question re: error message --- package error: "functionName" not resolved from current namespace

hello everyone

we are developing a package that has worked up until R3.0 which we just
tested.

the issue is as above .... when we call a function that works in R 2.15.2
from  R 3.0 we get an error

Error in .Call("antsImageRead", filename, pixeltype, dimension) :
 "antsImageRead" not resolved from current namespace (ANTsR)

this Error occurs when the .Call is made from within the .R function
wrapper that eases access to the C++ version of antsImageRead.

however, a direct  .Call("antsImageRead", etc. ) works as usual.

this happens for some of our functions and not others - not all are .Calls
...

i don't see a pattern to it.

a hack resolution that "works" is to source the .R files again within the R
shell.

of course, this is not a satisfying solution.

finally, if anyone cares to try to reproduce this error, here is what you
would do:


If you have CMake installed, then open R 3.0 and do:


install.packages(c("devtools", "Rcpp", "methods", "signal", "parallel",
   "timeSeries", "mFilter", "MASS", "robust", "magic", "knitr",
"pixmap", "rgl", "misc3d"))

then Clone or Pull ANTsR from this repository as follows:

$ git clone git at github.com:stnava/ANTsR.git

From the parent directory of the new ANTsR directory, install the package

as follows:

$ R CMD INSTALL ANTsR


finally - the error can be reproduced in R 3.0 as :

library(ANTsR)
fi<-antsImageRead( getANTsRData('r16') ,2)

any help would be appreciated -

brian

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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"

the problem is when we call this function:

antsImageRead <- function( filename , dimension , pixeltype = "float" )
{
     rval <- (.Call("antsImageRead", filename, pixeltype, dimension))
     return(rval)
}

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)

etcetera ....

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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 ....

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.

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 <mailto: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 ....


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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 ....

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.

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 ....


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