date:20170420

Re: [R-pkg-devel] Issue with including vignettes without building package

2017-04-20 Thread Zhian Kamvar

Perhaps you could add a Makefile with a rule that compiles the vignettes into 
the inst/doc directory? This might avoid the build process.

-
Zhian N. Kamvar, Ph. D.
Postdoctoral Researcher (Everhart Lab)
Department of Plant Pathology
University of Nebraska-Lincoln



> On Apr 20, 2017, at 15:30 , Alexandre Courtiol  
> wrote:
> 
> Thanks but I don't think so, that would imply them to rebuild the
> vignettes, which is exactly what I want to avoid.
> Without knitr cached chunk it would take forever on their laptops and they
> would also need to install tons of packages...
> ++
> 
> On 20 April 2017 at 21:01, Sven E Templer  > wrote:
> 
>> Hi Alex,
>> 
>> 
>> what if you run
>> 
>> devtools::install_github(build_vignettes = TRUE)
>> 
>> on your students computer?
>> 
>> See ?devtools::install
>> 
>> 
>> Best,
>> 
>> Sven
>> 
>> 
>>> On 20. Apr 2017, at 15:09, Alexandre Courtiol <
>> alexandre.court...@gmail.com> wrote:
>>> 
>>> Dear all,
>>> 
>>> I am using a package for teaching:
>>> my slides are html vignettes, and it is convenient for students to
>> control
>>> which packages they must install, provide code and datasets.
>>> 
>>> As I am often editing the package live during the course, it would be
>> great
>>> if I could just push to github and that the student would just have to
>> run
>>> a devtools::install_github() to get my updated vignettes. I would rather
>>> not to have to build the package before pushing to save time.
>>> 
>>> The issues is that I do not want to build the vignettes on install as
>> they
>>> are very slow to build. On my computer however it is quick because I have
>>> cached the knitr chunks output. So I was hoping to just have to run
>>> devtools::build_vignettes() on my machine before pushing the files
>> thereby
>>> created (./inst/doc) and that the student could just
>>> devtools::install_github().
>>> 
>>> I cannot make this work: no vignettes are found after install. When I do
>>> check the repository beeing installed on their computers, the html, Rmd
>> and
>>> R files corresponding to the vignettes are present in ./doc, so it is not
>>> an issue of having the wrong .gitgnore configuration.
>>> 
>>> I have read about many vignettes related issues on the net, but I did not
>>> find something dealing with this precise issue.
>>> 
>>> PS: I know about the R.rsp hack, but I would prefer to find a solution
>> more
>>> direct.
>>> 
>>> Best,
>>> 
>>> Alex
>>> 
>>> 
>>> 
>>> 
>>> --
>>> Alexandre Courtiol
>>> 
>>> http://sites.google.com/site/alexandrecourtiol/home
>>> 
>>> *"Science is the belief in the ignorance of experts"*, R. Feynman
>>> 
>>>  [[alternative HTML version deleted]]
>>> 
>>> __
>>> R-package-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> 
>> 
> 
> 
> -- 
> Alexandre Courtiol
> 
> http://sites.google.com/site/alexandrecourtiol/home 
> 
> 
> *"Science is the belief in the ignorance of experts"*, R. Feynman
> 
>   [[alternative HTML version deleted]]
> 
> __
> 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] Issue with including vignettes without building package

2017-04-20 Thread Alexandre Courtiol

To rephrase my needs, I need to find a way to create the file
/Meta/vignette.rds at install, not build, as all other files for the
vignettes to run are being installed properly.
Has anyone managed to do that?
For now my horrible hack is to have a function calling the vignette through
a call to browseURL(paste0(find.package("XXX"), "/doc/")).
It opens the folder with all the vignette, but it is not as nice as opening
the index in the web browser.
Doing a browseURL on the index.html works but then the links do not... so
that does not help.
Best
Alex

On 20 April 2017 at 22:30, Alexandre Courtiol 
wrote:

