[R-pkg-devel] Best practise in including third party code

[Wolfgang Lenhard]

Dear R developer list,
in general, if functionality from other packages are used in one's own 
package, it is of course the best way to declare the other package as an 
import. What is the straight forward way for only minor functions or 
functionality, especially when the other package comes with a lot 
dependencies itself? Is it advisable or ok to only use the according 
third party source code snippet and cite the other package (of course if 
the license of the package allows it; own package is AGPL, third package 
is GPL)? Or should the third party package always be installed as a 
dependency? I want to avoid bloating the installation process but it is 
very important for me not to violate academic standards, intellectual 
properties and best practise.


Thanks,
Wolfgang

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Re: [R-pkg-devel] How to submit to CRAN from GitHub?

[Wolfgang Lenhard]

Dear Spencer,
release: not directly, but via devtools in RStudio. Please have a look 
at the fantastic description from Hadley Wickham: 
http://r-pkgs.had.co.nz/release.html


Best,
    Wolfgang

Am 22.09.19 um 20:33 schrieb Spencer Graves:

Hello:


    Two questions:


HOW TO SUBMIT TO CRAN FROM GITHUB:  Is there a standard method for
submitting to CRAN from GitHub?  (There's a simple protocol for
submitting to CRAN from R-Forge, but I've experienced insurmountable
problems using R-Forge recently.)


PACKAGE STILL FAILING TRAVIS CI:  The latest report from
bui...@travis-ci.org on my Ecdat package for R on GitHub ends with
"Found warnings, treating as errors (as requested)."  The word "warning"
appears in that report over 100 times.  I didn't see anything there that
suggested to me anything I understand how to change.


NOTE:  "R CMD build Ecdat --resave-data" followed by "R CMD check
Ecdat_0.3.3-tar.gz" completed with no errors, warnings or notes under
macOS 10.14.6 and Windows 7 and 10.


    Thanks,
    Spencer Graves


 Forwarded Message 
Subject:Still Failing: sbgraves237/Ecdat#9 (master - c680f08)
Date:   Sun, 22 Sep 2019 15:21:08 +
From:   Travis CI 
To: spencer.gra...@effectivedefense.org



sbgraves237

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Ecdat




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Re: [R-pkg-devel] References in package description file

[Wolfgang Lenhard]

Fantastic! Thanks!

Am 16.09.2019 um 10:05 schrieb David Hugh-Jones:
> Hi Wolfgang,
>
> You can use the CITATION file. See ?citation and ?bibentry.
>
> Cheers,
> David
>
>
> On Mon, 16 Sep 2019 at 08:55, Wolfgang Lenhard 
>  <mailto:wolfgang.lenh...@uni-wuerzburg.de>> wrote:
>
> Hello world,
> is there a standard way of adding references (scientific papers
> ...) to
> the description file in R packages other than putting the DOI in the
> description text? Does a best practise exist on how much
> references are
> advisable in order not to clutter the package information? Or
> should I
> put these things in the vignette instead?
>
> Thanks and best regards,
>  Wolfgang
>
> __
> R-package-devel@r-project.org
> <mailto:R-package-devel@r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

-- 
Prof. Dr. Wolfgang Lenhard
Lehrstuhl Psychologie IV
Raum 02.130
Wittelsbacherplatz 1
D-97070 Würzburg

Tel.: 0931 3189791
FAX:  0931 3184891
URL:  https://go.uniwue.de/lenhard
Map:  https://go.uni-wuerzburg.de/3b


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[R-pkg-devel] References in package description file

[Wolfgang Lenhard]

Hello world,
is there a standard way of adding references (scientific papers ...) to 
the description file in R packages other than putting the DOI in the 
description text? Does a best practise exist on how much references are 
advisable in order not to clutter the package information? Or should I 
put these things in the vignette instead?


Thanks and best regards,
    Wolfgang

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Re: [R-pkg-devel] Package update submission to CRAN fails on pretest

[Wolfgang Lenhard]

Dear Hadley,
many thanks for your comment and much more for your fantastic tutorial 
and packages! I essentially learned (and still learn) package 
development by your tutorial. In the concrete case, changing some 
settings finally did it and devtools worked like charm. I want to thank 
you for your really great work.


There was a strange thing, though, that I do not yet understand. The 
submission failed on some systems (fedora and Mac OS X; not on Win and 
Ubuntu) because of errors building the vignette. Adding rmarkdown to 
imports in the description file solved the pretest rejection and the new 
version of cNORM is on CRAN, but now, I have the following note:

checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.


Apart from the note, it works now. Maybe, I remove the code from the 
vignette in future releases and.


Best regards,
Wolfgang

Am 08.12.2018 um 15:31 schrieb Hadley Wickham:

You might try reinstalling devtools and dependencies - there was
unfortunately a brief combination of versions that lead to build()
failing to overwrite existing files.

