Re: [R-pkg-devel] fixing problems in submitted R package

2020-09-04 Thread Duncan Murdoch 

On 04/09/2020 12:41 p.m., Vitor Hugo Moreau wrote:

Hello, all.

I have submitted a R package and it returns some NOTES from the automatic
checks. It is the first time I create and deposit a package so I would like
to know what to do. My package was built with Rstudio and it gave some of
these NOTES too, bby I don't know how to solve them.
These are the NOTES:

1.
The build time stamp is missing.


This is because you didn't use R CMD build to build your package.


2.
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘The package maintainer ’

"I don't even know what is wrong here, this is my professional email.
Should I just ignore it?"


If the text "The package maintainer" is in your DESCRIPTION file, you 
should replace it with your name.




3.
* checking DESCRIPTION meta-information ... NOTE
Checking should be performed on sources prepared by ‘R CMD build’.


Same as 1.



4.
checking R code for possible problems ... [4s/4s] NOTE

likelihood: no visible binding for global variable ‘xi’
likelihood: no visible binding for global variable ‘yi’
weibull4.fit: no visible binding for '<<-' assignment to ‘xi’
weibull4.fit: no visible binding for '<<-' assignment to ‘yi’
weibull4.fit: no visible binding for global variable ‘yi’
weibull4.fit: no visible binding for global variable ‘xi’
Undefined global functions or variables:
   xi yi

"There are two variable defined globally (xi and yi) and they are used
for some - not all - functions. Is this really a problem or can I
ignore it too?"


You can't ignore it.  You need to make sure xi and yi are defined in the 
source of your package, and they shouldn't be the top level if you are 
modifying them. It's possible but tricky to have global in packages, and 
it would be best to just avoid the problem by not having them.


5.
* checking Rd files ... NOTE
prepare_Rd: likelihood.Rd:15-16: Dropping empty section \details
prepare_Rd: likelihood.Rd:25-26: Dropping empty section \note
prepare_Rd: likelihood.Rd:28-29: Dropping empty section \seealso
prepare_Rd: posterior.Rd:17-18: Dropping empty section \details
prepare_Rd: posterior.Rd:28-29: Dropping empty section \note
prepare_Rd: posterior.Rd:31-32: Dropping empty section \seealso
prepare_Rd: prior.Rd:17-18: Dropping empty section \details
prepare_Rd: prior.Rd:28-29: Dropping empty section \note
prepare_Rd: prior.Rd:31-32: Dropping empty section \seealso
prepare_Rd: proposalfunction.Rd:15-16: Dropping empty section \details
prepare_Rd: proposalfunction.Rd:26-27: Dropping empty section \note
prepare_Rd: proposalfunction.Rd:29-30: Dropping empty section \seealso
prepare_Rd: run_metropolis_MCMC.Rd:20-21: Dropping empty section \details
prepare_Rd: run_metropolis_MCMC.Rd:31-32: Dropping empty section \note
prepare_Rd: run_metropolis_MCMC.Rd:34-35: Dropping empty section \seealso
prepare_Rd: weibull4.Rd:37-38: Dropping empty section \seealso
prepare_Rd: weibull4.fit.Rd:57-58: Dropping empty section \seealso

"Is it a real problem to drop some empty sections in some MAN files. These
functions will not be direct used by users"


If they aren't functions that the users will see, then they don't need 
to be exported and documented.


Duncan Murdoch



Thank you a lot and sorry for so basic questions.

Prof. Vitor Hugo Moreau, Ph.D.
Departamento de Biotecnologia
Universidade Federal da Bahia - UFBA

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[R-pkg-devel] fixing problems in submitted R package

2020-09-04 Thread Vitor Hugo Moreau 
Hello, all.

I have submitted a R package and it returns some NOTES from the automatic
checks. It is the first time I create and deposit a package so I would like
to know what to do. My package was built with Rstudio and it gave some of
these NOTES too, bby I don't know how to solve them.
These are the NOTES:

1.
The build time stamp is missing.

2.
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘The package maintainer ’

"I don't even know what is wrong here, this is my professional email.
Should I just ignore it?"

3.
* checking DESCRIPTION meta-information ... NOTE
Checking should be performed on sources prepared by ‘R CMD build’.

