On 11/09/2012 13:09, 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...
Actually, an incorrect check got re-activated by 2.15.1. NEWS for
R-devel says
• The functions .C(), .Call(), .External() and .Fortran() now check
that they are called with an unnamed first argument: the formal
arguments were changed from name= to .NAME= in R 2.13.0, but some
packages were still using the old name.
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.
Actually the CRAN message explicitly asked Master Dunn to use an unnamed
first argument ....
Or even follow the advice of the ?.Fortran help page in R-patched/R-devel:
These functions are all primitive, and ‘.NAME’ is always matched
to the first argument supplied (which should not be named). The
other named arguments follow ‘...’ and so cannot be abbreviated.
The reason for that advice is that only unnamed first arguments will
work for all recent versions of R.
As the posting guide says
'f you are using an old version of R and think it does not work
properly, upgrade to the latest version and try that, before posting. If
possible, try the current R-patched or R-devel version of R (see the FAQ
for details), to see if the problem has already been addressed.'
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: pdu...@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
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______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
