Re: [R-pkg-devel] proper way to cite an invalid URL

[Ivan Krylov via R-package-devel]

В Wed, 2 Apr 2025 21:20:19 -0400
Jason Cory Brunson  пишет:

> in case you're curious, www.ibge.Goiásv.br/

I went looking for links to this domain on the Web, found the link in
the documentation for the 'ripserr' package, and then found what looks
like a domain where the desired page could be found. Could it be

https://www.ibge.gov.br/geociencias/organizacao-do-territorio/estrutura-territorial/15761-areas-dos-municipios.html?edicao=30133&t=acesso-ao-produto

instead of the original link?

https://www.ibge.Goiasv.br/geociencias/organizacao-do-territorio/estrutura-territorial/15761-areas-dos-municipios.html?edicao=30133&t=acesso-ao-produto⁠

> But i got a new error from Win-Builder (the development version via 
> devtools::check_win_devel() but not the release version via 
> devtools::check_win_release()). It seems to apply to all URLs and
> DOIs, though i did not get it on any previous check:
> 
> Checking URLs failed with message:
>    there is no package called 'curl'
> 
> Checking DOIs failed with message:
>    there is no package called 'curl'

Looks like Win-Builder for R-devel is having transient problems:
https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64/curl-00install.html

("ERROR: cannot remove earlier installation, is it in use?", and then
it fails to overwrite libs\x64\curl.dll with "Permission denied".)

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] proper way to cite an invalid URL

[Jason Cory Brunson]

Thank you both!

Nicholas, i did check the Wayback Machine; the URL was never archived, 
nor was the domain itself (in case you're curious, www.ibge.Goiásv.br/).

Duncan, that worked at preventing the hyperlink locally; thank you. But 
i got a new error from Win-Builder (the development version via 
devtools::check_win_devel() but not the release version via 
devtools::check_win_release()). It seems to apply to all URLs and DOIs, 
though i did not get it on any previous check:

Checking URLs failed with message:
   there is no package called 'curl'

Checking DOIs failed with message:
   there is no package called 'curl'

Cory

On 4/2/25 20:28, Nicholas Tierney wrote:
> Could you potentially look for the original website in the internet 
> archive / wayback machine: https://web.archive.org/ and cite that instead?
>
> On Thu, 3 Apr 2025 at 08:42, Duncan Murdoch  
> wrote:
>
> On 2025-04-02 1:28 p.m., Jason Cory Brunson wrote:
> > Hello,
> >
> > I'm trying to submit a new version of a package to CRAN. Among the
> > additions is an RMarkdown vignette that uses data from a website
> that is
> > no longer active. For completeness, i'd still like to cite the
> invalid
> > URL, but without formatting it as a hyperlink. What is the
> preferred way
> > to do this?
> >
> > One StackExchange answer is to surround the URL with
> , but
> > this did not remove the hyperlink when i rendered the vignette
> locally.
> > Instead, i surrounded it with back-ticks, which works locally,
> but i've
> > been unable to run Win-Builder checks to see whether this
> prevents the
> > "invalid URLs" NOTE. And, even if the NOTE is prevented, i'm not
> sure
> > this is preferred.
>
> Why not leave off the scheme, e.g. "www.r-project.org
> " instead of
> "https://www.r-project.org";.
>
> Duncan Murdoch
>
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>

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Re: [R-pkg-devel] proper way to cite an invalid URL

[Nicholas Tierney]

Could you potentially look for the original website in the internet archive
/ wayback machine: https://web.archive.org/ and cite that instead?

On Thu, 3 Apr 2025 at 08:42, Duncan Murdoch 
wrote:

> On 2025-04-02 1:28 p.m., Jason Cory Brunson wrote:
> > Hello,
> >
> > I'm trying to submit a new version of a package to CRAN. Among the
> > additions is an RMarkdown vignette that uses data from a website that is
> > no longer active. For completeness, i'd still like to cite the invalid
> > URL, but without formatting it as a hyperlink. What is the preferred way
> > to do this?
> >
> > One StackExchange answer is to surround the URL with , but
> > this did not remove the hyperlink when i rendered the vignette locally.
> > Instead, i surrounded it with back-ticks, which works locally, but i've
> > been unable to run Win-Builder checks to see whether this prevents the
> > "invalid URLs" NOTE. And, even if the NOTE is prevented, i'm not sure
> > this is preferred.
>
> Why not leave off the scheme, e.g. "www.r-project.org" instead of
> "https://www.r-project.org";.
>
> Duncan Murdoch
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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Re: [R-pkg-devel] Connection time-out when checking a package

[Thierry Onkelinx]

Dear Ivan,

Thanks for the feedback. Skipping all URL checks is not an ideal solution.
Getting a NOTE for a broken link is valuable. Given that the problem occurs
over several repositories but always with the gnu.org domain, I was hoping
for a more tailored solution.

Removing the problematic URL is probably the best solution for now.

