Re: [R-pkg-devel] Do I need to namespace and import functions from 'methods' package?
On 12/07/2015 4:01 PM, Dean Attali wrote: I have a package that is using the 'is' function from the 'methods' package. My package has been on CRAN for some time now and has had 3 different versions already. Yesterday when submitting, I got a response with: * checking R code for possible problems ... NOTE ggMarginal: no visible global function definition for 'is' Undefined global functions or variables: is So I fixed it by changing 'is' to 'methods::is', and then I got a response * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘methods’ So I suppose I need to declare 'methods' in my imported packages. My question is: is this a new requirement, to explicitly import 'methods' and namespace functions from it, or has it always been a requirement but I just wasn't caught? Or is it not even a requirement and the R CMD check was being weird? It is a new requirement. As Joshua Ulrich posted on Friday, Yes, this is expected. See: http://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2015/06/29#n2015-06-29 And an earlier email on this list: https://stat.ethz.ch/pipermail/r-package-devel/2015q2/000171.html __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Do I need to namespace and import functions from 'methods' package?
I see there have been several messages about this recently. I apologize, I wasn't aware of the fact that I could search old messages on the board - will do that next time, thanks --- http://deanattali.com On 12 July 2015 at 13:36, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 12/07/2015 4:01 PM, Dean Attali wrote: I have a package that is using the 'is' function from the 'methods' package. My package has been on CRAN for some time now and has had 3 different versions already. Yesterday when submitting, I got a response with: * checking R code for possible problems ... NOTE ggMarginal: no visible global function definition for 'is' Undefined global functions or variables: is So I fixed it by changing 'is' to 'methods::is', and then I got a response * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘methods’ So I suppose I need to declare 'methods' in my imported packages. My question is: is this a new requirement, to explicitly import 'methods' and namespace functions from it, or has it always been a requirement but I just wasn't caught? Or is it not even a requirement and the R CMD check was being weird? It is a new requirement. As Joshua Ulrich posted on Friday, Yes, this is expected. See: http://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2015/06/29#n2015-06-29 And an earlier email on this list: https://stat.ethz.ch/pipermail/r-package-devel/2015q2/000171.html [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R-devel problem with temporary files or decompression?
I don't see any particular wrong with your code, so it seems like
R.utils doesn't handle your 'file' / 'tmp' pathnames correctly.
However, I cannot reproduce this (know what 'file' and 'tmp' are would
help), so I cannot fix it either.
Either way, instead of using low-level decompressFile(), you can
achieve what you want with:
rsk - R.utils::gunzip(file, temporary=TRUE, remove=FALSE)
If you don't use temporary=TRUE, then 'rsk' with point to 'sample.rsk'
in the current directory.
/Henrik
(author of R.utils)
On Sun, Jul 12, 2015 at 8:45 AM, Daniel Kelley dan.kel...@dal.ca wrote:
Uwe, thanks very much. How silly of me. It was because my code creates full
pathnames except if the first char of a filename is “/“ or “~”, etc. I have
never really used windows/msdos (went from 1970s unix to OSX) and so I was
being very silly. Dan.
On Jul 12, 2015, at 12:38 PM, Uwe Ligges lig...@statistik.tu-dortmund.de
wrote:
On 12.07.2015 17:33, Daniel Kelley wrote:
A data file that I’d like to use in my “oce” package is quite large, and
compresses well, so I thought of putting a compressed version into
inst/extdata. I want my documentation to show how to uncompress the file,
partly because these files tend to compress so well that I think users
might like to store them in gzipped form.
Naturally, I want to test my code using R-devel in addition to the
‘release’ version that I have on my box. Since I’ve never been able to get
R-devel installed properly on OSX, I thought of submitting to win-builder.
I got errors as below my signature line. What I don’t understand is the
“Invalid argument”, which seems to be different from the “No such file or
directory” that I would expect to get if there were no file. Any ideas on
how to proceed?
