Re: [R-pkg-devel] Need help with "Lost braces" in R under development checks

2024-04-07 Thread Duncan Murdoch 

On 06/04/2024 11:58 p.m., adi...@pdx.edu wrote:


Hello,

I would appreciate help with two build NOTEs:


First, On the Winbuilder check, the check for R version 4.4.0 alpha
(2024-04-05 r86346 ucrt) and also under the Debian R Under development
(unstable) (2024-04-05 r86348) I got a NOTE about a bunch of 'Lost
braces' in my .Rd files. I am confused because my braces appear to match
when I count them, and I don't *think* I am runing into an item/itemize
situation. Here's an example (all the reported issues in this NOTE are
within \references sections ):

   checkRd: (-1) LoopAnalyst-package.Rd:14: Lost braces
 14 |  Dambacher, J. M. and Li, H. W. and Rossignol, P. A. (2002)
   \doi{10.2307/3071950}{Relevance of community structure in assessing
   indeterminacy of ecological predictions}. \emph{Ecology},
   \bold{83(5)},1372--1385.


It appears you are trying to pass two arguments to \doi, but it only 
takes one.  I would have thought that would be fine, but apparently not.


So add a space after "\doi{10.2307/3071950}" and/or remove the braces 
around "{Relevance of community structure in assessing indeterminacy of 
ecological predictions}".


Duncan Murdoch



Here's the Winbuilder log:
https://win-builder.r-project.org/incoming_pretest/LoopAnalyst_1.2-7_20240406_215835/Windows/00check.log

And here's the Debian log:
https://win-builder.r-project.org/incoming_pretest/LoopAnalyst_1.2-7_20240406_215835/Debian/00check.log


The second NOTE is about "(possibly) invalid URLs:"
   URL: https://www.journals.uchicago.edu/doi/10.1086/367590
 Status: 403
 Message: Forbidden

However, when I follow this URL in my browser it appears to link
appropriately to the intended page. If I use a \doi{10.1086/367590}
instead of an \href I get the same behavior: check says "(possibly)
invalid URLs" but https://doi.org/10.1086/367590 appears to work just
fine in the browser. Not sure what I am doing wrong here.



Thank you!


Alexis Dinno
Associate Professor
OHSU-PSU School of Public Health
Pronouns: she/her/hers

610-R Vanport Building
1810 SW 5th Avenue, Suite 610
Portland, OR 97201-5202

p: (503) 725-3076
f: (503) 725-5100
e: alexis.di...@pdx.edu

Note: I do not use a networked calendar, so meeting dates should be 
communicated directly via email.

__
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] Need help with "Lost braces" in R under development checks

2024-04-07 Thread Georgi Boshnakov 
The braces are lost in the sense that they are superfluous (not typeset in the 
pdf manual but may be typeset in other formats. In your example \doi has one 
argument, so the braces enclosing the following phrase are superfluous.

This may not be harmful here but since CRAN introduced the NOTE it has 
uncovered thousands of actual typos and similar.

As to the 'invalid url', you can ignore it when you are sure that it is correct 
- some sites don't like being accessed programatically and start blocking the 
caller (eg if you run R checks several times in succession).


Georgi Boshnakov

Sent from Outlook for Android

From: R-package-devel  on behalf of 
adi...@pdx.edu 
Sent: Sunday, April 7, 2024 5:58:57 AM
To: r-package-devel@r-project.org 
Subject: [R-pkg-devel] Need help with "Lost braces" in R under development 
checks


Hello,

I would appreciate help with two build NOTEs:


First, On the Winbuilder check, the check for R version 4.4.0 alpha
(2024-04-05 r86346 ucrt) and also under the Debian R Under development
(unstable) (2024-04-05 r86348) I got a NOTE about a bunch of 'Lost
braces' in my .Rd files. I am confused because my braces appear to match
when I count them, and I don't *think* I am runing into an item/itemize
situation. Here's an example (all the reported issues in this NOTE are
within \references sections ):

  checkRd: (-1) LoopAnalyst-package.Rd:14: Lost braces
14 |  Dambacher, J. M. and Li, H. W. and Rossignol, P. A. (2002)
  \doi{10.2307/3071950}{Relevance of community structure in assessing
  indeterminacy of ecological predictions}. \emph{Ecology},
  \bold{83(5)},1372--1385.

Here's the Winbuilder log:
https://urldefense.com/v3/__https://win-builder.r-project.org/incoming_pretest/LoopAnalyst_1.2-7_20240406_215835/Windows/00check.log__;!!PDiH4ENfjr2_Jw!A109ZbFKcZjQ25lSt1JJSlLziJ-IyfouQzdKPv5pnUKRq_3-RoKd52MVDkHUoho-VQ5Ld85q6WmdGwh5eSSWPstUjY95nA$
 [win-builder[.]r-project[.]org]

And here's the Debian log:
https://urldefense.com/v3/__https://win-builder.r-project.org/incoming_pretest/LoopAnalyst_1.2-7_20240406_215835/Debian/00check.log__;!!PDiH4ENfjr2_Jw!A109ZbFKcZjQ25lSt1JJSlLziJ-IyfouQzdKPv5pnUKRq_3-RoKd52MVDkHUoho-VQ5Ld85q6WmdGwh5eSSWPstlRfRWeA$
 [win-builder[.]r-project[.]org]


