Re: [R-pkg-devel] Category (Subjection) in R documentation for package
In roxygen2 you do
@section Section name:
The colon is important.
David
On 1 October 2017 at 19:50, Duncan Murdoch wrote:
> On 01/10/2017 12:42 PM, Mohammad Tanvir Ahamed via R-package-devel wrote:
>
>> I am building package R-studio (Roxygen2).
>> In the package function documentation, now the standard format is to show
>> all function name.
>>
>> Now I want to categorize those function under some section/heading.
>> Can any one please hey me regarding this issue?
>> Is there any way or idea how one can do it ?
>>
>
>
> I don't know how to do this with Roxygen2, but what you want to get is a
> package help page (typically yourpackage-package.Rd with
> \alias{yourpackage-package}, and maybe also \alias{yourpackage}). On that
> page you can have sections using
>
> \section{section_title}{
>some content
> }
>
> The "some content" can be a list of links to your help topics using
> \itemize, \enumerate, or \tabular. See the built-in manual "Writing R
> Extensions", and presumably some Roxygen2 documentation to tell you how to
> let all of this get through to the .Rd file.
>
> Duncan Murdoch
>
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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[R-pkg-devel] Confusion over CRAN build error for package Brundle
Forgive me for possibly being naive. I have run the current version of my package, Brundle, through the test systems on win-builder, and the development and stable tests both pass. The package builds on my desktop (MacOS) still runs fine. Yet for the last two days I the package has caused warnings from CRAN. https://cran.r-project.org/web/checks/check_results_Brundle.html From the logs it appears to me that several of the errors are due missing BioConductor package. e.g. Packages required but not available: ‘DiffBind’ ‘Rsamtools’ ‘DESeq2’ Am I missing something obvious? I understood that the test environment included these packages. -- Dr Andrew Holding Fellow of Biochemistry / Senior Research Associate Downing College / Cancer Research UK Cambridge Institute CRUK CI: 01223 769696 Mobile: 07595 666459 [[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] Category (Subjection) in R documentation for package
--- Begin Message ---
Thanks.
But @section makes some section in individual functions help file. But I am in
interested to add section in main index file of the package.
This is more or less like sort functions by alphabetic order on the main help
index of the package. But here I want to add section by my own, not with
alphabetic order.
Regards.
Tanvir Ahamed
Stockholm, Sweden | mashra...@yahoo.com
On Monday, October 2, 2017, 9:59:06 AM GMT+2, David Hugh-Jones
wrote:
In roxygen2 you do
@section Section name:
The colon is important.
David
On 1 October 2017 at 19:50, Duncan Murdoch wrote:
> On 01/10/2017 12:42 PM, Mohammad Tanvir Ahamed via R-package-devel wrote:
>
>> I am building package R-studio (Roxygen2).
>> In the package function documentation, now the standard format is to show
>> all function name.
>>
>> Now I want to categorize those function under some section/heading.
>> Can any one please hey me regarding this issue?
>> Is there any way or idea how one can do it ?