> Thanks but I don't think so, that would imply them to rebuild the
> vignettes, which is exactly what I want to avoid.
> Without knitr cached chunk it would take forever on their laptops and they
> would also need to install tons of packages...
> ++
>
> On 20 April 2017 at 21:01, Sven E Templer  wrote:
>
>> Hi Alex,
>>
>>
>> what if you run
>>
>> devtools::install_github(build_vignettes = TRUE)
>>
>> on your students computer?
>>
>> See ?devtools::install
>>
>>
>> Best,
>>
>> Sven
>>
>>
>> > On 20. Apr 2017, at 15:09, Alexandre Courtiol <
>> alexandre.court...@gmail.com> wrote:
>> >
>> > Dear all,
>> >
>> > I am using a package for teaching:
>> > my slides are html vignettes, and it is convenient for students to
>> control
>> > which packages they must install, provide code and datasets.
>> >
>> > As I am often editing the package live during the course, it would be
>> great
>> > if I could just push to github and that the student would just have to
>> run
>> > a devtools::install_github() to get my updated vignettes. I would rather
>> > not to have to build the package before pushing to save time.
>> >
>> > The issues is that I do not want to build the vignettes on install as
>> they
>> > are very slow to build. On my computer however it is quick because I
>> have
>> > cached the knitr chunks output. So I was hoping to just have to run
>> > devtools::build_vignettes() on my machine before pushing the files
>> thereby
>> > created (./inst/doc) and that the student could just
>> > devtools::install_github().
>> >
>> > I cannot make this work: no vignettes are found after install. When I do
>> > check the repository beeing installed on their computers, the html, Rmd
>> and
>> > R files corresponding to the vignettes are present in ./doc, so it is
>> not
>> > an issue of having the wrong .gitgnore configuration.
>> >
>> > I have read about many vignettes related issues on the net, but I did
>> not
>> > find something dealing with this precise issue.
>> >
>> > PS: I know about the R.rsp hack, but I would prefer to find a solution
>> more
>> > direct.
>> >
>> > Best,
>> >
>> > Alex
>> >
>> >
>> >
>> >
>> > --
>> > Alexandre Courtiol
>> >
>> > http://sites.google.com/site/alexandrecourtiol/home
>> >
>> > *"Science is the belief in the ignorance of experts"*, R. Feynman
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> > __
>> > R-package-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>>
>
>
> --
> Alexandre Courtiol
>
> http://sites.google.com/site/alexandrecourtiol/home
>
> *"Science is the belief in the ignorance of experts"*, R. Feynman
>



-- 
Alexandre Courtiol

http://sites.google.com/site/alexandrecourtiol/home

*"Science is the belief in the ignorance of experts"*, R. Feynman

[[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] Issue with including vignettes without building package

2017-04-20 Thread Alexandre Courtiol

Thanks but I don't think so, that would imply them to rebuild the
vignettes, which is exactly what I want to avoid.
Without knitr cached chunk it would take forever on their laptops and they
would also need to install tons of packages...
++

On 20 April 2017 at 21:01, Sven E Templer  wrote:

> Hi Alex,
>
>
> what if you run
>
> devtools::install_github(build_vignettes = TRUE)
>
> on your students computer?
>
> See ?devtools::install
>
>
> Best,
>
> Sven
>
>
> > On 20. Apr 2017, at 15:09, Alexandre Courtiol <
> alexandre.court...@gmail.com> wrote:
> >
> > Dear all,
> >
> > I am using a package for teaching:
> > my slides are html vignettes, and it is convenient for students to
> control
> > which packages they must install, provide code and datasets.
> >
> > As I am often editing the package live during the course, it would be
> great
> > if I could just push to github and that the student would just have to
> run
> > a devtools::install_github() to get my updated vignettes. I would rather
> > not to have to build the package before pushing to save time.
> >
> > The issues is that I do not want to build the vignettes on install as
> they
> > are very slow to build. On my computer however it is quick because I have
> > cached the knitr chunks output. So I was hoping to just have to run
> > devtools::build_vignettes() on my machine before pushing the files
> thereby
> > created (./inst/doc) and that the student could just
> > devtools::install_github().
> >
> > I cannot make this work: no vignettes are found after install. When I do
> > check the repository beeing installed on their computers, the html, Rmd
> and
> > R files corresponding to the vignettes are present in ./doc, so it is not
> > an issue of having the wrong .gitgnore configuration.
> >
> > I have read about many vignettes related issues on the net, but I did not
> > find something dealing with this precise issue.
> >
> > PS: I know about the R.rsp hack, but I would prefer to find a solution
> more
> > direct.
> >
> > Best,
> >
> > Alex
> >
> >
> >
> >
> > --
> > Alexandre Courtiol
> >
> > http://sites.google.com/site/alexandrecourtiol/home
> >
> > *"Science is the belief in the ignorance of experts"*, R. Feynman
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>


