[R] .NAME in .Fortran

[Rolf Turner]

Duncan:

I experimented by using ".NAME =" in a call to .Fortran()
in one of my packages and got the same error as Peter.
I am definitely (!) using R version 2.15.1.

Doing args(.Fortran) gives:
> function (.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCODING)
> NULL
> <bytecode: 0x9e7762c>

If I replace ".NAME" by "name" in my call to .Fortran() everything works
smoothly.

Consequently:  It looks to me like there is a bug here.  An inconsistency
between .Fortran() and ".Primitive(".Fortran")" perhaps.

     cheers,

         Rolf

On 12/09/12 00:09, Duncan Murdoch wrote:
> On 12-09-10 9:21 PM, Peter Dunn wrote:
>> Hi all
>>
>> I've been getting some emails from the R package maintainers that I need
>> to update some code in a CRAN packge that uses FORTRAN, to comply with
>> (not so recent) changes.  I've been a little busy...
>>
>> I'm having trouble adjusting my code.  I hope someone can help.
>>
>> The package was working fine, and a few R functions in my package had
>> lines like this:
>>
>> tmp <- .Fortran( name="pdf", <other parameters here>)
>>
>> and similar.  The "pdf" is the name of the FORTRAN subroutine being
>> called, of course.
>>
>> When I replace that line with
>>
>> tmp <- .Fortran( .NAME="pdf", <other parameters here>)
>>
>>
>> ...the package then does not pass the checks.  The library package 
>> builds
>> OK with no errors or warnings, and then during "R CMD check" the 
>> examples
>> give this error:
>>
>> out <- tweedie.profile( y~1, p.vec=seq(1.1, 1.9, length=9),
>> do.plot=TRUE)
>> 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9
>> .Error in .Fortran(.NAME = "pdfun", as.double(power),
>> as.double(phi[i]/(y[i]^(2 -  :
>>    supplied argument name '.NAME' does not match 'name'
>> Calls: tweedie.profile -> dtweedie.inversion -> .Fortran
>> Execution halted
>>
>>
>>
>>
>> I've had a search--including a read of the "Writing R Extensions" manual
>> on CRAN (I did read it, but interestingly a search of that document did
>> not reveal any instance of .NAME)--and I cannot see the problem.  It's
>> probably obvious.
>>
>> Any help appreciated, even pointers to more info.
>
> I suspect you are doing your checks with an old version, not with the 
> one listed below.  The first argument was called "name" until R 2.13.0 
> was released; at that point it was changed to ".NAME" (to prevent 
> conflicts with something or other).  It seems someone forgot to note 
> this in the NEWS file...
>
> You can find which version did the checks by looking at the header in 
> the 00check.log file created during the check.  You could also follow 
> Rolf's advice and not name the first arg.
>
> Duncan Murdoch
>
>
>>
>> P.
>>
>> sessionInfo()
>> R version 2.15.1 (2012-06-22)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods base
>>
>>
>>
>>
>> The output from R CMD check:
>>
>>
>>
>> R CMD check tweedie
>> * using log directory
>> '/Users/pdunn2/Documents/SharedFiles/pkd/Research/Rlibraries/tweedie/tweedi 
>>
>> e.Rcheck'
>> * using R version 2.15.1 (2012-06-22)
>> * using platform: x86_64-apple-darwin9.8.0 (64-bit)
>> * using session charset: UTF-8
>> * checking for file 'tweedie/DESCRIPTION' ... OK
>> * this is package 'tweedie' version '2.1.2'
>> * checking package namespace information ... OK
>> * checking package dependencies ... OK
>> * checking if this is a source package ... OK
>> * checking if there is a namespace ... OK
>> * checking for executable files ... OK
>> * checking whether package 'tweedie' can be installed ... OK
>> * checking installed package size ... OK
>> * checking package directory ... OK
>> * checking for portable file names ... OK
>> * checking for sufficient/correct file permissions ... OK
>> * checking DESCRIPTION meta-information ... OK
>> * checking top-level files ... OK
>> * checking index information ... OK
>> * checking package subdirectories ... OK
>> * checking R files for non-ASCII characters ... OK
>> * checking R files for syntax errors ... OK
>> * loading checks for arch 'i386'
>> ** checking whether the package can be loaded ... OK
>> ** checking whether the package can be loaded with stated 
>> dependencies ...
>> OK
>> ** checking whether the package can be unloaded cleanly ... OK
>> ** checking whether the namespace can be loaded with stated dependencies