>>
>
>
> I don't know how to do this with Roxygen2, but what you want to get is a
> package help page (typically yourpackage-package.Rd with
> \alias{yourpackage-package}, and maybe also \alias{yourpackage}). On that
> page you can have sections using
>
> \section{section_title}{
> some content
> }
>
> The "some content" can be a list of links to your help topics using \itemize,
> \enumerate, or \tabular. See the built-in manual "Writing R Extensions", and
> presumably some Roxygen2 documentation to tell you how to let all of this get
> through to the .Rd file.Duncan Murdoch
>
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/l istinfo/r-package-devel
>
[[alternative HTML version deleted]]
--- End Message ---
__
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Re: [R-pkg-devel] Confusion over CRAN build error for package Brundle
On 02.10.2017 08:23, Andrew Holding wrote: Forgive me for possibly being naive. I have run the current version of my package, Brundle, through the test systems on win-builder, and the development and stable tests both pass. The package builds on my desktop (MacOS) still runs fine. Yet for the last two days I the package has caused warnings from CRAN. https://cran.r-project.org/web/checks/check_results_Brundle.html From the logs it appears to me that several of the errors are due missing BioConductor package. e.g. Packages required but not available: ‘DiffBind’ ‘Rsamtools’ ‘DESeq2’ Am I missing something obvious? I understood that the test environment included these packages. The problem with missing BioC dependencies can be ignored as well as the R-devel Windows error. THe latter will be auto-resolved, the BioC stuff depends on the fact that CRAN upgraded to BioC 3.6 which is in development and will be released before R-devel, hence we check against it, but it is rather instable and sometimes we cannot intsall the BioC packagess yet. Best, Uwe Ligges __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Confusion over CRAN build error for package Brundle
Dear Uwe, Thanks for your response. Andy On Mon, 2 Oct 2017 at 13:16 Uwe Ligges wrote: > > > On 02.10.2017 08:23, Andrew Holding wrote: > > Forgive me for possibly being naive. I have run the current version of my > > > > package, Brundle, through the test systems on win-builder, and the > > development and stable tests both pass. The package builds on my desktop > > (MacOS) still runs fine. > > > > Yet for the last two days I the package has caused warnings from CRAN. > > > > https://cran.r-project.org/web/checks/check_results_Brundle.html > > > > From the logs it appears to me that several of the errors are due > missing > > BioConductor package. > > > > e.g. Packages required but not available: ‘DiffBind’ ‘Rsamtools’ > ‘DESeq2’ > > > > Am I missing something obvious? I understood that the test environment > > included these packages. > > > > The problem with missing BioC dependencies can be ignored as well as the > R-devel Windows error. THe latter will be auto-resolved, the BioC stuff > depends on the fact that CRAN upgraded to BioC 3.6 which is in > development and will be released before R-devel, hence we check against > it, but it is rather instable and sometimes we cannot intsall the BioC > packagess yet. > > Best, > Uwe Ligges > > -- Dr Andrew Holding Fellow of Biochemistry / Senior Research Associate Downing College / Cancer Research UK Cambridge Institute CRUK CI: 01223 769696 Mobile: 07595 666459 [[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] Category (Subjection) in R documentation for package
On 02/10/2017 8:10 AM, Mohammad Tanvir Ahamed wrote:
Thanks.
But @section makes some section in individual functions help file.
No, I said to put it in the package help file, not an individual
function help file.
But
I am in interested to add section in main index file of the package.
This is more or less like sort functions by alphabetic order on the main
help index of the package. But here I want to add section by my own, not
with alphabetic order.
There are at least a couple of different locations where a "help index"
is stored. One is in the file <...>/html/00Index.html, where <..> is
the path given by system.file(package="yourpackage"). This file is
produced automatically when the package is built or installed (I forget
which), and there's no way to control the formatting at the level you
want. So a gross hack would be to replace that file with a file of your
own choosing, but you would certainly not be allowed to do that if you
wanted your package to appear on CRAN.
Duncan Murdoch
Regards.
Tanvir Ahamed
Stockholm, Sweden | mashra...@yahoo.com
On Monday, October 2, 2017, 9:59:06 AM GMT+2, David Hugh-Jones
wrote:
In roxygen2 you do
@section Section name:
The colon is important.
David
On 1 October 2017 at 19:50, Duncan Murdoch wrote:
> On 01/10/2017 12:42 PM, Mohammad Tanvir Ahamed via R-package-devel wrote:
>
>> I am building package R-studio (Roxygen2).
>> In the package function documentation, now the standard format is to
show all function name.
>>
>> Now I want to categorize those function under some section/heading.
>> Can any one please hey me regarding this issue?
>> Is there any way or idea how one can do it ?
>>
>
>
> I don't know how to do this with Roxygen2, but what you want to get
is a package help page (typically yourpackage-package.Rd with
\alias{yourpackage-package}, and maybe also \alias{yourpackage}). On
that page you can have sections using
>
> \section{section_title}{
> some content
> }
>
> The "some content" can be a list of links to your help topics using
\itemize, \enumerate, or \tabular. See the built-in manual "Writing R
Extensions", and presumably some Roxygen2 documentation to tell you how
to let all of this get through to the .Rd file.Duncan Murdoch
>
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/l istinfo/r-package-devel
>
__
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