[R-pkg-devel] GitHub Action failed re-building 'sos.Rnw'

[Duncan Murdoch]

For ks, if you look here: 
https://github.com/sbgraves237/sos/runs/2650960959?check_suite_focus=true

in the "Install Dependencies" section, you'll see these errors:

trying URL 'https://cloud.r-project.org/src/contrib/ks_1.13.0.tar.gz'
Content type 'application/x-gzip' length 1076044 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

* installing *source* package ‘plot3D’ ...
** package ‘plot3D’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: Error: .onLoad failed in loadNamespace() for 'tcltk', details:
ERROR: lazy loading failed for package ‘plot3D’
   call: fun(libname, pkgname)
* removing ‘/Users/runner/work/_temp/Library/plot3D’
   error: X11 library is missing: install XQuartz from www.xquartz.org
Execution halted
ERROR: dependency ‘plot3D’ is not available for package ‘ks’
* removing ‘/Users/runner/work/_temp/Library/ks’

so the problem is really with plot3D, and indirectly with rgl and tcltk. 
I'm familiar with problems like that!  Here are the lines from the rgl 
workflow to work around the XQuartz issues:

     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       _R_CHECK_FORCE_SUGGESTS_: false
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       RGL_USE_NULL: true

The last line might be enough for you, but I think the 2nd line

_R_CHECK_FORCE_SUGGESTS_: false

may be more important:  you use ks, it imports plot3D, plot3D imports 
misc3d, but it only suggests rgl and tkrplot:  so that would let ks load 
without XQuartz support.

Duncan Murdoch

On 23/05/2021 3:09 p.m., Spencer Graves wrote:
> Hi, Duncan et al.:
> 
> 
> 	  Thanks again to Duncan.  Your suggestions worked for the LaTeX
> problem, though it required multiple iterations, adding a total of 7
> different "tinytex::parse_install" clauses to overcome other LaTeX and
> pdfTeX errors.
> 
> 
> 	  However, macOS still says, "there is no package called 'ks'", even
> though I added 'install.packages("ks")' as you suggested -- to three
> different places, all without solving the problem.  I posted this
> question to
> "https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions",
> as suggested in line 2 of "~/.github/workflows/R-CMD-check.yaml".  See:
> 
> 
> 	  Spencer
> 
> 
> On 5/23/21 11:03 AM, Duncan Murdoch wrote:
>> This page
>>
>> https://bookdown.org/yihui/rmarkdown-cookbook/install-latex-pkgs.html
>>
>> suggests that executing this in R should fix the tikz issue:
>>
>> tinytex::parse_install(
>>     text = "! LaTeX Error: File `tikz.sty' not found."
>> )
>>
>> The "ks" message looks like a missing R package rather than a missing
>> LaTeX package, so running install.packages("ks") would fix it.
>>
>> So the only question is how to do these things in a Github action.  I
>> don't know if there's a pre-made recipe for this, but this one should do
>> it:
>>
>>         - name: Install tikz.tex and ks
>>           run: |
>>             install.packages(c('tinytex', 'ks')) # Maybe tinytex is
>> already there?
>>             tinytex::parse_install(
>>                text = "! LaTeX Error: File `tikz.sty' not found."
>>             )
>>           shell: Rscript {0}
>>
>> Duncan Murdoch
>>
>> On 23/05/2021 11:28 a.m., Spencer Graves wrote:
>>> Hi, Duncan et al.:
>>>
>>>
>>>        Thanks very much to Duncan for his suggestion.  I did added the
>>> line
>>> Duncan suggested in three slightly different places.  That fixed the
>>> problems with missing tex and pdflatex, but exposed two new problems:
>>>
>>>
>>>        On Windows and ubuntu (both release and devel) I now get:
>>>
>>>
>>> LaTeX Error: File `tikz.sty' not found.
>>>
>>>
>>>        On macOS, I got a different error:
>>>
>>>
>>> there is no package called 'ks'
>>>
>>>
>>>        I added "ks" to "suggests" in DESCRIPTON but still got "no package
>>> called 'ks'.  And I studied README in https://github.com/r-lib/actions,
>>> and I did some other searches without figuring out how to fix
>>> "`tikz.sty' not found."
>>>
>>>
>>>        For more details, see:
>>>
>>>
>>> https://github.com/sbgraves237/sos
>>>
>>>
>>>        Suggestions?
>>>        Thanks,
>>>        Spencer
>>>
>>>
>>> On 5/23/21 4:43 AM, Duncan Murdoch wrote:
>>>> On 22/05/2021 10:05 p.m., Spencer Graves wrote:
>>>>> Hello:
>>>>>
>>>>>
>>>>>         What do you suggest I do to enable GitHub Action to process
>>>>> "sos.Rnw"
>>>>> properly?
>>>>>
>>>>>
>>>>>         The development version of my "sos" package passes "R CMD
>>>>> check" on
>>>>> my Mac but fails in all four platforms under GitHub Action on
>>>>>
>>>>>
>>>>> https://github.com/sbgraves237/sos
>>>>>
>>>>>
>>>>>         The error messages on macOS and Ubuntu release and devel all
>>>>> seems
>>>>> the same:
>>>>>
>>>>>
>>>>>               * Error: processing vignette 'sos.Rnw' failed with
>>>>> diagnostics:
>>>>> Running 'texi2dvi' on 'sos.tex' failed.  Messages: You don't have a
>>>>> working TeX binary (tex) installed anywhere in your PATH, and texi2dvi
>>>>> cannot proceed without one.
>>>>>
>>>>>
>>>>>         The error message under Windows seemed crudely similar but
>>>>> different:
>>>>>
>>>>>
>>>>>               * Error: processing vignette 'sos.Rnw' failed with
>>>>> diagnostics:
>>>>> pdflatex is not available
>>>>>
>>>>>
>>>>>         What do you suggest?
>>>>
>>>> The virtual machines that run Github actions have lots of tools
>>>> installed, but apparently not LaTeX.  So you need to figure out the
>>>> "step" to install it.  I'm not currently using Rnw with Github actions,
>>>> but by looking at the README for https://github.com/r-lib/actions, I'm
>>>> pretty sure all you need is to add
>>>>
>>>>      - uses: r-lib/actions/setup-tinytex using v1
>>>>
>>>> somewhere after
>>>>
>>>>      - uses: actions/checkout using master
>>