-- 
Alexandre Courtiol

http://sites.google.com/site/alexandrecourtiol/home

*"Science is the belief in the ignorance of experts"*, R. Feynman

[[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] Issue with including vignettes without building package

2017-04-20 Thread Sven E Templer

Hi Alex,


what if you run

devtools::install_github(build_vignettes = TRUE)

on your students computer?

See ?devtools::install


Best,

Sven


> On 20. Apr 2017, at 15:09, Alexandre Courtiol  
> wrote:
> 
> Dear all,
> 
> I am using a package for teaching:
> my slides are html vignettes, and it is convenient for students to control
> which packages they must install, provide code and datasets.
> 
> As I am often editing the package live during the course, it would be great
> if I could just push to github and that the student would just have to run
> a devtools::install_github() to get my updated vignettes. I would rather
> not to have to build the package before pushing to save time.
> 
> The issues is that I do not want to build the vignettes on install as they
> are very slow to build. On my computer however it is quick because I have
> cached the knitr chunks output. So I was hoping to just have to run
> devtools::build_vignettes() on my machine before pushing the files thereby
> created (./inst/doc) and that the student could just
> devtools::install_github().
> 
> I cannot make this work: no vignettes are found after install. When I do
> check the repository beeing installed on their computers, the html, Rmd and
> R files corresponding to the vignettes are present in ./doc, so it is not
> an issue of having the wrong .gitgnore configuration.
> 
> I have read about many vignettes related issues on the net, but I did not
> find something dealing with this precise issue.
> 
> PS: I know about the R.rsp hack, but I would prefer to find a solution more
> direct.
> 
> Best,
> 
> Alex
> 
> 
> 
> 
> -- 
> Alexandre Courtiol
> 
> http://sites.google.com/site/alexandrecourtiol/home
> 
> *"Science is the belief in the ignorance of experts"*, R. Feynman
> 
>   [[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] R CMD check not finding my vignettes

2017-04-20 Thread David Hugh-Jones

Hi guys,

Thanks very much for all of your comments. I now have a good sense of what
the possibilities are, and I will think about what works best for my
package.

Cheers,
David


On 20 April 2017 at 14:42, Duncan Murdoch  wrote:

> On 20/04/2017 4:57 AM, Brian G. Peterson wrote:
>
>> David,
>>
>> I'd suggest creating a vignette for each of HTML and PDF, and including
>> a source file that contains the common code.  e.g. have a pdf header and
>> an html header file, and then include the 'main' Rmd as a child doc from
>> each header Rmd.  This way R CMD build could build both pdf and html
>> versions of the output.
>>
>
> That's another solution.  My suggestion would be simpler:  just pick one
> of PDF or HTML, and give the user instructions to produce the other if
> necessary, but don't produce it for them.
>
> Duncan Murdoch
>
>
>
>> Regards,
>>
>> Brian
>>
>> On 04/20/2017 03:38 AM, David Hugh-Jones wrote:
>>
>>> Hi Duncan,
>>>
>>> Thank you very much for taking the time to look at this.
>>>
>>> I tried rebuilding the tar file so as to include only the .Rmd files, not
>>> the HTML files, in 'vignettes':
>>>
>>> drwxr-xr-x  0 david  staff   0 20 Apr 09:21 huxtable/vignettes/
>>>
>>> -rw-r--r--  0 david  staff1633  6 Apr 16:26
>>> huxtable/vignettes/comparison.csv
>>>
>>> -rw-r--r--  0 david  staff6697  6 Apr 14:44
>>> huxtable/vignettes/design-principles.Rmd
>>>
>>> -rw-r--r--  0 david  staff5521  6 Apr 14:30
>>> huxtable/vignettes/huxreg.Rmd
>>>
>>> -rw-r--r--  0 david  staff   20552  6 Apr 16:19
>>> huxtable/vignettes/huxtable.Rmd
>>>
>>> -rw-r--r--  0 david  staff  22 17 Mar 00:19
>>> huxtable/vignettes/placeins-header.tex
>>>
>>>
>>> But when I run R CMD check, I still get the same warning:
>>>
>>> * checking package vignettes in ‘inst/doc’ ... WARNING
>>>
>>> Package vignettes without corresponding PDF/HTML:
>>>
>>>‘design-principles.Rmd’
>>>
>>>‘huxreg.Rmd’
>>>
>>>‘huxtable.Rmd’
>>>
>>> So, the warning does not seem to be related to the presence of HTML files
>>> in vignettes.
>>>
>>> I also tried manually removing .Rmd files from inst/doc (leaving them
>>> only
>>> in vignettes) but this still gave the same error.
>>>
>>> My goal here is that for package-specific reasons, I would like both pdf
>>> and HTML versions of my vignettes to be available (I am writing code that
>>> prints HTML and LaTeX tables and want my users to have examples of how
>>> both
>>> output formats work). This is why I build those files manually, and place
>>> them in inst/doc.
>>>
>>> Side comment: at the moment, I feel as if I am running through the
>>> combinatorics of including and excluding files from vignettes and
>>> inst/doc,
>>> without much insight into what I am doing. Would it be fair to say that
>>> the
>>> current system is not very easy to comprehend?
>>>
>>> Cheers,
>>>
>>> David
>>>
>>> On 19 April 2017 at 21:24, Duncan Murdoch 
>>> wrote:
>>>
>>> On 19/04/2017 1:00 PM, David Hugh-Jones wrote:

 Hi Uwe,
>
> I'm not sure if you ever got my off-list message with my tarball or
> subsequent messages. I can't send a tarball on-list - it gets rejected
> as
> too large - but here is a dropbox link. If you could confirm receipt,
> that
> would be extremely helpful!
>
> https://www.dropbox.com/s/179jrm19kx9o7dz/huxtable_0.2.0.tar.gz?dl=0
>
>
> Not sure if Uwe has had a chance to look, but I just ran R CMD check on
 your tarball using the latest version of R-devel.  It reported the
 following problems:

 * checking CRAN incoming feasibility ... NOTE
 Maintainer: ‘David Hugh-Jones ’

 Found the following (possibly) invalid URLs:
   URL: http://cran.rstudio.com/web/packages/huxtable/index.html
 From: README.md
 CRAN URL not in canonical form
   Canonical CRAN.R-project.org URLs use https.

 The URL for your package should be in the form

 https://CRAN.R-project.org/package=huxtable

 * checking top-level files ... NOTE
 Non-standard file/directory found at top level:
   ‘multirow.rds’

 I'm not sure where that file belongs, but not there.

 * checking files in ‘vignettes’ ... WARNING
 Files in the 'vignettes' directory newer than all files in 'inst/doc':
   ‘huxreg.html’, ‘huxtable.html’

 Those files shouldn't be in the vignettes directory, they are products
 of
 building the vignettes.  Only the source should normally be in the
 vignettes directory.

