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.
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.
I don't understand at all what the problem is, but a workaround
is simply not to specify the "pdf" argument in "name=value"
form
but rather in positional form. I.e. just make it the first argument
to .Fortran(). As in:
tmp <- .Fortran("pdf", <other parameters here>)
Works for me! :-)
cheers,
Rolf
On 11/09/12 13:21, 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.
<SNIP>
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. > > ______________________________________________ > 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. >