4.
checking R code for possible problems ... [4s/4s] NOTE

likelihood: no visible binding for global variable ‘xi’
likelihood: no visible binding for global variable ‘yi’
weibull4.fit: no visible binding for '<<-' assignment to ‘xi’
weibull4.fit: no visible binding for '<<-' assignment to ‘yi’
weibull4.fit: no visible binding for global variable ‘yi’
weibull4.fit: no visible binding for global variable ‘xi’
Undefined global functions or variables:
  xi yi

"There are two variable defined globally (xi and yi) and they are used
for some - not all - functions. Is this really a problem or can I
ignore it too?"

5.
* checking Rd files ... NOTE
prepare_Rd: likelihood.Rd:15-16: Dropping empty section \details
prepare_Rd: likelihood.Rd:25-26: Dropping empty section \note
prepare_Rd: likelihood.Rd:28-29: Dropping empty section \seealso
prepare_Rd: posterior.Rd:17-18: Dropping empty section \details
prepare_Rd: posterior.Rd:28-29: Dropping empty section \note
prepare_Rd: posterior.Rd:31-32: Dropping empty section \seealso
prepare_Rd: prior.Rd:17-18: Dropping empty section \details
prepare_Rd: prior.Rd:28-29: Dropping empty section \note
prepare_Rd: prior.Rd:31-32: Dropping empty section \seealso
prepare_Rd: proposalfunction.Rd:15-16: Dropping empty section \details
prepare_Rd: proposalfunction.Rd:26-27: Dropping empty section \note
prepare_Rd: proposalfunction.Rd:29-30: Dropping empty section \seealso
prepare_Rd: run_metropolis_MCMC.Rd:20-21: Dropping empty section \details
prepare_Rd: run_metropolis_MCMC.Rd:31-32: Dropping empty section \note
prepare_Rd: run_metropolis_MCMC.Rd:34-35: Dropping empty section \seealso
prepare_Rd: weibull4.Rd:37-38: Dropping empty section \seealso
prepare_Rd: weibull4.fit.Rd:57-58: Dropping empty section \seealso

"Is it a real problem to drop some empty sections in some MAN files. These
functions will not be direct used by users"

Thank you a lot and sorry for so basic questions.

Prof. Vitor Hugo Moreau, Ph.D.
Departamento de Biotecnologia
Universidade Federal da Bahia - UFBA

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Re: [R-pkg-devel] CRAN, API packages, Keys and tests

2020-09-04 Thread Joshua Ulrich 
On Fri, Sep 4, 2020 at 9:20 AM Joshua Ulrich  wrote:
>
> Hi Rainer,
>
> You could set an environment variable with the API key, and only run
> the tests if the variable is set.
>
Sorry, I missed that you're already doing this.  I confirm that it
works for CRAN.  I also set my API key as a private/secure variable on
TravisCI, so the tests will run there.

IIRC, testthat does something similar. You could look at that pattern,
since it works on CRAN for many packages.

> Here's an example that I use:
> https://github.com/joshuaulrich/quantmod/blob/master/tests/test_getSymbols.R#L4
>
> Best,
> Josh
>
> On Fri, Sep 4, 2020 at 3:25 AM Rainer M Krug  wrote:
> >
> > I know this has been asked a few times - but I can’t find anything which 
> > might help me.
> >
> > I have a package (https://github.com/rkrug/ROriginStamp) which wraps around 
> > API calls to OriginStamp (https://originstamp.com) to obtain trusted time 
> > stamps.
> >
> > The package works, but the tests are the problem on remote machines.
> >
> > My question is:
> >
> > 1) I have disabled all tests and all examples if there is no environmental 
> > variable set with the API Key - is this OK for CRAN?
> > 2) If not, how can I make this CRAN compliant?
> >
> > Thanks,
> >
> > Rainer
> >
> >
> > --
> > Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
> > UCT), Dipl. Phys. (Germany)
> >
> > Orcid ID: -0002-7490-0066
> >
> > Department of Evolutionary Biology and Environmental Studies
> > University of Zürich
> > Office Y34-J-74
> > Winterthurerstrasse 190
> > 8075 Zürich
> > Switzerland
> >
> > Office: +41 (0)44 635 47 64
> > Cell:   +41 (0)78 630 66 57
> > email:  rainer.k...@uzh.ch
> > rai...@krugs.de
> > Skype: RMkrug
> >
> > PGP: 0x0F52F982
> >
> >
> >
> >
> >
> > --
> > Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
> > UCT), Dipl. Phys. (Germany)
> >
> > Orcid ID: -0002-7490-0066
> >
> > Department of Evolutionary Biology and Environmental Studies
> > University of Zürich
> > Office Y34-J-74
> > Winterthurerstrasse 190
> > 8075 Zürich
> > Switzerland
> >
> > Office: +41 (0)44 635 47 64
> > Cell:   +41 (0)78 630 66 57
> > email:  rainer.k...@uzh.ch
> > rai...@krugs.de
> > Skype: RMkrug
> >
> > PGP: 0x0F52F982
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
>
> --
> Joshua Ulrich  |  about.me/joshuaulrich
> FOSS Trading  |  www.fosstrading.com