 * checking package vignettes in ‘inst/doc’ ... WARNING
 Package vignettes without corresponding PDF/HTML:
‘design-principles.Rmd’
‘huxreg.Rmd’
‘huxtable.Rmd’

 I think this is the warning you were asking about.  If I look at just
 the
 first of those files, I see that design-principles.Rmd exists in
 vignettes
 and is set

Re: [R-pkg-devel] How to fix errors in R headers when uploading my package to win-builer

2017-04-20 Thread GSC

I figured it out as header clash. Putting #include R headers after Windows
headers works for me.

GSC 于2017年4月18日周二 上午9:54写道：

> That link is deprecated, new link to log:
> https://win-builder.r-project.org/I3u4Z9BbLHsC/ .
>
> GSC 于2017年4月17日周一 下午10:47写道：
>
>> I have no idea how I could fix these compiling errors in R headers.
>> Testing my package locally on archlinux is fine. The link to build log is:
>> https://win-builder.r-project.org/08H2Ne0lShbY/ . Please help.
>>
>> Thanks!
>>
>

[[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 CMD check not finding my vignettes

2017-04-20 Thread Brian G. Peterson


David,

I'd suggest creating a vignette for each of HTML and PDF, and including 
a source file that contains the common code.  e.g. have a pdf header and 
an html header file, and then include the 'main' Rmd as a child doc from 
each header Rmd.  This way R CMD build could build both pdf and html 
versions of the output.


Regards,

Brian

On 04/20/2017 03:38 AM, David Hugh-Jones wrote:

Hi Duncan,

Thank you very much for taking the time to look at this.

I tried rebuilding the tar file so as to include only the .Rmd files, not
the HTML files, in 'vignettes':

drwxr-xr-x  0 david  staff   0 20 Apr 09:21 huxtable/vignettes/

-rw-r--r--  0 david  staff1633  6 Apr 16:26
huxtable/vignettes/comparison.csv

-rw-r--r--  0 david  staff6697  6 Apr 14:44
huxtable/vignettes/design-principles.Rmd

-rw-r--r--  0 david  staff5521  6 Apr 14:30
huxtable/vignettes/huxreg.Rmd

-rw-r--r--  0 david  staff   20552  6 Apr 16:19
huxtable/vignettes/huxtable.Rmd

-rw-r--r--  0 david  staff  22 17 Mar 00:19
huxtable/vignettes/placeins-header.tex


But when I run R CMD check, I still get the same warning:

* checking package vignettes in ‘inst/doc’ ... WARNING

Package vignettes without corresponding PDF/HTML:

   ‘design-principles.Rmd’

   ‘huxreg.Rmd’

   ‘huxtable.Rmd’

So, the warning does not seem to be related to the presence of HTML files
in vignettes.

I also tried manually removing .Rmd files from inst/doc (leaving them only
in vignettes) but this still gave the same error.

My goal here is that for package-specific reasons, I would like both pdf
and HTML versions of my vignettes to be available (I am writing code that
prints HTML and LaTeX tables and want my users to have examples of how both
output formats work). This is why I build those files manually, and place
them in inst/doc.

Side comment: at the moment, I feel as if I am running through the
combinatorics of including and excluding files from vignettes and inst/doc,
without much insight into what I am doing. Would it be fair to say that the
current system is not very easy to comprehend?

Cheers,

David

On 19 April 2017 at 21:24, Duncan Murdoch  wrote:


On 19/04/2017 1:00 PM, David Hugh-Jones wrote:


Hi Uwe,

I'm not sure if you ever got my off-list message with my tarball or
subsequent messages. I can't send a tarball on-list - it gets rejected as
too large - but here is a dropbox link. If you could confirm receipt, that
would be extremely helpful!

https://www.dropbox.com/s/179jrm19kx9o7dz/huxtable_0.2.0.tar.gz?dl=0



Not sure if Uwe has had a chance to look, but I just ran R CMD check on
your tarball using the latest version of R-devel.  It reported the
following problems:

* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘David Hugh-Jones ’

Found the following (possibly) invalid URLs:
  URL: http://cran.rstudio.com/web/packages/huxtable/index.html
From: README.md
CRAN URL not in canonical form
  Canonical CRAN.R-project.org URLs use https.