Hadley
On Fri, Dec 7, 2018 at 10:46 AM Wolfgang Lenhard
 wrote:

Many thanks for the remark. It seems, it has something to do with
submitting via the devtools (maybe I did something wrong with tagging
the prior release). Submitting it manually at least does not result in
pretest rejection. I guess there is something out of sync which resulted
in rechecking and old version.

Am 07.12.2018 um 13:46 schrieb Georgi Boshnakov:

The link you gave, 
https://cran.r-project.org/web/checks/check_results_cNORM.html,
is to the check results for the package currently on CRAN and it is indeed v. 
1.0.1
(it is linked from https://CRAN.R-project.org/package=cNORM).

Was this really the link you got from CRAN's pretest? Sometimes they ask if 
care has been taken about NOTEs/WARNINGs for the current CRAN version, since 
some tests are not done during submission, but this doesn't seem the case here.

Georgi Boshnakov


-Original Message-
From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf 
Of Wolfgang Lenhard
Sent: 07 December 2018 07:55
To: r-package-devel@r-project.org
Subject: [R-pkg-devel] Package update submission to CRAN fails on pretest

Dear list,
I am getting problems when trying to submit an update of the package
cNORM to CRAN. I am developing the package with RStudio and devtools and
I am using Travis for automatic testing. The package is tested locally
on Win10 and Mac OS X and on Travis with Ubuntu and Mac both for
development and release versions of R. All local tests and tests on
Travis work flawlessly - no errors, warning or notes. When submitting to
CRAN, a note and an error show up on some of the Linux OS (Fedora &
Solaris) and Mac OS X, while others display an 'OK' (Win, Debian). The
results: https://cran.r-project.org/web/checks/check_results_cNORM.html

- error: This seems to be related to the vignette with the following
message:

* checking examples ... ERROR
Running examples in ‘cNORM-Ex.R’ failed

I can however not identify the location of the error

- Note: Check: data for non-ASCII characters

The strange thing is: I checked all data files multiple times. They
mainly consist of data.frames with numerics and all colnames  are ASCII.
I am not able to replicate the issue. The same is true for the error,
which does not show up on Travis and as well locally. And finally, the
results state, that the version of the package is 1.0.1, which had been
the first submission to CRAN a month ago. The current version of the
package is 1.1.1. Could this be the reason for the problem?

Do you have an idea how to progress with the testing or how to locate
the errors? Any help is welcome.

Best regards,
   Wolfgang Lenhard


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--
Prof. Dr. Wolfgang Lenhard
Lehrstuhl Psychologie IV
Raum 02.130
Wittelsbacherplatz 1
D-97070 Würzburg

Tel.: 0931 3189791
FAX:  0931 3184891
URL:  https://go.uniwue.de/lenhard
Map:  https://go.uni-wuerzburg.de/3b

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Re: [R-pkg-devel] Package update submission to CRAN fails on pretest

[Wolfgang Lenhard]

Thanks for pointing that out. I rebuilt everything from scratch. Indeed 
I thought, there were no UTF-8 encodings in the data and neither Travis, 
checking it locally and R-Hub (all kinds of OS) resulted in errors.


Am 07.12.2018 um 13:58 schrieb peter dalgaard:

Hmm, no ERRORs in the CRAN checks at this moment?

Re. utf-8, on Mac OS, the CRAN checks have a note about 90 strings marked as 
utf8.

I see 57 of them in



life$Country[Encoding(life$Country)!="unknown"]

  [1] "Korea, Dem. People’s Rep." "Korea, Dem. People’s Rep."
  [3] "Korea, Dem. People’s Rep." "Korea, Dem. People’s Rep."
  [5] "Korea, Dem. People’s Rep." "Korea, Dem. People’s Rep."
...

and 32 more in "mortality". You go find the remaining 1...

This seems to be an issue with the quote symbol:



u <- life$Country[Encoding(life$Country)!="unknown"][1]
Encoding(u)

[1] "UTF-8"

Encoding(u) <- "bytes"
u

[1] "Korea, Dem. People\\xe2\\x80\\x99s Rep."


I have no clue why this is not an issue on only some platforms.

-pd



On 7 Dec 2018, at 08:54 , Wolfgang Lenhard  
wrote:

Dear list,
I am getting problems when trying to submit an update of the package
cNORM to CRAN. I am developing the package with RStudio and devtools and
I am using Travis for automatic testing. The package is tested locally
on Win10 and Mac OS X and on Travis with Ubuntu and Mac both for
development and release versions of R. All local tests and tests on
Travis work flawlessly - no errors, warning or notes. When submitting to
CRAN, a note and an error show up on some of the Linux OS (Fedora &
Solaris) and Mac OS X, while others display an 'OK' (Win, Debian). The
results: https://cran.r-project.org/web/checks/check_results_cNORM.html

- error: This seems to be related to the vignette with the following
message:

* checking examples ... ERROR
Running examples in ‘cNORM-Ex.R’ failed

I can however not identify the location of the error

- Note: Check: data for non-ASCII characters

The strange thing is: I checked all data files multiple times. They
mainly consist of data.frames with numerics and all colnames  are ASCII.
I am not able to replicate the issue. The same is true for the error,
which does not show up on Travis and as well locally. And finally, the
results state, that the version of the package is 1.0.1, which had been
the first submission to CRAN a month ago. The current version of the
package is 1.1.1. Could this be the reason for the problem?

