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

[Spencer Graves]

Hi, Uwe et al.:


	  Uwe suggests I postprocess output with gsub("_", "\\\\_", output). 
It's not clear to me where I should apply this.  The "WARN" flags the 
sos vignette sos.Rnw, but the offending code refers to pspline_checker, 
which is not in the version of the vignette available on CRAN.[1] The 
text of sos.Rnw is available on GitHub.[2] I am not eager to change the 
code in the package, because it could break something else that's 
currently working.


	  Suggestions?
	  Thanks,
	  Spencer Graves


[1]


https://cran.r-project.org/web/packages/sos/vignettes/sos.pdf


[2]


https://github.com/sbgraves237/sos/blob/master/vignettes/sos.Rnw


On 5/16/23 7:41 AM, Uwe Ligges wrote:
> 
> 
> 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
>>>>