Re: [R-pkg-devel] What's recommended to do on "Suggests or Enhances not in mainstream repositories: ..."?

[Balamuta, James Joseph]

Greetings and Salutations Marius,

For implementation help with “Additional_repositories”, which lacks a bit of 
documentation, please see: 
http://thecoatlessprofessor.com/programming/r-data-packages-in-external-data-repositories-using-the-additional_repositories-field/

Under this approach, I am able use `imudata` package 
[https://github.com/smac-group/imudata] to build the vignettes within the 
`gmwm` package [https://github.com/smac-group/gmwm] with the suggests field 
filled in as: “Suggests: imudata”. Otherwise, CRAN would not accept the `gmwm` 
package as-is. 

(Regarding the package size claim, there really are not that many packages 
greater than 5 mb… For some figures on this, see: 
http://thecoatlessprofessor.com/programming/size-and-limitations-of-packages-on-cran/
 )

Sincerely,

JJB

On 5/21/16, 10:22 AM, "R-package-devel on behalf of Marius Hofert" 
 
wrote:

>Hi,
>
>I have (co-)developed two packages: 'qrmtools' and 'qrmdata'. The
>latter contains data sets and is currently only available on R-Forge
>(as it is larger than 5MB and thus not accepted for CRAN [although
>there are much larger packages, but that's a different story...]).
>'qrmtools' contains mainly tools that show what can be done with data
>such as the one contained in 'qrmdata' -- and thus has 'qrmdata' in
>Suggests. The check shows 'Suggests or Enhances not in mainstream
>repositories: qrmdata'; I also added 'Additional_repositories:
>http://r-forge.r-project.org/' to DESCRIPTION but of course
>winbuilder reports errors as it can't find 'qrmdata'.
>
>I'm wondering about what I am supposed to do: Remove everything about
>'qrmdata' from 'qrmtools'? Clearly, the easiest solution, but that's a
>bit dull as the 'qrmtools' can be nicely used to deal with the data
>from 'qrmdata'.
>
>How 'severe' is this issue for vignettes? I guess since they are
>checked as well, one would run into the same problem. But then a
>vignette even more so should show/replicate the functionality of a
>paper, say, and there one would definitely like to work with the
>data...
>
>The only partially related thread I found was
>https://stat.ethz.ch/pipermail/r-package-devel/2015q2/02.html
>
>In any case, I continue to pray to the R gods in the hope that the 5MB
>limit will change for data-related packages (which are updated very
>rarely) at some point in the future... Some 'adaptive limits' would be
>nice: The less often you submit, the larger the data package can be
>(for example), up to a certain larger limit more suitable for
>data-related packages.
>
>Any ideas on (all of) that?
>
>Cheers,
>Marius
>
>__
>R-package-devel@r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-package-devel

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Re: [R-pkg-devel] What's recommended to do on "Suggests or Enhances not in mainstream repositories: ..."?

[Marius Hofert]

On Sat, May 21, 2016 at 7:45 PM, Henrik Bengtsson
 wrote:
> On Sat, May 21, 2016 at 8:22 AM, Marius Hofert
>  wrote:
>> Hi,
>>
>> I have (co-)developed two packages: 'qrmtools' and 'qrmdata'. The
>> latter contains data sets and is currently only available on R-Forge
>> (as it is larger than 5MB and thus not accepted for CRAN [although
>> there are much larger packages, but that's a different story...]).
>> 'qrmtools' contains mainly tools that show what can be done with data
>> such as the one contained in 'qrmdata' -- and thus has 'qrmdata' in
>> Suggests. The check shows 'Suggests or Enhances not in mainstream
>> repositories: qrmdata'; I also added 'Additional_repositories:
>> http://r-forge.r-project.org/' to DESCRIPTION but of course
>> winbuilder reports errors as it can't find 'qrmdata'.
>
> First, there are plenty of CRAN package using:
>
> Additional_repositories: http://r-forge.r-project.org/
>
> is used, cf. 
> https://github.com/search?q=org%3Acran+Additional_repositories%3A+http%3A%2F%2Fr-forge.r-project.org=Code
>
> so this should be ok. I'm using it too.
>
>>
>> I'm wondering about what I am supposed to do: Remove everything about
>> 'qrmdata' from 'qrmtools'? Clearly, the easiest solution, but that's a
>> bit dull as the 'qrmtools' can be nicely used to deal with the data
>> from 'qrmdata'.
>
> It sounds that one of your vignettes, examples or package tests
> requires the qrmdata package.  It is ok to use:
>
> Suggests: qrmdata
>
> but then you should make sure it is truly optional throughout, i.e. use
>
> if (require("qrmdata")) {
>   ## Use qrmdata functions here
> }

Hi Henrik,

Thanks a lot. That's indeed a good idea.