Best regards,

Thierry

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
*Postadres:* Koning Albert II-laan 15 bus 186, 1210 Brussel
*Poststukken die naar dit adres worden gestuurd, worden ingescand en
digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar
dossiers volledig digitaal behandelen. Poststukken met de vermelding
‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de geadresseerde
bezorgd.*
www.inbo.be

///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///




Op wo 2 apr 2025 om 11:45 schreef Ivan Krylov :

> В Tue, 1 Apr 2025 14:28:04 +0200
> Thierry Onkelinx  пишет:
>
> > Any suggestions how to fix this note without removing the
> > URL for the README?
>
> I think it should be possible to set the environment variable
> _R_CHECK_CRAN_INCOMING_REMOTE_=FALSE to disable the "remote" checks [*]
> (including checks for repository content) or
> _R_CHECK_CRAN_INCOMING_SKIP_URL_CHECKS_IF_REMOTE_=TRUE to only skip the
> URL checks.
>
> --
> Best regards,
> Ivan
>
> [*]
>
> https://cran.r-project.org/doc/manuals/r-devel/R-ints.html#index-_005fR_005fCHECK_005fCRAN_005fINCOMING_005fREMOTE_005f
>

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Re: [R-pkg-devel] Connection time-out when checking a package

[Ivan Krylov via R-package-devel]

В Tue, 1 Apr 2025 14:28:04 +0200
Thierry Onkelinx  пишет:

> Any suggestions how to fix this note without removing the
> URL for the README?

I think it should be possible to set the environment variable
_R_CHECK_CRAN_INCOMING_REMOTE_=FALSE to disable the "remote" checks [*]
(including checks for repository content) or
_R_CHECK_CRAN_INCOMING_SKIP_URL_CHECKS_IF_REMOTE_=TRUE to only skip the
URL checks.

-- 
Best regards,
Ivan

[*]
https://cran.r-project.org/doc/manuals/r-devel/R-ints.html#index-_005fR_005fCHECK_005fCRAN_005fINCOMING_005fREMOTE_005f

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Re: [R-pkg-devel] proper way to cite an invalid URL

[Duncan Murdoch]

On 2025-04-02 1:28 p.m., Jason Cory Brunson wrote:

Hello,

I'm trying to submit a new version of a package to CRAN. Among the
additions is an RMarkdown vignette that uses data from a website that is
no longer active. For completeness, i'd still like to cite the invalid
URL, but without formatting it as a hyperlink. What is the preferred way
to do this?

One StackExchange answer is to surround the URL with , but
this did not remove the hyperlink when i rendered the vignette locally.
Instead, i surrounded it with back-ticks, which works locally, but i've
been unable to run Win-Builder checks to see whether this prevents the
"invalid URLs" NOTE. And, even if the NOTE is prevented, i'm not sure
this is preferred.


Why not leave off the scheme, e.g. "www.r-project.org" instead of 
"https://www.r-project.org";.


Duncan Murdoch

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Re: [R-pkg-devel] Connection time-out when checking a package

[Simon Urbanek]

FWIW: connectivity from GH runners is notoriously patchy*, so I wouldn’t rely 
on those for URL checks, so I’d recommend using the solution by Ivan in actions 
and simply running a separate check without the option once in a while locally 
(e.g., before submission) to detect such issues. After all, the point of GHAs 
is to detect things you cannot detect locally (because of OS etc.) which this 
not the case here.

* - the failure rate is so high that pretty much all actions involving remote 
files include provisions for several retries, otherwise your actions will fail 
on a regular basis. That said, GNU servers are notoriously unreliable 
themselves, compounding the problem. Even in our macOS recipes I had to create 
a provision for automatic rewriting of gnu.org URLs to more reliable GNU 
mirrors as the master site is either slow or unresponsive very often, so this 
is not an unusual problem.

Cheers,
Simon


> On 3 Apr 2025, at 00:01, Thierry Onkelinx  wrote:
> 
> Dear Ivan,
> 
> Thanks for the feedback. Skipping all URL checks is not an ideal solution.
> Getting a NOTE for a broken link is valuable. Given that the problem occurs
> over several repositories but always with the gnu.org domain, I was hoping
> for a more tailored solution.
> 
> Removing the problematic URL is probably the best solution for now.
> 
> Best regards,
> 
> Thierry
> 
> ir. Thierry Onkelinx
> Statisticus / Statistician
> 
> Vlaamse Overheid / Government of Flanders
> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
> FOREST
> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> thierry.onkel...@inbo.be
> Havenlaan 88 bus 73, 1000 Brussel
> *Postadres:* Koning Albert II-laan 15 bus 186, 1210 Brussel
> *Poststukken die naar dit adres worden gestuurd, worden ingescand en
> digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar
> dossiers volledig digitaal behandelen. Poststukken met de vermelding
> ‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de geadresseerde
> bezorgd.*
> www.inbo.be
> 
> ///
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
> ///
> 
> 
> 
> 
> Op wo 2 apr 2025 om 11:45 schreef Ivan Krylov :
> 
>> В Tue, 1 Apr 2025 14:28:04 +0200
>> Thierry Onkelinx  пишет:
>> 
>>> Any suggestions how to fix this note without removing the
>>> URL for the README?
>> 
>> I think it should be possible to set the environment variable
>> _R_CHECK_CRAN_INCOMING_REMOTE_=FALSE to disable the "remote" checks [*]
>> (including checks for repository content) or
>> _R_CHECK_CRAN_INCOMING_SKIP_URL_CHECKS_IF_REMOTE_=TRUE to only skip the
>> URL checks.
>> 
>> --
>> Best regards,
>> Ivan
>> 
>> [*]
>> 
>> https://cran.r-project.org/doc/manuals/r-devel/R-ints.html#index-_005fR_005fCHECK_005fCRAN_005fINCOMING_005fREMOTE_005f
>> 
> 
> [[alternative HTML version deleted]]
> 
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