
not found.

 > getNativeSymbolInfo("antsImageRead")$package
DLL name: libRantsImageRead
Filename:
 
/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.0-2.13/ANTsR/libs/libRantsImageRead.so
Dynamic lookup: TRUE

 > getCallingDLLe(getNamespace("ANTsR"))
DLL name: libRantsRegistration
Filename:
 
/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.0-2.13/ANTsR/libs/libRantsRegistration.so
Dynamic lookup: TRUE

> if i source the file
>
> source("ANTsR/R/antsImageRead.R")
>
> after loading the library, then it works fine in 3.0.x without the direct
> call to PACKAGE=ANTsR.

from the command line, we are not in a NAMESPACE so R uses R_FindSymbol at 
dotcode.c:259; this performs a more general search and finds the appropriate symbol.

The change was somewhere around

------------------------------------------------------------------------
r60607 | ripley | 2012-09-07 10:56:35 -0700 (Fri, 07 Sep 2012) | 1 line
Changed paths:
    M /trunk/doc/NEWS.Rd
    M /trunk/src/main/dotcode.c

confine .C etc in a package to the registered DLL.


>
> anyway - i hope this clarifies things a bit -
>
> does anyone know of something that might have changed between 2.x and 3.x
> that would relate to this issue?
>
>
>
>
>
> brian
>
>
>
>
> On Wed, Apr 10, 2013 at 3:53 PM, Duncan Murdoch <murdoch.duncan at gmail.com>wrote:
>
>> On 10/04/2013 2:25 PM, brian avants wrote:
>>
>>> hi simon
>>>
>>> thank you for your questions ---- answers here:
>>>
>>> I won't answer your question directly but some suggestions:
>>>> a) does adding PACKAGE="ANTsR" to .Call change anything? (It should
>>> really
>>>> be there if you are using strings as names)
>>>>
>>>
>>> this does change things .... for instance, this works:
>>>
>>> library(ANTsR)
>>> filename<-getANTsRData('r16')
>>> .Call("antsImageRead", filename,'double',2) #  Succeeds!
>>> .Call("antsImageRead", filename,'double',2,PACKAGE=**ANTsR) #  Fails!
>>> # Error in .Call("antsImageRead", filename, "double", 2, PACKAGE =
>>> "ANTsR")
>>> :
>>> #  "antsImageRead" not available for .Call() for package "ANTsR"
>>>
>>
>> That makes it look as though it is finding that entry point somewhere
>> other than in the ANTsR.{so|dll} file installed with the package.
>>
>>
>>> the problem is when we call this function:
>>>
>>> antsImageRead <- function( filename , dimension , pixeltype = "float" )
>>> {
>>>       rval <- (.Call("antsImageRead", filename, pixeltype, dimension))
>>>       return(rval)
>>> }
>>>
>>
>> That's the one where you should be using the PACKAGE declaration.
>>
>>
>>
>>> the we get the error   antsImageRead not resolved from current namespace ,
>>> e.g.:
>>>
>>>> antsImageRead(filename,2)
>>> Error in .Call("antsImageRead", filename, pixeltype, dimension) :
>>>     "antsImageRead" not resolved from current namespace (ANTsR)
>>>>
>>>
>>>
>>> b) you may want to consider use the more efficient registration - either
>>>> explicit or in NAMESPACE - so in your case you could use
>>>> NAMESPACE: useDynLib(ANTsR, antsImageRead, ...)
>>>> foo.R: .Call(antsImageRead, ...)
>>>>
>>>
>>> yes - we have all of our shared libraries registered in the NAMESPACE file
>>> e.g.
>>>
>>> useDynLib(libRantsImageRead)
>>>
>>
>> But this doesn't register the entry point.  List it explicitly, and it
>> will create an object called antsImageRead in the package namespace that
>> has entry point information.
>>
>> Duncan Murdoch
>>
>>>
>>> etcetera ....
>>>
>>>
>>>          [[alternative HTML version deleted]]
>>>
>>> ______________________________**________________
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>>> https://stat.ethz.ch/mailman/**listinfo/r-devel<https://stat.ethz.ch/mailman/listinfo/r-devel>
>>>
>>
>>
>
> 	[[alternative HTML version deleted]]
>
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[Rd] question re: error message --- package error: "functionName" not resolved from current namespace
Martin Morgan