[R-pkg-devel] The Help (e.g. links) is not working for my packages

David.Kaethner at dlr.de David.Kaethner at dlr.de
Thu Aug 10 19:34:45 CEST 2017 

sorry, I got sloppy - I had played around before with the DESCRIPTION file, that does not seem to be the culprit. But you are right of course, it should run without warnings in any case.



* using log directory ‘/Users/spaceicons/code/R_package_dev/helpers2/helpers2.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘helpers2/DESCRIPTION’ ... OK
* this is package ‘helpers2’ version ‘0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘helpers2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK



________________________________
Von: Dason Kurkiewicz [dasonk at gmail.com]
Gesendet: Donnerstag, 10. August 2017 18:42
An: Käthner, David
Cc: Duncan Murdoch; R package devel; edd at debian.org; lists at dewey.myzen.co.uk
Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages

It tells you what the warning is. You need to specify a license in your DESCRIPTION file. You should really fill the entire thing out properly anyways.

On Aug 10, 2017 12:39 PM, <David.Kaethner at dlr.de<mailto:David.Kaethner at dlr.de>> wrote:
Thank you for pointing that out, this solved the ERROR in the R CMD check. I've updated the repo.

Unfortunately, it did not solve the problem. So when you clone/pull the repo now, the error should persist.


* using log directory ‘/Users/spaceicons/code/R_package_dev/helpers2/helpers2.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘helpers2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘helpers2’ version ‘0.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘helpers2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  What license is it under?
Standardizable: FALSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING



________________________________________
Von: Michael Dewey [lists at dewey.myzen.co.uk<mailto:lists at dewey.myzen.co.uk>]
Gesendet: Donnerstag, 10. August 2017 17:38
An: Käthner, David; edd at debian.org<mailto:edd at debian.org>; murdoch.duncan at gmail.com<mailto:murdoch.duncan at gmail.com>
Cc: r-package-devel at r-project.org<mailto:r-package-devel at r-project.org>
Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages

Your log says you have no examples but you do in your Rd file.
Your examples look the wrong way round x(function) rather than function(x)

Not sure whether those are relevant issues but perhaps they help.

On 10/08/2017 15:47, David.Kaethner at dlr.de<mailto:David.Kaethner at dlr.de> wrote:
> Thank you for the replies!
>
> First of all, here is the test package:
>     https://github.com/c06n/helpers2
>
> Session info and the log of R CMD check at the end. There is an error: "LaTeX errors when creating PDF version." However, it says "checking Rd files ... OK".
>
> I have tried the install now on 4 different computers (via devtools::install_github), they all did not work.
>
> Further points:
> - Unfortunately, installation from a tarball did not work either. I build the tarball from the command line (Cygwin), then used R CMD, but tried it also from within RStudio ("Build Source Package", then "install.packages")
> - I have managed to create another package WHICH WORKS. I have not been able to do it again though, I just don't know what I did differently.
> - I played around with the documentation lines in the test package, to no avail.
>
> I am sure that it is something very minor where I went wrong, and in all likelihood the problem is on my side. I just cannot figure out what it might be.
>
> David
>
> -----
>> sessionInfo()
> R version 3.4.1 (2017-06-30)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
> [5] LC_TIME=German_Germany.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] _0.1.0
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.1 tools_3.4.1
>
> --------
> * using log directory '/cygdrive/d/Home/projects/R_package_dev/helpers2.Rcheck'
> * using R version 3.4.0 (2017-04-21)
> * using platform: x86_64-unknown-cygwin (64-bit)
> * using session charset: ISO8859-1
> * checking for file 'helpers2/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'helpers2' version '0.1.0'
> * package encoding: UTF-8
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking for hidden files and directories ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking whether package 'helpers2' can be installed ... OK
> * checking installed package size ... OK
> * checking package directory ... OK
> * checking DESCRIPTION meta-information ... WARNING
> Non-standard license specification:
>   testlicense
> Standardizable: FALSE
> * checking top-level files ... OK
> * checking for left-over files ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking R files for non-ASCII characters ... OK
> * checking R files for syntax errors ... OK
> * checking whether the package can be loaded ... OK
> * checking whether the package can be loaded with stated dependencies ... OK
> * checking whether the package can be unloaded cleanly ... OK
> * checking whether the namespace can be loaded with stated dependencies ... OK
> * checking whether the namespace can be unloaded cleanly ... OK
> * checking loading without being on the library search path ... OK
> * checking dependencies in R code ... OK
> * checking S3 generic/method consistency ... OK
> * checking replacement functions ... OK
> * checking foreign function calls ... OK
> * checking R code for possible problems ... OK
> * checking Rd files ... OK
> * checking Rd metadata ... OK
> * checking Rd cross-references ... OK
> * checking for missing documentation entries ... OK
> * checking for code/documentation mismatches ... OK
> * checking Rd \usage sections ... OK
> * checking Rd contents ... OK
> * checking for unstated dependencies in examples ... OK
> * checking examples ... NONE
> * checking PDF version of manual ... WARNING
> LaTeX errors when creating PDF version.
> This typically indicates Rd problems.
> * checking PDF version of manual without hyperrefs or index ... ERROR
> * DONE
> Status: 1 ERROR, 2 WARNINGs
>
>
>
>
>
>
>
>
>
>
>
>
> -----Ursprüngliche Nachricht-----
> Von: Dirk Eddelbuettel [mailto:dirk.eddelbuettel at gmail.com<mailto:dirk.eddelbuettel at gmail.com>] Im Auftrag von Dirk Eddelbuettel
> Gesendet: Donnerstag, 10. August 2017 14:32
> An: Duncan Murdoch
> Cc: Käthner, David; r-package-devel at r-project.org<mailto:r-package-devel at r-project.org>
> Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages
>
>
> On 9 August 2017 at 08:38, Duncan Murdoch wrote:
> | Nothing that you've written is reproducible by others.  See if you can
> | put together a short self-contained series of instructions that
> | display the problems (or just one of them).  It might involve
> | installing from Github, or making a package tarball available somewhere.
>
> I am fairly certain I have observed this myself, and I *think* it simply stems from running R CMD INSTALL (and alike) from a source directory, as opposed to a tarball.  I filed it under minor nuisance and didn't care too much either as the official two-step of 'R CMD build ...; R CMD INSTALL ...'
> is just that: the official and recommended way. With which things work.
>
> Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org<mailto:edd at debian.org>
>
> ______________________________________________
> R-package-devel at r-project.org<mailto:R-package-devel at r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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>
>

--
Michael
http://www.dewey.myzen.co.uk/home.html

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