[R-pkg-devel] FW: CRAN submission berryFunctions 1.8.0
Hi, after submitting my package update, CRAN (Brian Ripley) found a couple of warnings / messages. URLs that are not longer existent, a non-ASCII character from copypasting, incorrect title case. Stuff that I should and could definitely solve before submitting. Why did the latest Rdevel (2015-06-01 r68455) CMD check --as-cran not find them? Below are the relevant excerpts. Thanks for any hints about what I may have done wrong, Berry - > Found the following (possibly) invalid URLs: >URL: http://cran.r-project.org/web/packages/denstrip (moved to > http://cran.r-project.org/web/packages/denstrip/) > From: man/betaPlot.Rd >man/normPlot.Rd > Status: 200 > Message: OK > CRAN URL not in canonical form >URL: http://www.geolinde.musin.de/afrika/pic/klimamuenchen.gif > From: man/climateGraph.Rd > Status: 404 > Message: Not Found [...] >The canonical URL of the CRAN page for a package is >http://cran.r-project.org/package=pkgname > No package encoding and non-ASCII characters in the following R files: >R/groupHist.R > 19: # ignore messages like: argument col is not made use of > The Title field should be in title case, current version then in title case: > �Function Collection related to Plotting and Hydrology� > �Function Collection Related to Plotting and Hydrology� > [[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] FW: CRAN submission berryFunctions 1.8.0
On 03.06.2015 09:48, Berry Boessenkool wrote: Hi, after submitting my package update, CRAN (Brian Ripley) found a couple of warnings / messages. URLs that are not longer existent, a non-ASCII character from copypasting, incorrect title case. Stuff that I should and could definitely solve before submitting. Why did the latest Rdevel (2015-06-01 r68455) CMD check --as-cran not find them? Your R was not libcurl enabled nor had you the spellchecker installed, I guess. Best, Uwe Ligges Below are the relevant excerpts. Thanks for any hints about what I may have done wrong, Berry - Found the following (possibly) invalid URLs: URL: http://cran.r-project.org/web/packages/denstrip (moved to http://cran.r-project.org/web/packages/denstrip/) From: man/betaPlot.Rd man/normPlot.Rd Status: 200 Message: OK CRAN URL not in canonical form URL: http://www.geolinde.musin.de/afrika/pic/klimamuenchen.gif From: man/climateGraph.Rd Status: 404 Message: Not Found [...] The canonical URL of the CRAN page for a package is http://cran.r-project.org/package=pkgname No package encoding and non-ASCII characters in the following R files: R/groupHist.R 19: # ignore messages like: argument col is not made use of The Title field should be in title case, current version then in title case: �Function Collection related to Plotting and Hydrology� �Function Collection Related to Plotting and Hydrology� [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] FW: CRAN submission berryFunctions 1.8.0
I found the actual reason: I was really stupid. At the time of testing, I had killed the internet acces. Sorry for bothering you all ... Berry PS: If you want to know why on earth I did that: Yesterday, I got the error: unable to connect to CRAN.R-project.org on port 80. I couldn't find an effective solution online except for turning of the internet connection while testing - which I did. And hooray, the error changed into a warning - which I felt safe to ignore. Apparently, I should just have waited longer and tried again later, as the condition seems to be temporary in nature. Pretty clear that, if I turn off the internet, checks can't find false URLs. > From: plumm...@iarc.fr > To: berryboessenk...@hotmail.com; lig...@statistik.tu-dortmund.de > CC: r-package-devel@r-project.org > Subject: Re: [R-pkg-devel] FW: CRAN submission berryFunctions 1.8.0 > Date: Wed, 3 Jun 2015 08:02:19 + > > On Wed, 2015-06-03 at 09:51 +0200, Uwe Ligges wrote: >> >> On 03.06.2015 09:48, Berry Boessenkool wrote: >>> >>> Hi, >>> >>> after submitting my package update, CRAN (Brian Ripley) found a couple of >>> warnings / messages. >>> URLs that are not longer existent, a non-ASCII character from copypasting, >>> incorrect title case. >>> Stuff that I should and could definitely solve before submitting. >>> >>> Why did the latest Rdevel (2015-06-01 r68455) CMD check --as-cran not find >>> them? >> >> Your R was not libcurl enabled nor had you the spellchecker installed, I >> guess. > > I got the package source from https://github.com/brry/berryFunctions and > I do get these messages. > > Martyn > >> Best, >> Uwe Ligges >> >> >>> Below are the relevant excerpts. >>> >>> Thanks for any hints about what I may have done wrong, >>> Berry >>> >>> - >>> Found the following (possibly) invalid URLs: URL: http://cran.r-project.org/web/packages/denstrip (moved to http://cran.r-project.org/web/packages/denstrip/) From: man/betaPlot.Rd man/normPlot.Rd Status: 200 Message: OK CRAN URL not in canonical form >>> URL: http://www.geolinde.musin.de/afrika/pic/klimamuenchen.gif From: man/climateGraph.Rd Status: 404 Message: Not Found >>> >>> [...] >>> The canonical URL of the CRAN page for a package is http://cran.r-project.org/package=pkgname >>> >>> No package encoding and non-ASCII characters in the following R files: R/groupHist.R 19: # ignore messages like: argument col is not made use of >>> >>> The Title field should be in title case, current version then in title case: �Function Collection related to Plotting and Hydrology� �Function Collection Related to Plotting and Hydrology� >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> __ >>> R-package-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel >>> >> >> __ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[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] FW: CRAN submission berryFunctions 1.8.0