Dan Kelley / Oceanography / Dalhousie University / Halifax NS Canada
### ** Examples
library(oce)
## A CTD-style rsk
if (requireNamespace(R.utils)) {
+ file - system.file(extdata, sample.rsk.gz, package=oce)
+ tmp - tempfile(fileext=.rsk)
+ R.utils::decompressFile(file, destname=tmp, ext=gz, FUN=gzfile,
remove=FALSE)
+ rsk - read.rsk(tmp)
+ ctd - as.ctd(rsk)
+ plot(ctdTrim(ctd))
+ }
Loading required namespace: R.utils
Warning in file(file, r) :
cannot open file
'd:/RCompile/CRANguest/R-devel/oce.Rcheck/examples_i386/D:\temp\RtmpGUYumI\file29ac3bed3fed.rsk':
Apparently you have put together the location of the current path and the
one of the tempfile which does not make sense.
So very likely a bug in your code. Surprise you do not see it on your end.
Best,
Uwe Ligges
Invalid argument
Error in file(file, r) : cannot open the connection
Calls: read.rsk - file
Execution halted
** running examples for arch 'x64' ... ERROR
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[R-pkg-devel] Do I need to namespace and import functions from 'methods' package?
I have a package that is using the 'is' function from the 'methods' package. My package has been on CRAN for some time now and has had 3 different versions already. Yesterday when submitting, I got a response with: * checking R code for possible problems ... NOTE ggMarginal: no visible global function definition for 'is' Undefined global functions or variables: is So I fixed it by changing 'is' to 'methods::is', and then I got a response * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘methods’ So I suppose I need to declare 'methods' in my imported packages. My question is: is this a new requirement, to explicitly import 'methods' and namespace functions from it, or has it always been a requirement but I just wasn't caught? Or is it not even a requirement and the R CMD check was being weird? --- http://deanattali.com [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R-devel problem with temporary files or decompression?
Uwe, thanks very much. How silly of me. It was because my code creates full
pathnames except if the first char of a filename is “/“ or “~”, etc. I have
never really used windows/msdos (went from 1970s unix to OSX) and so I was
being very silly. Dan.
On Jul 12, 2015, at 12:38 PM, Uwe Ligges lig...@statistik.tu-dortmund.de
wrote:
On 12.07.2015 17:33, Daniel Kelley wrote:
A data file that I’d like to use in my “oce” package is quite large, and
compresses well, so I thought of putting a compressed version into
inst/extdata. I want my documentation to show how to uncompress the file,
partly because these files tend to compress so well that I think users might
like to store them in gzipped form.
Naturally, I want to test my code using R-devel in addition to the ‘release’
version that I have on my box. Since I’ve never been able to get R-devel
installed properly on OSX, I thought of submitting to win-builder. I got
errors as below my signature line. What I don’t understand is the “Invalid
argument”, which seems to be different from the “No such file or directory”
that I would expect to get if there were no file. Any ideas on how to
proceed?
Dan Kelley / Oceanography / Dalhousie University / Halifax NS Canada
### ** Examples
library(oce)
## A CTD-style rsk
if (requireNamespace(R.utils)) {
+ file - system.file(extdata, sample.rsk.gz, package=oce)
+ tmp - tempfile(fileext=.rsk)
+ R.utils::decompressFile(file, destname=tmp, ext=gz, FUN=gzfile,
remove=FALSE)
+ rsk - read.rsk(tmp)
+ ctd - as.ctd(rsk)
+ plot(ctdTrim(ctd))
+ }
Loading required namespace: R.utils
Warning in file(file, r) :
cannot open file
'd:/RCompile/CRANguest/R-devel/oce.Rcheck/examples_i386/D:\temp\RtmpGUYumI\file29ac3bed3fed.rsk':
Apparently you have put together the location of the current path and the one
of the tempfile which does not make sense.
So very likely a bug in your code. Surprise you do not see it on your end.
Best,
Uwe Ligges
Invalid argument
Error in file(file, r) : cannot open the connection
Calls: read.rsk - file
Execution halted
** running examples for arch 'x64' ... ERROR
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