The URL for your package should be in the form

https://CRAN.R-project.org/package=huxtable

* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘multirow.rds’

I'm not sure where that file belongs, but not there.

* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘huxreg.html’, ‘huxtable.html’

Those files shouldn't be in the vignettes directory, they are products of
building the vignettes.  Only the source should normally be in the
vignettes directory.

* checking package vignettes in ‘inst/doc’ ... WARNING
Package vignettes without corresponding PDF/HTML:
   ‘design-principles.Rmd’
   ‘huxreg.Rmd’
   ‘huxtable.Rmd’

I think this is the warning you were asking about.  If I look at just the
first of those files, I see that design-principles.Rmd exists in vignettes
and is set to produce PDF output (only the first output entry in the YAML
counts).  You also have a .html file in vignettes; it shouldn't be there.
In inst/doc, you have source, .html and .pdf versions of that file.

The warning isn't very helpful, but I think it is triggered by the fact
that you've got the .html file in your vignettes directory.  If I remove
everything but the source from that directory, and everything from the
inst/doc directory, then all the vignette warnings go away.

(I haven't traced through the code, but I think the warning may be
literally correct.  Since you had .html files that looked like vignette
outputs but weren't, you have vignettes without *corresponding* HTML. It
would have been nicer if it suggested how to fix this, but that vignette
code is quite tricky, because any file could be source, and any html, tex
or pdf file could be output.  At some point I may try to clean it up a bit
and then maybe the error messages will be less obscure.)

Duncan Murdoch



[[alternative HTML version deleted]]

Re: [R-pkg-devel] R CMD check not finding my vignettes

2017-04-20 Thread David Hugh-Jones

Hi Duncan,

Thank you very much for taking the time to look at this.

I tried rebuilding the tar file so as to include only the .Rmd files, not
the HTML files, in 'vignettes':

drwxr-xr-x  0 david  staff   0 20 Apr 09:21 huxtable/vignettes/

-rw-r--r--  0 david  staff1633  6 Apr 16:26
huxtable/vignettes/comparison.csv

-rw-r--r--  0 david  staff6697  6 Apr 14:44
huxtable/vignettes/design-principles.Rmd

-rw-r--r--  0 david  staff5521  6 Apr 14:30
huxtable/vignettes/huxreg.Rmd

-rw-r--r--  0 david  staff   20552  6 Apr 16:19
huxtable/vignettes/huxtable.Rmd

-rw-r--r--  0 david  staff  22 17 Mar 00:19
huxtable/vignettes/placeins-header.tex


But when I run R CMD check, I still get the same warning:

* checking package vignettes in ‘inst/doc’ ... WARNING

Package vignettes without corresponding PDF/HTML:

   ‘design-principles.Rmd’

   ‘huxreg.Rmd’

   ‘huxtable.Rmd’

So, the warning does not seem to be related to the presence of HTML files
in vignettes.

I also tried manually removing .Rmd files from inst/doc (leaving them only
in vignettes) but this still gave the same error.

My goal here is that for package-specific reasons, I would like both pdf
and HTML versions of my vignettes to be available (I am writing code that
prints HTML and LaTeX tables and want my users to have examples of how both
output formats work). This is why I build those files manually, and place
them in inst/doc.

Side comment: at the moment, I feel as if I am running through the
combinatorics of including and excluding files from vignettes and inst/doc,
without much insight into what I am doing. Would it be fair to say that the
current system is not very easy to comprehend?