Note that current devtools 1.8.0 attempts to use the spell checker when you say devtools::check(check_version = TRUE), and warns if no spell checker could be found. Perhaps a simpler option is to build on win-builder before submission (e.g., by running devtools::build_win() ), which is a good idea unless your package doesn't support Windows. Best regards Kirill On 03.06.2015 09:51, Uwe Ligges wrote: On 03.06.2015 09:48, Berry Boessenkool wrote: Hi, after submitting my package update, CRAN (Brian Ripley) found a couple of warnings / messages. URLs that are not longer existent, a non-ASCII character from copypasting, incorrect title case. Stuff that I should and could definitely solve before submitting. Why did the latest Rdevel (2015-06-01 r68455) CMD check --as-cran not find them? Your R was not libcurl enabled nor had you the spellchecker installed, I guess. Best, Uwe Ligges Below are the relevant excerpts. Thanks for any hints about what I may have done wrong, Berry - Found the following (possibly) invalid URLs: URL: http://cran.r-project.org/web/packages/denstrip (moved to http://cran.r-project.org/web/packages/denstrip/) From: man/betaPlot.Rd man/normPlot.Rd Status: 200 Message: OK CRAN URL not in canonical form URL: http://www.geolinde.musin.de/afrika/pic/klimamuenchen.gif From: man/climateGraph.Rd Status: 404 Message: Not Found [...] The canonical URL of the CRAN page for a package is http://cran.r-project.org/package=pkgname No package encoding and non-ASCII characters in the following R files: R/groupHist.R 19: # ignore messages like: argument col is not made use of The Title field should be in title case, current version then in title case: �Function Collection related to Plotting and Hydrology� �Function Collection Related to Plotting and Hydrology� [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] FW: CRAN submission berryFunctions 1.8.0
On Wed, 2015-06-03 at 09:51 +0200, Uwe Ligges wrote: > > On 03.06.2015 09:48, Berry Boessenkool wrote: > > > > Hi, > > > > after submitting my package update, CRAN (Brian Ripley) found a couple of > > warnings / messages. > > URLs that are not longer existent, a non-ASCII character from copypasting, > > incorrect title case. > > Stuff that I should and could definitely solve before submitting. > > > > Why did the latest Rdevel (2015-06-01 r68455) CMD check --as-cran not find > > them? > > Your R was not libcurl enabled nor had you the spellchecker installed, I > guess. I got the package source from https://github.com/brry/berryFunctions and I do get these messages. Martyn > Best, > Uwe Ligges > > > > Below are the relevant excerpts. > > > > Thanks for any hints about what I may have done wrong, > > Berry > > > > - > > > >> Found the following (possibly) invalid URLs: > >> URL: http://cran.r-project.org/web/packages/denstrip (moved to > >> http://cran.r-project.org/web/packages/denstrip/) > >> From: man/betaPlot.Rd > >> man/normPlot.Rd > >> Status: 200 > >> Message: OK > >> CRAN URL not in canonical form > > > >> URL: http://www.geolinde.musin.de/afrika/pic/klimamuenchen.gif > >> From: man/climateGraph.Rd > >> Status: 404 > >> Message: Not Found > > > > [...] > > > >> The canonical URL of the CRAN page for a package is > >> http://cran.r-project.org/package=pkgname > > > > > >> No package encoding and non-ASCII characters in the following R files: > >> R/groupHist.R > >> 19: # ignore messages like: argument col is not made use of > > > > > >> The Title field should be in title case, current version then in title > >> case: > >> �Function Collection related to Plotting and Hydrology� > >> �Function Collection Related to Plotting and Hydrology� > >> > > > > > > [[alternative HTML version deleted]] > > > > > > > > __ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Running a script after a package has been installed.
Dear all, I am writing a package that contains some binaries that should be linked in /usr/bin after the package has been installed (I placed them in Rpackage/inst/bin) I know I can use a script "configure" or "configure.win" to be run before the package has been installed, is there a way I can write a script that is run after the package has been correctly installed? Thanks a lot in advance for the help, Cheers, Luca __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Running a script after a package has been installed.
