Re: [Rd] R-3.2.5 Mac OS X package
On 5/2/16 4:25 PM, David Winsemius wrote: On May 2, 2016, at 3:45 PM, Mick Jordan wrote: When is the R-3.2.5 binary for Mac OS X likely to show up? Where did you look? I see both Mavericks and SnowLeopard fork binaries with or without r.app GUI at http://r.research.att.com/ I've been using the 3.3.0 RC for a while with only relative minor and mostly expected difficulties relating to packages that have external dependencies. I was looking at https://cran.r-project.org/ which only shows a 3.2.4 pkg. Anyway as 3.3.0 is release this is probably moot. Mick __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-3.2.5 Mac OS X package
On Tue, May 3, 2016 at 1:25 AM, David Winsemius wrote: > >> On May 2, 2016, at 3:45 PM, Mick Jordan wrote: >> >> When is the R-3.2.5 binary for Mac OS X likely to show up? > > Where did you look? I see both Mavericks and SnowLeopard fork binaries with > or without r.app GUI at http://r.research.att.com/ AFAICT there is only 3.2.5-pathed there, which is not exactly the same. Gabor [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-3.2.5 Mac OS X package
On May 3, 2016, at 10:40 AM, Mick Jordan wrote: > On 5/2/16 4:25 PM, David Winsemius wrote: >>> On May 2, 2016, at 3:45 PM, Mick Jordan wrote: >>> >>> When is the R-3.2.5 binary for Mac OS X likely to show up? >> Where did you look? I see both Mavericks and SnowLeopard fork binaries with >> or without r.app GUI at http://r.research.att.com/ >> >> I've been using the 3.3.0 RC for a while with only relative minor and mostly >> expected difficulties relating to packages that have external dependencies. >> >> > I was looking at https://cran.r-project.org/ which only shows a 3.2.4 pkg. > > Anyway as 3.3.0 is release this is probably moot. > 3.2.5 is just re-named 3.2.4-revised which is at https://cran.r-project.org/bin/macosx/R-3.2.4-revised.pkg There is a bit of an issue since 3.2.5 was supposed to be just re-named 3.2.4-revised, but in the meantime there were changes like the R logo which makes it hard to do a release without reverting the sources in the repos. So 3.2.5 may or may not happen, but 3.3.0 is the priority now. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] vignette/knitr help
I need some help understanding a problem running the tests on the
'digest' package. Initially, I got the message that the 'knitr' package
was needed to run vignettes:
Running vignettes for package ‘digest’
Error in loadVignetteBuilder(vigns$pkgdir) :
vignette builder 'knitr' not found
So I installed the knitr package and all its dependents (‘mime’,
‘stringi’, ‘magrittr’, ‘evaluate’, ‘formatR’, ‘highr’, ‘markdown’,
‘stringr’, ‘yaml’) . Now I get some different warnings:
Running vignettes for package ‘digest’
Running ‘sha1.Rmd’
Warning messages:
1: In readLines(if (is.character(input2)) { :
cannot open file 'sha1.Rmd': No such file or directory
2: In engine$weave(file, quiet = TRUE, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the
rmarkdown package is not installed. Please install it.
3: In readLines(con) :
cannot open file 'sha1.Rmd': No such file or directory
So why is sha1.Rmd missing? And why is it complaining about rmarkdown?
Or more precisely why did it not install it as a dependent? It installed
plain markdown.
Mick Jordan
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Re: [Rd] vignette/knitr help
Dear Mick,
Note that both knitr and rmarkdown are listed under Suggests: both are
required to compile the vignette. Installing rmarkdown should solve
the problem. If not, please provide more information. OS, R version,
digest version, ...
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data. ~ John Tukey
2016-05-03 20:10 GMT+02:00 Mick Jordan :
> I need some help understanding a problem running the tests on the 'digest'
> package. Initially, I got the message that the 'knitr' package was needed to
> run vignettes:
>
> Running vignettes for package ‘digest’
> Error in loadVignetteBuilder(vigns$pkgdir) :
> vignette builder 'knitr' not found
>
> So I installed the knitr package and all its dependents (‘mime’, ‘stringi’,
> ‘magrittr’, ‘evaluate’, ‘formatR’, ‘highr’, ‘markdown’, ‘stringr’, ‘yaml’) .
