[R] .NAME in .Fortran
Duncan Murdoch
murdoch.duncan at gmail.com
Wed Sep 12 00:50:26 CEST 2012
On 12-09-11 4:44 PM, Rolf Turner wrote:
>
> 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.
Yes, Peter told me the same.
>
> 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.
There was a bug; it was fixed in August (also without a NEWS entry).
You shouldn't see it in R-patched, or 2.15.2, when that is released.
Duncan Murdoch
>
> 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.
>>> CRICOS Provider No: 01595D
>>> Please consider the environment before printing this email.
>>> This email is confidential. If received in error, please delete it
>>> from your system.
>>>
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>>> http://www.R-project.org/posting-guide.html
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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.
>>
>
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