-- 
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FOSS Trading  |  www.fosstrading.com

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Re: [R-pkg-devel] CRAN, API packages, Keys and tests

2020-09-04 Thread Joshua Ulrich 
Hi Rainer,

You could set an environment variable with the API key, and only run
the tests if the variable is set.

Here's an example that I use:
https://github.com/joshuaulrich/quantmod/blob/master/tests/test_getSymbols.R#L4

Best,
Josh

On Fri, Sep 4, 2020 at 3:25 AM Rainer M Krug  wrote:
>
> I know this has been asked a few times - but I can’t find anything which 
> might help me.
>
> I have a package (https://github.com/rkrug/ROriginStamp) which wraps around 
> API calls to OriginStamp (https://originstamp.com) to obtain trusted time 
> stamps.
>
> The package works, but the tests are the problem on remote machines.
>
> My question is:
>
> 1) I have disabled all tests and all examples if there is no environmental 
> variable set with the API Key - is this OK for CRAN?
> 2) If not, how can I make this CRAN compliant?
>
> Thanks,
>
> Rainer
>
>
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
> UCT), Dipl. Phys. (Germany)
>
> Orcid ID: -0002-7490-0066
>
> Department of Evolutionary Biology and Environmental Studies
> University of Zürich
> Office Y34-J-74
> Winterthurerstrasse 190
> 8075 Zürich
> Switzerland
>
> Office: +41 (0)44 635 47 64
> Cell:   +41 (0)78 630 66 57
> email:  rainer.k...@uzh.ch
> rai...@krugs.de
> Skype: RMkrug
>
> PGP: 0x0F52F982
>
>
>
>
>
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
> UCT), Dipl. Phys. (Germany)
>
> Orcid ID: -0002-7490-0066
>
> Department of Evolutionary Biology and Environmental Studies
> University of Zürich
> Office Y34-J-74
> Winterthurerstrasse 190
> 8075 Zürich
> Switzerland
>
> Office: +41 (0)44 635 47 64
> Cell:   +41 (0)78 630 66 57
> email:  rainer.k...@uzh.ch
> rai...@krugs.de
> Skype: RMkrug
>
> PGP: 0x0F52F982
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel



-- 
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FOSS Trading  |  www.fosstrading.com

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Re: [R-pkg-devel] Submission to CRAN Contributed Documentation

2020-09-04 Thread Stefan Evert 
Did you read the notice

Note: The CRAN area for contributed documentation is frozen and no 
longer actively maintained

at the top of that page?

