[R-pkg-devel] help fixing CRAN package sos

[Uwe Ligges]

On 16.05.2023 14:02, Spencer Graves wrote:
> 
> 
> On 5/16/23 6:06 AM, Uwe Ligges wrote:
>>
>>
>> On 16.05.2023 01:46, Spencer Graves wrote:
>>> Hello, All:
>>>
>>>
>>>        The sos package is failing some CRAN checks, complaining:[1]
>>>
>>>
>>> LaTeX errors:
>>> ! Missing $ inserted.
>>> <inserted text>
>>>                  $
>>> l.303 {\tt pspline_
>>>                     checker} in the
>>
>>
>> I can only guess this is part of the response you got from some sos 
>> request? I cannot reproduce it currently.
>>
>> So check:
>> Does your package pass check if some function names including an 
>> underscore in the name is returned from an sos request?
> 
> 
> Hi, Uwe et al.:
> 
> 
>        Thanks, Uwe, for your reply.
> 
> 
>        It's complaining about something in a vignette that has been part 
> of the package since it appeared in The R Journal in Volume 1/2 in 
> 2009.  I received an email from Prof. Ripley complaining that it 
> reported problems ("WARN") on some of the CRAN checks.  When I asked, 
> Prof. Ripley reply's reply included:
> 
> 
>  >>      l.303 {\tt pspline_
>  >>       checker} in the
>  >>      ! ==> Fatal error occurred, no output PDF file produced!
>  >>
>  >> Underlines need to be escaped in LaTeX.  And as your results depend on
>  >> Internet downloads,
>  >>
>  >> "Packages which use Internet resources should fail gracefully with an
>  >> informative message if the resource is not available or has changed
>  >> (and not give a check warning nor error)."
>  >>
>  >> applies: you need to anticipate that the results might include
>  >> underlines.
> 
> 
>        I don't know how to detect, let alone fix the "Underlines" that 
> "need to be escaped in LaTeX."

If you receive an output, postprocess it via

gsub("_", "\\\\_", output)



> 
> 
>        Regarding the other issue that "Packages which use Internet 
> resources should fail gracefully with an informative message if the 
> resource is not available or has changed (and not give a check warning 
> nor error)", I assume I should wrap in "try" all tests in *.Rd files 
> that access the Internet and make sure that they don't fail "R CMD 
> check" if the Internet is not available.

Yes.

Best,
Uwe Ligges


> 
>        Comments?
>        Thanks again,
>        Spencer Graves
> 
> 
> p.s.  Yesterday I remember I got "WARN" on three of six CRAN checks 
> against r-devel on different platforms and NOTE on four of the seven 
> other CRAN checks.  Today I see "WARN" on only two.  If I just wait, 
> these "WARN" problems may go away by themselves.  However, Prof. Ripley 
> gave me other problems to fix, and I want to support our kind, smart and 
> generous English professor.
> 
>>
>> Best,
>> Uwe Ligges
>>
>>
>>
>>
>>
>>
>>> ! Emergency stop.
>>> <inserted text>
>>>                  $
>>> l.303 {\tt pspline_
>>>                     checker} in the
>>> ! ==> Fatal error occurred, no output PDF file produced!
>>> --- failed re-building 'sos.Rnw'
>>>
>>>
>>>        I can NOT replicate these locally nor with GitHub action, and 
>>> I failed to find 'psp' in 'sos.Rnw'.[2]  This raises two issue:
>>>
>>>
>>> OBVIOUS:  What can I do to fix this error, or at least to understand 
>>> it better?
>>>
>>>
>>> SUBTLE:  How can I configure "github action", so it can replicate the 
>>> errors reported on CRAN?
>>>
>>>
>>>        Thanks,
>>>        Spencer
>>>
>>>
>>> [1]
>>>
>>>
>>> https://cran.r-project.org
>>>
>>>
>>> [2]
>>>
>>>
>>> https://github.com/sbgraves237/sos
>>>
>>>
>>> -------- Forwarded Message --------
>>> Subject: Re: CRAN package sos
>>> Date: Sun, 14 May 2023 14:46:06 +0100
>>> From: Prof Brian Ripley <ripley using stats.ox.ac.uk>
>>> Reply-To: CRAN <CRAN using r-project.org>
>>> To: Spencer Graves <spencer.graves using prodsyse.com>
>>> CC: CRAN using R-project.org
>>>
>>> <snip>
>>>
>>>
>>> On 12/05/2023 13:03, Spencer Graves wrote:
>>>> Hello, All:
>>>
>>> You have just spammed my personal email address, contrary to the CRAN 
>>> policy and done so deliberately and/or recklessly, overriding the 
>>> Reply-To header.
>>>
>>>>        Is MASS being withdrawn along with multiple other packages 
>>>> (mgcv, survival, boot, lattice)?
>>>
>>> Not so.  And that was a failure to do your own homework as you should 
>>> have looked on CRAN to see that they are still available.
>>>
>>> Further
>>>
>>> options(repos=c(CRAN="http://cran.cnr.berkeley.edu"))
>>>
>>> does not respect the user's choice of repository: that seems to make 
>>> re-making it unreasonably slow.  On my very fast MacBook Pro
>>>
>>> * checking re-building of vignette outputs ...^R
>>>   [26s/265s] OK
>>>
>>> so it is waiting 90% of the time.
>>>
>>>
>>>>        That's responsible for 3 of the 4 'warnings' listed there. 
>>>> The warning for r-devel-linux-x86_64-fedora-gcc says "LaTeX errors:
>>>> ! Missing $ inserted ... Fatal error occurred, no output PDF file 
>>>> produced! ... Vignette re-building failed."
>>>>
>>>>
>>>>        These all sound to me like operating system errors.  If 
>>>> there's something here I should do, I could use help in 
>>>> understanding what.
>>>
>>> Do read the message -- it is a LaTeX error in the LaTeX code your 
>>> package's vignettes generates.
>>>
>>>     LaTeX errors:
>>>      ! Missing $ inserted.
>>>      <inserted text>
>>>       $
>>>      l.303 {\tt pspline_
>>>       checker} in the
>>>      ! Emergency stop.
>>>      <inserted text>
>>>       $
>>>      l.303 {\tt pspline_
>>>       checker} in the
>>>      ! ==> Fatal error occurred, no output PDF file produced!
>>>
>>> Underlines need to be escaped in LaTeX.  And as your results depend 
>>> on Internet downloads,
>>>
>>> "Packages which use Internet resources should fail gracefully with an 
>>> informative message if the resource is not available or has changed 
>>> (and not give a check warning nor error)."
>>>
>>> applies: you need to anticipate that the results might include 
>>> underlines.
>>>
>>>>
>>>>
>>>>        Thanks,
>>>>        Spencer Graves
>>>> m:  1-408-655-4567
>>>>
>>>>
>>>> On 5/12/23 1:38 AM, Prof Brian Ripley wrote:
>>>>> Dear maintainer,
>>>>>
>>>>> Please see the problems shown on
>>>>> <https://cran.r-project.org/web/checks/check_results_sos.html>.
>>>>>
>>>>> Please correct before 2023-05-26 to safely retain your package on 
>>>>> CRAN.
>>>>>
>>>>> The CRAN Team
>>>