Cheers,
Marius


>
> in your tests, examples etc.
>
> This is common practice. See also Writing R Extensions.
>
> Maybe there's something else to it?  It would help clarify your
> problem if we could see the R CMD check issues and the code (online
> repository?).
>
> My $.02
>
> Henrik
>
>>
>> How 'severe' is this issue for vignettes? I guess since they are
>> checked as well, one would run into the same problem. But then a
>> vignette even more so should show/replicate the functionality of a
>> paper, say, and there one would definitely like to work with the
>> data...
>>
>> The only partially related thread I found was
>> https://stat.ethz.ch/pipermail/r-package-devel/2015q2/02.html
>>
>> In any case, I continue to pray to the R gods in the hope that the 5MB
>> limit will change for data-related packages (which are updated very
>> rarely) at some point in the future... Some 'adaptive limits' would be
>> nice: The less often you submit, the larger the data package can be
>> (for example), up to a certain larger limit more suitable for
>> data-related packages.
>>
>> Any ideas on (all of) that?
>>
>> Cheers,
>> Marius
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel

__
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Re: [R-pkg-devel] What's recommended to do on "Suggests or Enhances not in mainstream repositories: ..."?

[Henrik Bengtsson]

On Sat, May 21, 2016 at 8:22 AM, Marius Hofert
 wrote:
> Hi,
>
> I have (co-)developed two packages: 'qrmtools' and 'qrmdata'. The
> latter contains data sets and is currently only available on R-Forge
> (as it is larger than 5MB and thus not accepted for CRAN [although
> there are much larger packages, but that's a different story...]).
> 'qrmtools' contains mainly tools that show what can be done with data
> such as the one contained in 'qrmdata' -- and thus has 'qrmdata' in
> Suggests. The check shows 'Suggests or Enhances not in mainstream
> repositories: qrmdata'; I also added 'Additional_repositories:
> http://r-forge.r-project.org/' to DESCRIPTION but of course
> winbuilder reports errors as it can't find 'qrmdata'.

First, there are plenty of CRAN package using:

Additional_repositories: http://r-forge.r-project.org/

is used, cf. 
https://github.com/search?q=org%3Acran+Additional_repositories%3A+http%3A%2F%2Fr-forge.r-project.org=Code

so this should be ok. I'm using it too.

>
> I'm wondering about what I am supposed to do: Remove everything about
> 'qrmdata' from 'qrmtools'? Clearly, the easiest solution, but that's a
> bit dull as the 'qrmtools' can be nicely used to deal with the data
> from 'qrmdata'.

It sounds that one of your vignettes, examples or package tests
requires the qrmdata package.  It is ok to use:

Suggests: qrmdata

but then you should make sure it is truly optional throughout, i.e. use

if (require("qrmdata")) {
  ## Use qrmdata functions here
}

in your tests, examples etc.

This is common practice. See also Writing R Extensions.

Maybe there's something else to it?  It would help clarify your
problem if we could see the R CMD check issues and the code (online
repository?).

My $.02

Henrik

>
> How 'severe' is this issue for vignettes? I guess since they are
> checked as well, one would run into the same problem. But then a
> vignette even more so should show/replicate the functionality of a
> paper, say, and there one would definitely like to work with the
> data...
>
> The only partially related thread I found was
> https://stat.ethz.ch/pipermail/r-package-devel/2015q2/02.html
>
> In any case, I continue to pray to the R gods in the hope that the 5MB
> limit will change for data-related packages (which are updated very
> rarely) at some point in the future... Some 'adaptive limits' would be
> nice: The less often you submit, the larger the data package can be
> (for example), up to a certain larger limit more suitable for
> data-related packages.
>
> Any ideas on (all of) that?
>
> Cheers,
> Marius
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

__
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[R-pkg-devel] What's recommended to do on "Suggests or Enhances not in mainstream repositories: ..."?

[Marius Hofert]

Hi,

I have (co-)developed two packages: 'qrmtools' and 'qrmdata'. The
latter contains data sets and is currently only available on R-Forge
(as it is larger than 5MB and thus not accepted for CRAN [although
there are much larger packages, but that's a different story...]).
'qrmtools' contains mainly tools that show what can be done with data
such as the one contained in 'qrmdata' -- and thus has 'qrmdata' in
Suggests. The check shows 'Suggests or Enhances not in mainstream
repositories: qrmdata'; I also added 'Additional_repositories:
http://r-forge.r-project.org/' to DESCRIPTION but of course
winbuilder reports errors as it can't find 'qrmdata'.

I'm wondering about what I am supposed to do: Remove everything about
'qrmdata' from 'qrmtools'? Clearly, the easiest solution, but that's a
bit dull as the 'qrmtools' can be nicely used to deal with the data
from 'qrmdata'.

How 'severe' is this issue for vignettes? I guess since they are
checked as well, one would run into the same problem. But then a
vignette even more so should show/replicate the functionality of a
paper, say, and there one would definitely like to work with the
data...

The only partially related thread I found was
https://stat.ethz.ch/pipermail/r-package-devel/2015q2/02.html

In any case, I continue to pray to the R gods in the hope that the 5MB
limit will change for data-related packages (which are updated very
rarely) at some point in the future... Some 'adaptive limits' would be
nice: The less often you submit, the larger the data package can be
(for example), up to a certain larger limit more suitable for
data-related packages.

Any ideas on (all of) that?

Cheers,
Marius

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