>> ... OK
>> ** checking whether the namespace can be unloaded cleanly ... OK
>> * loading checks for arch 'x86_64'
>> ** checking whether the package can be loaded ... OK
>> ** checking whether the package can be loaded with stated 
>> dependencies ...
>> OK
>> ** checking whether the package can be unloaded cleanly ... OK
>> ** checking whether the namespace can be loaded with stated dependencies
>> ... OK
>> ** checking whether the namespace can be unloaded cleanly ... OK
>> * checking for unstated dependencies in R code ... OK
>> * checking S3 generic/method consistency ... OK
>> * checking replacement functions ... OK
>> * checking foreign function calls ... OK
>> * checking R code for possible problems ... NOTE
>> dtweedie.stable: no visible global function definition for 'dstable'
>> * checking Rd files ... OK
>> * checking Rd metadata ... OK
>> * checking Rd cross-references ... OK
>> * checking for missing documentation entries ... OK
>> * checking for code/documentation mismatches ... WARNING
>> Codoc mismatches from documentation object 'tweedie.plot':
>> tweedie.plot
>>    Code: function(y, xi = power, mu, phi, type = "pdfun", power = NULL,
>>                   add = FALSE, ...)
>>    Docs: function(y, xi, mu, phi, type = "pdf", power = NULL, add =
>>                   FALSE, ...)
>>    Mismatches in argument default values:
>>      Name: 'xi' Code: power Docs:
>>      Name: 'type' Code: "pdfun" Docs: "pdf"
>>
>> * checking Rd \usage sections ... OK
>> * checking Rd contents ... OK
>> * checking for unstated dependencies in examples ... OK
>> * checking line endings in C/C++/Fortran sources/headers ... OK
>> * checking line endings in Makefiles ... OK
>> * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
>> * checking compiled code ... OK
>> * checking examples ...
>> ** running examples for arch 'i386' ... ERROR
>> Running examples in 'tweedie-Ex.R' failed
>> The error most likely occurred in:
>>
>> ### Name: tweedie-package
>> ### Title: Tweedie Distributions
>> ### Aliases: tweedie-package Tweedie
>> ### Keywords: models
>> ### ** Examples
>> # Generate random numbers
>> set.seed(314)
>> y <- rtweedie( 500, p=1.5, mu=1, phi=1)
>>          # With index  p  between 1 and 2, this produces continuous
>>          # data with exact zeros
>> x <- rnorm( length(y), 0, 1)  # Unrelated predictor
>> # With exact zeros, index  p  must be between 1 and 2
>> # Fit the tweedie distribution; expect p about 1.5
>> out <- tweedie.profile( y~1, p.vec=seq(1.1, 1.9, length=9), 
>> do.plot=TRUE)
>> 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9
>> .Error in .Fortran(.NAME = "pdfun", as.double(power),
>> as.double(phi[i]/(y[i]^(2 -  :
>>    supplied argument name '.NAME' does not match 'name'
>> Calls: tweedie.profile -> dtweedie.inversion -> .Fortran
>> Execution halted
>> ** running examples for arch 'x86_64' ... ERROR
>> Running examples in 'tweedie-Ex.R' failed
>> The error most likely occurred in:
>>
>> ### Name: tweedie-package
>> ### Title: Tweedie Distributions
>> ### Aliases: tweedie-package Tweedie
>> ### Keywords: models
>> ### ** Examples
>> # Generate random numbers
>> set.seed(314)
>> y <- rtweedie( 500, p=1.5, mu=1, phi=1)
>>          # With index  p  between 1 and 2, this produces continuous
>>          # data with exact zeros
>> x <- rnorm( length(y), 0, 1)  # Unrelated predictor
>> # With exact zeros, index  p  must be between 1 and 2
>> # Fit the tweedie distribution; expect p about 1.5
>> out <- tweedie.profile( y~1, p.vec=seq(1.1, 1.9, length=9), 
>> do.plot=TRUE)
>> 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9
>> .Error in .Fortran(.NAME = "pdfun", as.double(power),
>> as.double(phi[i]/(y[i]^(2 -  :
>>    supplied argument name '.NAME' does not match 'name'
>> Calls: tweedie.profile -> dtweedie.inversion -> .Fortran
>> Execution halted
>>
>>
>>
>> -- 
>> Dr Peter Dunn
>> Biostatistician
>> Faculty of Science, Health, Education and
>> Engineering (T3.03; ML 33)
>> Ph: +61 7 5456 5085 | Fax: +61 7 5430 2896 | Email: pdunn2 at usc.edu.au |
>> Web: www.usc.edu.au <http://www.usc.edu.au/>
>>
>>
>>
>>
>>
>> University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, 
>> Queensland, 4558 Australia.
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>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>