> Now I get some different warnings:
>
> Running vignettes for package ‘digest’
> Running ‘sha1.Rmd’
> Warning messages:
> 1: In readLines(if (is.character(input2)) { :
> cannot open file 'sha1.Rmd': No such file or directory
> 2: In engine$weave(file, quiet = TRUE, encoding = enc) :
> The vignette engine knitr::rmarkdown is not available, because the
> rmarkdown package is not installed. Please install it.
> 3: In readLines(con) :
> cannot open file 'sha1.Rmd': No such file or directory
>
> So why is sha1.Rmd missing? And why is it complaining about rmarkdown? Or
> more precisely why did it not install it as a dependent? It installed plain
> markdown.
>
> Mick Jordan
>
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> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
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Re: [Rd] vignette/knitr help
On 5/3/16 11:29 AM, Thierry Onkelinx wrote: Dear Mick, Note that both knitr and rmarkdown are listed under Suggests: both are required to compile the vignette. Installing rmarkdown should solve the problem. If not, please provide more information. OS, R version, digest version, ... This is occurring in the context of an automated testing environment that compares the output of GnuR and FastR. I'm using tools::testInstalledPackage with the default values for 'types'. I guess the problem is that there is no connection between this step and the previous package install step (that did use --install-tests) but didn't install the "Suggests" dependencies because in general these are not needed. But I still am not clear why knitr doesn't list rmarkdown as a dependency when it clearly will try to use it. To me that is is not "Suggests" dependency. Mick __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] vignette/knitr help
Dear Mick, knitr doesn't depends on rmarkdown. It's the vignette that depends on both knitr (for handle the R chunks) and rmarkdown (for the output format rmarkdown::html_vignette). https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies states: "The ‘Suggests’ field ...snip... lists packages that are not necessarily needed. This includes packages used only in examples, tests or vignettes ...snip... Then it is not necessary to have bar use foo unless one wants to execute all the examples/tests/vignettes" So packages in Suggests might be required to compile vignettes. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey 2016-05-03 21:05 GMT+02:00 Mick Jordan : > On 5/3/16 11:29 AM, Thierry Onkelinx wrote: >> >> Dear Mick, >> >> Note that both knitr and rmarkdown are listed under Suggests: both are >> required to compile the vignette. Installing rmarkdown should solve >> the problem. If not, please provide more information. OS, R version, >> digest version, ... >> >> > This is occurring in the context of an automated testing environment that > compares the output of GnuR and FastR. I'm using tools::testInstalledPackage > with the default values for 'types'. I guess the problem is that there is no > connection between this step and the previous package install step (that did > use --install-tests) but didn't install the "Suggests" dependencies because > in general these are not needed. But I still am not clear why knitr doesn't > list rmarkdown as a dependency when it clearly will try to use it. To me > that is is not "Suggests" dependency. > > Mick > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] vignette/knitr help
On 5/3/16 12:19 PM, Thierry Onkelinx wrote:
Dear Mick,
knitr doesn't depends on rmarkdown. It's the vignette that depends on
both knitr (for handle the R chunks) and rmarkdown (for the output
format rmarkdown::html_vignette).
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies
states: "The ‘Suggests’ field ...snip... lists packages that are not
necessarily needed. This includes packages used only in examples,
tests or vignettes ...snip... Then it is not necessary to have bar
use foo unless one wants to execute all the examples/tests/vignettes"
So packages in Suggests might be required to compile vignettes.
Ok, I get it now, and a more careful reading of the Writing Extensions
manual would have helped prevent the surprise. Anyway, FastR can't
handle knitr yet so I am backing off to testing types=c("examples, "tests").
Thanks
Mick
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[Rd] R process killed when allocating too large matrix (Mac OS X)
Dear expeRts, The following code leads to R being killed (under Mac OS X 10.11.4; R installed from source; also happened under a previous unstable version): m <- matrix(0, 10, 10) I expected an error that a vector of this size could not be allocated. Besides the above (a bug?), how can I find out beforehand whether or not a square matrix can be allocated? Cheers, Marius PS: Here is the sessionInfo() output: R version 3.3.0 (2016-05-03) Platform: x86_64-apple-darwin15.4.0 (64-bit) Running under: OS X 10.11.4 (El Capitan) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
