"could not find function" error in "R CMD check"

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"could not find function" error in "R CMD check"

Spencer Graves
Hi, All:

      What might cause "R CMD check" to report, "could not find
function" for a function that has long been in the 'fda' package?

      Both Jim Ramsay in Ottawa, Canada, and I in San Jose, CA, get this
same error.  I replicated it with a fresh, anonymous checkout from
R-Forge (svn checkout svn://svn.r-forge.r-project.org/svnroot/fda).  
With this, I did "R CMD build pkg", then "R CMD check fda_2.1.0.tar.gz",
with the following result:


D:\spencerg\statmtds\splines\fda\tmp\fda>R CMD check fda_2.1.0.tar.gz
* checking for working pdflatex ... OK
* using log directory 'D:/spencerg/statmtds/splines/fda/tmp/fda/fda.Rcheck'
* using R version 2.8.0 (2008-10-20)
* using session charset: ISO8859-1
* checking for file 'fda/DESCRIPTION' ... OK
* this is package 'fda' version '2.1.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for .dll and .exe files ... OK
* checking whether package 'fda' can be installed ... ERROR
Installation failed.
See 'D:/spencerg/statmtds/splines/fda/tmp/fda/fda.Rcheck/00install.out'
for deta
ils.

     
####################################
      "00install.out" is as follows:

####################################

installing R.css in D:/spencerg/statmtds/splines/fda/tmp/fda/fda.Rcheck


---------- Making package fda ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing demos
  installing inst files
  installing data files
  preparing package fda for lazy loading
Loading required package: splines
Loading required package: zoo

Attaching package: 'zoo'


    The following object(s) are masked from package:base :

     as.Date.numeric

Error in basisfd(type = type, rangeval = rangeval, nbasis = nbasis,
params = params,  :
  could not find function "use.proper.basis"
Error: unable to load R code in package 'fda'
Execution halted
make[2]: *** [lazyload] Error 1
make[1]: *** [all] Error 2
make: *** [pkg-fda] Error 2
*** Installation of fda failed ***

Removing 'D:/spencerg/statmtds/splines/fda/tmp/fda/fda.Rcheck/fda'


####################################

      Both "basisfd" and "use.proper.basis" have been in the "fda"
package for years and have passed "R CMD check" many times.  I'm running
Windows XP Pro and Jim is running Vista.

      Any suggestions?
      Thanks,
      Spencer Graves
   

 sessionInfo()
R version 2.8.0 (2008-10-20)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    
 >

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Re: "could not find function" error in "R CMD check"

Duncan Murdoch
On 16/12/2008 10:55 AM, Spencer Graves wrote:
> Hi, All:
>
>       What might cause "R CMD check" to report, "could not find
> function" for a function that has long been in the 'fda' package?

I would guess that you are calling it from within your *.R files.  It's
called from a lot of places, so I couldn't spot the one that's causing
the trouble, but something like this could do it:

f <- function() { }  # Function is done, by mistake

   basisfd()          # This is a top level call, not within f

}                    # Not sure why the parser wouldn't see this
                      # so this guess may be wrong

In general, you can call functions from within the *.R files, but you
have to be careful to make sure they are already defined (and you
shouldn't count on any side effects from them.

Duncan Murdoch

>
>       Both Jim Ramsay in Ottawa, Canada, and I in San Jose, CA, get this
> same error.  I replicated it with a fresh, anonymous checkout from
> R-Forge (svn checkout svn://svn.r-forge.r-project.org/svnroot/fda).  
> With this, I did "R CMD build pkg", then "R CMD check fda_2.1.0.tar.gz",
> with the following result:
>
>
> D:\spencerg\statmtds\splines\fda\tmp\fda>R CMD check fda_2.1.0.tar.gz
> * checking for working pdflatex ... OK
> * using log directory 'D:/spencerg/statmtds/splines/fda/tmp/fda/fda.Rcheck'
> * using R version 2.8.0 (2008-10-20)
> * using session charset: ISO8859-1
> * checking for file 'fda/DESCRIPTION' ... OK
> * this is package 'fda' version '2.1.0'
> * checking package name space information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking for .dll and .exe files ... OK
> * checking whether package 'fda' can be installed ... ERROR
> Installation failed.
> See 'D:/spencerg/statmtds/splines/fda/tmp/fda/fda.Rcheck/00install.out'
> for deta
> ils.
>
>      
> ####################################
>       "00install.out" is as follows:
>
> ####################################
>
> installing R.css in D:/spencerg/statmtds/splines/fda/tmp/fda/fda.Rcheck
>
>
> ---------- Making package fda ------------
>   adding build stamp to DESCRIPTION
>   installing NAMESPACE file and metadata
>   installing R files
>   installing demos
>   installing inst files
>   installing data files
>   preparing package fda for lazy loading
> Loading required package: splines
> Loading required package: zoo
>
> Attaching package: 'zoo'
>
>
>     The following object(s) are masked from package:base :
>
>      as.Date.numeric
>
> Error in basisfd(type = type, rangeval = rangeval, nbasis = nbasis,
> params = params,  :
>   could not find function "use.proper.basis"
> Error: unable to load R code in package 'fda'
> Execution halted
> make[2]: *** [lazyload] Error 1
> make[1]: *** [all] Error 2
> make: *** [pkg-fda] Error 2
> *** Installation of fda failed ***
>
> Removing 'D:/spencerg/statmtds/splines/fda/tmp/fda/fda.Rcheck/fda'
>
>
> ####################################
>
>       Both "basisfd" and "use.proper.basis" have been in the "fda"
> package for years and have passed "R CMD check" many times.  I'm running
> Windows XP Pro and Jim is running Vista.
>
>       Any suggestions?
>       Thanks,
>       Spencer Graves
>    
>
>  sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base    
>  >
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: "could not find function" error in "R CMD check"

Duncan Murdoch
In reply to this post by Spencer Graves
Using Martin's sourceDir() function (from example(source)), I found your
problem:  You have some test code in your R dir.

smooth.bibasis.test.R :Error in basisfd(type = type, rangeval =
rangeval, nbasis = nbasis, params = params,  :
   could not find function "use.proper.basis"

That file smooth.bibasis.test.R probably belongs in the tests directory,
where it will be run after all the files have been sourced.

Duncan Murdoch

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Re: "could not find function" error in "R CMD check"

Spencer Graves
Hi, Duncan:

      Thanks very much.  That fixed that problem.

      I should have tried that myself;  I've heard essentially that
suggestion before, but couldn't think of it in this case.

      Best Wishes,
      Spencer Graves

Duncan Murdoch wrote:

> Using Martin's sourceDir() function (from example(source)), I found
> your problem:  You have some test code in your R dir.
>
> smooth.bibasis.test.R :Error in basisfd(type = type, rangeval =
> rangeval, nbasis = nbasis, params = params,  :
>   could not find function "use.proper.basis"
>
> That file smooth.bibasis.test.R probably belongs in the tests
> directory, where it will be run after all the files have been sourced.
>
> Duncan Murdoch
>

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