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

2017-08-07 Thread David.Kaethner
Hello,



I am hoping to post to the right mailing list, if not apologies!



I have recently written my first couple packages, relying on devtools and 
roxygen. Everything is done in RStudio (details regarding the setup: see end of 
text).



But the help is not working! Specifically:



On Windows 7:

* functions: I cannot click the links in the 'help'-panel. Or at least nothing 
happens when I click them.

* DESCRIPTION: If I build the package locally, it has the same issues as the 
packages. If I install the packages from Github (devtools::install_github) or 
from a network drive, it works.

* The "my_package::my_function" syntax throws an error. Once I enter 
'my_package::' and click TAB, the following error appears in the console: 
"Error in gzfile(file, "rb") : cannot open the connection"

* "?my_package::my_function" brings me to the function overview page for the 
package, but not to the help page for the my_function()

* the link itself (on the function overview page) looks inocuous: 
http://127.0.0.1:44391/help/library/helpers/html/my_function.html



I would love to do a Traceback on this, but I do not know how, since it only 
happens when hitting TAB. I have done a Traceback for 
"?my_package::my_function", it just returns the path to where the help should 
be, like "D:/Home/R/Rpackages/my_package/help/my_function".



On MacOS Sierra:

* DESCRIPTION can always be opened, no matter how the package is installed

* when clicking on functions in the help panel, the known error appears (as 
text in the help panel): "Error in gzfile(file, "rb") : cannot open the 
connection"



It gets much weirder: When installing the package for the very first time, it 
seems to work! But after that it quits working, even not when I delete the 
package, re-install R, re-install RStudio, and create the package from scratch.



I really wish I was kidding with all of this. I have tried every debugging-idea 
that came to my mind, including (but not limited to):

* the .Rd-files are generated, they definitely are not missing

* taking an auto-generated DESCRIPTION file

* removing every function file save for a test file

* copying content from a function file into the auto-generated "hello.R" file

* changing the encoding from UTF-8 to WINDOWS-1252

* as mentioned, trying everying both on Windows and MacOS, and trying different 
ways of installation

* as mentioned, re-installing both R and RStudio



I would enormously appreciate it if anyone has an idea how to get a handle on 
this, any suggestions are welcome!





David



__

My setup:

* Windows 7 / MacOS Sierra

* R 3.4.1

* RStudio 1.0.153

* devtools 1.13.3

* roxygen2 6.0.1


[[alternative HTML version deleted]]

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

2017-08-10 Thread David.Kaethner
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.eddelbuet...@gmail.com] Im Auftrag von Dirk 
Eddelbuettel
Gesendet: Donnerstag, 10. August 2017 14:32
An: Duncan Murdoch
Cc: Käthner, David; r-package-devel@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: 

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

2017-08-10 Thread David.Kaethner
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 [li...@dewey.myzen.co.uk]
Gesendet: Donnerstag, 10. August 2017 17:38
An: Käthner, David; e...@debian.org; murdoch.dun...@gmail.com
Cc: r-package-devel@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.kaeth...@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

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

2017-08-10 Thread David.Kaethner
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 [das...@gmail.com]
Gesendet: Donnerstag, 10. August 2017 18:42
An: K�thner, David
Cc: Duncan Murdoch; R package devel; e...@debian.org; li...@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, mailto:david.kaeth...@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 ..

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

2017-08-14 Thread David.Kaethner
Hello,

for the archive: I believe I found the solution, validated on Win7 and MacOS.

This error occurs for any package that starts with "help". So "hell" is ok, 
"help12345" is not ok as a package name.

Is this documented behavior? Apologies if I missed that.


-Ursprüngliche Nachricht-
Von: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] 
Gesendet: Mittwoch, 9. August 2017 14:39
An: Käthner, David; r-package-devel@r-project.org
Betreff: Re: [R-pkg-devel] The Help (e.g. links) is not working for my packages

On 07/08/2017 3:41 AM, david.kaeth...@dlr.de wrote:
> Hello,
>
>
>
> I am hoping to post to the right mailing list, if not apologies!
>
>
>
> I have recently written my first couple packages, relying on devtools and 
> roxygen. Everything is done in RStudio (details regarding the setup: see end 
> of text).
>
>
>
> But the help is not working! Specifically:
>
>
>
> On Windows 7:
>
> * functions: I cannot click the links in the 'help'-panel. Or at least 
> nothing happens when I click them.
>
> * DESCRIPTION: If I build the package locally, it has the same issues as the 
> packages. If I install the packages from Github (devtools::install_github) or 
> from a network drive, it works.
>
> * The "my_package::my_function" syntax throws an error. Once I enter 
> 'my_package::' and click TAB, the following error appears in the console: 
> "Error in gzfile(file, "rb") : cannot open the connection"
>
> * "?my_package::my_function" brings me to the function overview page 
> for the package, but not to the help page for the my_function()
>
> * the link itself (on the function overview page) looks inocuous: 
> http://127.0.0.1:44391/help/library/helpers/html/my_function.html
>
>
>
> I would love to do a Traceback on this, but I do not know how, since it only 
> happens when hitting TAB. I have done a Traceback for 
> "?my_package::my_function", it just returns the path to where the help should 
> be, like "D:/Home/R/Rpackages/my_package/help/my_function".
>
>
>
> On MacOS Sierra:
>
> * DESCRIPTION can always be opened, no matter how the package is 
> installed
>
> * when clicking on functions in the help panel, the known error appears (as 
> text in the help panel): "Error in gzfile(file, "rb") : cannot open the 
> connection"
>
>
>
> It gets much weirder: When installing the package for the very first time, it 
> seems to work! But after that it quits working, even not when I delete the 
> package, re-install R, re-install RStudio, and create the package from 
> scratch.
>
>
>
> I really wish I was kidding with all of this. I have tried every 
> debugging-idea that came to my mind, including (but not limited to):
>
> * the .Rd-files are generated, they definitely are not missing
>
> * taking an auto-generated DESCRIPTION file
>
> * removing every function file save for a test file
>
> * copying content from a function file into the auto-generated 
> "hello.R" file
>
> * changing the encoding from UTF-8 to WINDOWS-1252
>
> * as mentioned, trying everying both on Windows and MacOS, and trying 
> different ways of installation
>
> * as mentioned, re-installing both R and RStudio
>
>
>
> I would enormously appreciate it if anyone has an idea how to get a handle on 
> this, any suggestions are welcome!

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.

Duncan Murdoch

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