Do you have an idea how to progress with the testing or how to locate
the errors? Any help is welcome.

Best regards,
 Wolfgang Lenhard


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--
Prof. Dr. Wolfgang Lenhard
Lehrstuhl Psychologie IV
Raum 02.130
Wittelsbacherplatz 1
D-97070 Würzburg

Tel.: 0931 3189791
FAX:  0931 3184891
URL:  https://go.uniwue.de/lenhard
Map:  https://go.uni-wuerzburg.de/3b

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Re: [R-pkg-devel] Package update submission to CRAN fails on pretest

[Wolfgang Lenhard]

Many thanks for the remark. It seems, it has something to do with 
submitting via the devtools (maybe I did something wrong with tagging 
the prior release). Submitting it manually at least does not result in 
pretest rejection. I guess there is something out of sync which resulted 
in rechecking and old version.


Am 07.12.2018 um 13:46 schrieb Georgi Boshnakov:

The link you gave, 
https://cran.r-project.org/web/checks/check_results_cNORM.html,
is to the check results for the package currently on CRAN and it is indeed v. 
1.0.1
(it is linked from https://CRAN.R-project.org/package=cNORM).

Was this really the link you got from CRAN's pretest? Sometimes they ask if 
care has been taken about NOTEs/WARNINGs for the current CRAN version, since 
some tests are not done during submission, but this doesn't seem the case here.

Georgi Boshnakov


-Original Message-
From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf 
Of Wolfgang Lenhard
Sent: 07 December 2018 07:55
To: r-package-devel@r-project.org
Subject: [R-pkg-devel] Package update submission to CRAN fails on pretest

Dear list,
I am getting problems when trying to submit an update of the package
cNORM to CRAN. I am developing the package with RStudio and devtools and
I am using Travis for automatic testing. The package is tested locally
on Win10 and Mac OS X and on Travis with Ubuntu and Mac both for
development and release versions of R. All local tests and tests on
Travis work flawlessly - no errors, warning or notes. When submitting to
CRAN, a note and an error show up on some of the Linux OS (Fedora &
Solaris) and Mac OS X, while others display an 'OK' (Win, Debian). The
results: https://cran.r-project.org/web/checks/check_results_cNORM.html

- error: This seems to be related to the vignette with the following
message:

* checking examples ... ERROR
Running examples in ‘cNORM-Ex.R’ failed

I can however not identify the location of the error

- Note: Check: data for non-ASCII characters

The strange thing is: I checked all data files multiple times. They
mainly consist of data.frames with numerics and all colnames  are ASCII.
I am not able to replicate the issue. The same is true for the error,
which does not show up on Travis and as well locally. And finally, the
results state, that the version of the package is 1.0.1, which had been
the first submission to CRAN a month ago. The current version of the
package is 1.1.1. Could this be the reason for the problem?

Do you have an idea how to progress with the testing or how to locate
the errors? Any help is welcome.

Best regards,
      Wolfgang Lenhard


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--
Prof. Dr. Wolfgang Lenhard
Lehrstuhl Psychologie IV
Raum 02.130
Wittelsbacherplatz 1
D-97070 Würzburg

Tel.: 0931 3189791
FAX:  0931 3184891
URL:  https://go.uniwue.de/lenhard
Map:  https://go.uni-wuerzburg.de/3b

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[R-pkg-devel] Package update submission to CRAN fails on pretest

[Wolfgang Lenhard]

Dear list,
I am getting problems when trying to submit an update of the package 
cNORM to CRAN. I am developing the package with RStudio and devtools and 
I am using Travis for automatic testing. The package is tested locally 
on Win10 and Mac OS X and on Travis with Ubuntu and Mac both for 
development and release versions of R. All local tests and tests on 
Travis work flawlessly - no errors, warning or notes. When submitting to 
CRAN, a note and an error show up on some of the Linux OS (Fedora & 
Solaris) and Mac OS X, while others display an 'OK' (Win, Debian). The 
results: https://cran.r-project.org/web/checks/check_results_cNORM.html

- error: This seems to be related to the vignette with the following 
message:
> * checking examples ... ERROR
> Running examples in ‘cNORM-Ex.R’ failed
I can however not identify the location of the error

- Note: Check: data for non-ASCII characters

The strange thing is: I checked all data files multiple times. They 
mainly consist of data.frames with numerics and all colnames  are ASCII. 
I am not able to replicate the issue. The same is true for the error, 
which does not show up on Travis and as well locally. And finally, the 
results state, that the version of the package is 1.0.1, which had been 
the first submission to CRAN a month ago. The current version of the 
package is 1.1.1. Could this be the reason for the problem?

Do you have an idea how to progress with the testing or how to locate 
the errors? Any help is welcome.

Best regards,
     Wolfgang Lenhard


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