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

[Spencer Graves]

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."


	  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.


	  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
>>