Cheers,

David

On 19 April 2017 at 21:24, Duncan Murdoch  wrote:

> On 19/04/2017 1:00 PM, David Hugh-Jones wrote:
>
>> Hi Uwe,
>>
>> I'm not sure if you ever got my off-list message with my tarball or
>> subsequent messages. I can't send a tarball on-list - it gets rejected as
>> too large - but here is a dropbox link. If you could confirm receipt, that
>> would be extremely helpful!
>>
>> https://www.dropbox.com/s/179jrm19kx9o7dz/huxtable_0.2.0.tar.gz?dl=0
>>
>>
> Not sure if Uwe has had a chance to look, but I just ran R CMD check on
> your tarball using the latest version of R-devel.  It reported the
> following problems:
>
> * checking CRAN incoming feasibility ... NOTE
> Maintainer: ‘David Hugh-Jones ’
>
> Found the following (possibly) invalid URLs:
>   URL: http://cran.rstudio.com/web/packages/huxtable/index.html
> From: README.md
> CRAN URL not in canonical form
>   Canonical CRAN.R-project.org URLs use https.
>
> The URL for your package should be in the form
>
> https://CRAN.R-project.org/package=huxtable
>
> * checking top-level files ... NOTE
> Non-standard file/directory found at top level:
>   ‘multirow.rds’
>
> I'm not sure where that file belongs, but not there.
>
> * checking files in ‘vignettes’ ... WARNING
> Files in the 'vignettes' directory newer than all files in 'inst/doc':
>   ‘huxreg.html’, ‘huxtable.html’
>
> Those files shouldn't be in the vignettes directory, they are products of
> building the vignettes.  Only the source should normally be in the
> vignettes directory.
>
> * checking package vignettes in ‘inst/doc’ ... WARNING
> Package vignettes without corresponding PDF/HTML:
>‘design-principles.Rmd’
>‘huxreg.Rmd’
>‘huxtable.Rmd’
>
> I think this is the warning you were asking about.  If I look at just the
> first of those files, I see that design-principles.Rmd exists in vignettes
> and is set to produce PDF output (only the first output entry in the YAML
> counts).  You also have a .html file in vignettes; it shouldn't be there.
> In inst/doc, you have source, .html and .pdf versions of that file.
>
> The warning isn't very helpful, but I think it is triggered by the fact
> that you've got the .html file in your vignettes directory.  If I remove
> everything but the source from that directory, and everything from the
> inst/doc directory, then all the vignette warnings go away.
>
> (I haven't traced through the code, but I think the warning may be
> literally correct.  Since you had .html files that looked like vignette
> outputs but weren't, you have vignettes without *corresponding* HTML. It
> would have been nicer if it suggested how to fix this, but that vignette
> code is quite tricky, because any file could be source, and any html, tex
> or pdf file could be output.  At some point I may try to clean it up a bit
> and then maybe the error messages will be less obscure.)
>
> Duncan Murdoch
>

[[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] Interplay between knitr() and View()

2017-04-20 Thread Thierry Onkelinx

Dear Roy,

In case you create a HTML vignette you can use datatable() from the DT
package. That creates a dynamic table in the output.

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

2017-04-19 19:20 GMT+02:00 Roy Mendelssohn - NOAA Federal <
roy.mendelss...@noaa.gov>:

> Hi All:
>
> My package allows the user to search for information about the data
> available, and the information is returned in a dataframe. I had long been
> looking for a nice way to display the results  (the datasets' metadata),
> and wasn't too happy with anything until I tried the View() command,  which
> does exactly what I want.
>
> The problem is I can't seem to find a way to make View() and knitr() work
> nice together in creating the vignette. Given the way View() works I doubt
> there is a way,  but any suggestions of how I can show what the user will
> see when the given the command in the package from within my vignette?
>
> Thanks,
>
> -Roy
>
>
>
> **
> "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> **
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new street address***
> 110 McAllister Way
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK
> Jr.
>
> __
> 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] Issue with including vignettes without building package

Re: [R-pkg-devel] Issue with including vignettes without building package

Re: [R-pkg-devel] Issue with including vignettes without building package

Re: [R-pkg-devel] Issue with including vignettes without building package

Re: [R-pkg-devel] R CMD check not finding my vignettes

Re: [R-pkg-devel] How to fix errors in R headers when uploading my package to win-builer

Re: [R-pkg-devel] R CMD check not finding my vignettes

Re: [R-pkg-devel] R CMD check not finding my vignettes

Re: [R-pkg-devel] Interplay between knitr() and View()

9 matches

Site Navigation

Mail list logo

Footer information