Best,
Stefan


> On 4 Sep 2020, at 14:43, Jakub Nowosad  wrote:
> 
> Dear all,
> 
> I have tried to submit a textbook to the CRAN Contributed Documentation
> (https://cran.r-project.org/other-docs.html#nenglish).
> 
> However, the instruction on how to do that are vague. The Contributed
> Documentation page states "To submit, follow the submission instructions
> on the CRAN main page.", however, it is impossible to upload non-R
> package using the standard way (https://cran.r-project.org/submit.html).
> Therefore, I decided to follow another CRAN suggestion "If this fails,
> upload toftp://CRAN.R-project.org/incoming/  and send an email to
> cran-submissi...@r-project.org    
> following the policy.", uploaded the PDF to CRAN incoming FTP and wrote
> an email several days ago. I did not get any answers back.
> 
> Could you suggest me a proper way how to add a document to the CRAN
> Contributed Documentation?
> 
> Best,
> 
> Jakub Nowosad
> 
> -- 
> https://nowosad.github.io/ | @jakub_nowosad | nowosad.ja...@gmail.com
> 
> __
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[R-pkg-devel] Submission to CRAN Contributed Documentation

2020-09-04 Thread Jakub Nowosad 

Dear all,

I have tried to submit a textbook to the CRAN Contributed Documentation
(https://cran.r-project.org/other-docs.html#nenglish).

However, the instruction on how to do that are vague. The Contributed
Documentation page states "To submit, follow the submission instructions
on the CRAN main page.", however, it is impossible to upload non-R
package using the standard way (https://cran.r-project.org/submit.html).
Therefore, I decided to follow another CRAN suggestion "If this fails,
upload toftp://CRAN.R-project.org/incoming/  and send an email to
cran-submissi...@r-project.org    
following the policy.", uploaded the PDF to CRAN incoming FTP and wrote

an email several days ago. I did not get any answers back.

Could you suggest me a proper way how to add a document to the CRAN
Contributed Documentation?

Best,

Jakub Nowosad

--
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Re: [R-pkg-devel] Can these two notes be safely ignored?

2020-09-04 Thread Ben Bolker 
Yes

On Fri, Sep 4, 2020, 6:55 AM David Pleydell  wrote:

> Hi
>
>
> I've a package that I'd like to submit to CRAN.  When I run the command
> rhub::check_for_cran()  the checks on both Windows and Ubuntu virtual
> machines send me emails with the following two notes...
>
>
> * checking CRAN incoming feasibility ... NOTE
>
> Maintainer: 'David Pleydell '
> New submission
>
> * checking for future file timestamps ... NOTE
> unable to verify current time
>
>
> Could you please confirm my best-guess that I can safely ignore these
> notes: the first is just printing out correct information that is contained
> within the DESCRIPTION file. The second is related to a time check being
> performed on a website that is currently down - and so a check on any
> package would currently generate the same note.
>
>
> Many thanks
>
> David
>
>
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>
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[R-pkg-devel] Can these two notes be safely ignored?

2020-09-04 Thread David Pleydell 
Hi


I've a package that I'd like to submit to CRAN.  When I run the command  
rhub::check_for_cran()  the checks on both Windows and Ubuntu virtual machines 
send me emails with the following two notes...


* checking CRAN incoming feasibility ... NOTE

Maintainer: 'David Pleydell '
New submission

* checking for future file timestamps ... NOTE
unable to verify current time


Could you please confirm my best-guess that I can safely ignore these notes: 
the first is just printing out correct information that is contained within the 
DESCRIPTION file. The second is related to a time check being performed on a 
website that is currently down - and so a check on any package would currently 
generate the same note.


Many thanks

David


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[R-pkg-devel] CRAN, API packages, Keys and tests

2020-09-04 Thread Rainer M Krug 
I know this has been asked a few times - but I can’t find anything which might 
help me.

I have a package (https://github.com/rkrug/ROriginStamp) which wraps around API 
calls to OriginStamp (https://originstamp.com) to obtain trusted time stamps.

The package works, but the tests are the problem on remote machines.

My question is:

1) I have disabled all tests and all examples if there is no environmental 
variable set with the API Key - is this OK for CRAN?
2) If not, how can I make this CRAN compliant?

Thanks,

Rainer


--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Orcid ID: -0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland

Office: +41 (0)44 635 47 64
Cell:   +41 (0)78 630 66 57
email:  rainer.k...@uzh.ch
rai...@krugs.de
Skype: RMkrug

PGP: 0x0F52F982





--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Orcid ID: -0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland

Office: +41 (0)44 635 47 64
Cell:   +41 (0)78 630 66 57
email:  rainer.k...@uzh.ch
rai...@krugs.de
Skype: RMkrug

PGP: 0x0F52F982

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