On 3 June 2015 at 12:51, Luca Cerone wrote: | Dear all, | I am writing a package that contains some binaries that should be | linked in /usr/bin after the package [ Don't do that, /usr is for your system. Use /usr/local/bin. ] | has been installed (I placed them in Rpackage/inst/bin) | | I know I can use a script "configure" or "configure.win" to be run | before the package has been installed, is there a way I can write a | script that is run after the package has been correctly installed? You can't. I miss that too. We do the same thing at work -- scripts (often via Rscript or littler) go into into/scripts inside a package, we then have to (at least _one time_) create a softlink from /usr/local/bin into (on our systems with Debian/Ubuntu paths) /usr/local/lib/R/site-library/PKG/script/SCRIPT where PKG and SCRIPT vary. Having more 'hooks' in the R CMD INSTALL ... process would be nice, but it doesn't exist now. One alternative is to package the R package as a .deb package to use the proper postinst. But that may be overkill / does not help on other OS. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Running a script after a package has been installed.
On 3 June 2015 at 07:13, Dirk Eddelbuettel wrote:
|
| On 3 June 2015 at 12:51, Luca Cerone wrote:
| | Dear all,
| | I am writing a package that contains some binaries that should be
| | linked in /usr/bin after the package
|
| [ Don't do that, /usr is for your system. Use /usr/local/bin. ]
|
| | has been installed (I placed them in Rpackage/inst/bin)
| |
| | I know I can use a script "configure" or "configure.win" to be run
| | before the package has been installed, is there a way I can write a
| | script that is run after the package has been correctly installed?
|
| You can't. I miss that too.
|
| We do the same thing at work -- scripts (often via Rscript or littler) go
| into into/scripts inside a package, we then have to (at least _one time_)
| create a softlink from /usr/local/bin into (on our systems with Debian/Ubuntu
| paths) /usr/local/lib/R/site-library/PKG/script/SCRIPT where PKG and SCRIPT
| vary.
|
| Having more 'hooks' in the R CMD INSTALL ... process would be nice, but it
| doesn't exist now.
I just realized that you could abuse configure to create the link described
above. Not elegant, and in the wrong order ("don't know yet if build will
succeed") but a hack.
Dirk
| One alternative is to package the R package as a .deb package to use the
| proper postinst. But that may be overkill / does not help on other OS.
|
| Dirk
|
| --
| http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
|
| __
| R-package-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-package-devel
--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
__
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[R-pkg-devel] Vignette does not show up after loading package
Hi all,
I am developing a package for the interpretation of mass spectrometry data,
which can be found here: https://github.com/goat-anti-rabbit/labelpepmatch.R
I wrote a vignette that compiles fine into a .html using knitr in Rstudio.
The output line in the vignette.rmd file looks like :
??output: rmarkdown::html_vignette
However, when I use
devtools::install_github("goat-anti-rabbit/labelpepmatch.R") or
devtools::install_github("goat-anti-rabbit/labelpepmatch.R",build_vignettes =
TRUE), the package loads normally, but no vignette is found when using
browseVignettes("labelpepmatch") or vignette("labelpepmatch").
I don't really get this, because as far as I understood, shouldn't the package
be able to build the vignette from scratch?
I also tried with these lines for output:
output:
html_document:
theme: readable
pdf_document:
highlight: default
toc: yes
And it nicely knits into example html and pdf files, but no real files are
created in the labelpepmatch/vignettes directory. Any suggestions here?
So: recap of my questions:
1. Should it be possible for the vignette to be built from scratch and if yes,
what is missing in my package for this functionality to work?
2. How can I make knitr output a html AND pdf in my vignettes directory?
Looking forward to your replies.
Many, many thanks!
Rik
[[alternative HTML version deleted]]
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Re: [R-pkg-devel] Vignette does not show up after loading package
On 03/06/2015 12:16 PM, Rik Verdonck wrote:
> Hi all,
>
>
>
>
> I am developing a package for the interpretation of mass spectrometry data,
> which can be found here: https://github.com/goat-anti-rabbit/labelpepmatch.R
If your vignette is not written in Sweave, you need to tell R what
package handles it. See the "Non-Sweave vignettes" section 1.4.2 in
Writing R Extensions.
Duncan Murdoch
> I wrote a vignette that compiles fine into a .html using knitr in Rstudio.
> The output line in the vignette.rmd file looks like :
>
> ??output: rmarkdown::html_vignette
>
> However, when I use
> devtools::install_github("goat-anti-rabbit/labelpepmatch.R") or
> devtools::install_github("goat-anti-rabbit/labelpepmatch.R",build_vignettes =
> TRUE), the package loads normally, but no vignette is found when using
> browseVignettes("labelpepmatch") or vignette("labelpepmatch").
>
> I don't really get this, because as far as I understood, shouldn't the
> package be able to build the vignette from scratch?
>
> I also tried with these lines for output:
>
> output:
> html_document:
> theme: readable
> pdf_document:
> highlight: default
> toc: yes
>
> And it nicely knits into example html and pdf files, but no real files are
> created in the labelpepmatch/vignettes directory. Any suggestions here?
>
>
> So: recap of my questions:
> 1. Should it be possible for the vignette to be built from scratch and if
> yes, what is missing in my package for this functionality to work?
> 2. How can I make knitr output a html AND pdf in my vignettes directory?
>
> Looking forward to your replies.
> Many, many thanks!
> Rik
>
>
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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