The second NOTE is about "(possibly) invalid URLs:"
  URL: 
https://urldefense.com/v3/__https://www.journals.uchicago.edu/doi/10.1086/367590__;!!PDiH4ENfjr2_Jw!A109ZbFKcZjQ25lSt1JJSlLziJ-IyfouQzdKPv5pnUKRq_3-RoKd52MVDkHUoho-VQ5Ld85q6WmdGwh5eSSWPsuMHqle7Q$
 [journals[.]uchicago[.]edu]
Status: 403
Message: Forbidden

However, when I follow this URL in my browser it appears to link
appropriately to the intended page. If I use a \doi{10.1086/367590}
instead of an \href I get the same behavior: check says "(possibly)
invalid URLs" but 
https://urldefense.com/v3/__https://doi.org/10.1086/367590__;!!PDiH4ENfjr2_Jw!A109ZbFKcZjQ25lSt1JJSlLziJ-IyfouQzdKPv5pnUKRq_3-RoKd52MVDkHUoho-VQ5Ld85q6WmdGwh5eSSWPstaKkb77Q$
 [doi[.]org] appears to work just
fine in the browser. Not sure what I am doing wrong here.



Thank you!


Alexis Dinno
Associate Professor
OHSU-PSU School of Public Health
Pronouns: she/her/hers

610-R Vanport Building
1810 SW 5th Avenue, Suite 610
Portland, OR 97201-5202

p: (503) 725-3076
f: (503) 725-5100
e: alexis.di...@pdx.edu

Note: I do not use a networked calendar, so meeting dates should be 
communicated directly via email.

__
R-package-devel@r-project.org mailing list
https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-package-devel__;!!PDiH4ENfjr2_Jw!A109ZbFKcZjQ25lSt1JJSlLziJ-IyfouQzdKPv5pnUKRq_3-RoKd52MVDkHUoho-VQ5Ld85q6WmdGwh5eSSWPssk-Dl_sw$
 [stat[.]ethz[.]ch]

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[R-pkg-devel] Need help with "Lost braces" in R under development checks

2024-04-07 Thread adinno 


Hello,

I would appreciate help with two build NOTEs:


First, On the Winbuilder check, the check for R version 4.4.0 alpha 
(2024-04-05 r86346 ucrt) and also under the Debian R Under development 
(unstable) (2024-04-05 r86348) I got a NOTE about a bunch of 'Lost 
braces' in my .Rd files. I am confused because my braces appear to match 
when I count them, and I don't *think* I am runing into an item/itemize 
situation. Here's an example (all the reported issues in this NOTE are 
within \references sections ):

  checkRd: (-1) LoopAnalyst-package.Rd:14: Lost braces
14 |  Dambacher, J. M. and Li, H. W. and Rossignol, P. A. (2002) 
  \doi{10.2307/3071950}{Relevance of community structure in assessing 
  indeterminacy of ecological predictions}. \emph{Ecology}, 
  \bold{83(5)},1372--1385.

Here's the Winbuilder log:
https://win-builder.r-project.org/incoming_pretest/LoopAnalyst_1.2-7_20240406_215835/Windows/00check.log

And here's the Debian log:
https://win-builder.r-project.org/incoming_pretest/LoopAnalyst_1.2-7_20240406_215835/Debian/00check.log


The second NOTE is about "(possibly) invalid URLs:"
  URL: https://www.journals.uchicago.edu/doi/10.1086/367590
Status: 403
Message: Forbidden

However, when I follow this URL in my browser it appears to link 
appropriately to the intended page. If I use a \doi{10.1086/367590} 
instead of an \href I get the same behavior: check says "(possibly) 
invalid URLs" but https://doi.org/10.1086/367590 appears to work just 
fine in the browser. Not sure what I am doing wrong here.



Thank you!


Alexis Dinno
Associate Professor
OHSU-PSU School of Public Health
Pronouns: she/her/hers

610-R Vanport Building
1810 SW 5th Avenue, Suite 610
Portland, OR 97201-5202

p: (503) 725-3076
f: (503) 725-5100
e: alexis.di...@pdx.edu

Note: I do not use a networked calendar, so meeting dates should be 
communicated directly via email.

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Linking Tutorial Site to CRAN Package site.

2024-04-07 Thread Ivan Krylov via R-package-devel 
В Sat, 6 Apr 2024 18:27:24 +
"Ruff, Sergej"  пишет:

> The CRAN site
> (https://cran.r-project.org/web/packages/RepeatedHighDim/index.html)
> has a "documentation" part with the refrence pdf.
> 
> Can I link to our tutorial site (https://software.klausjung-lab.de/.)
> under documentation?

Since your tutorial is relatively short and contains R code intermixed
with the results of running it, it could make a great vignette.
Vignettes are linked on the CRAN page for a package right under the
PDF reference manual. For example, the BiocManager package has one
vignette: https://cran.r-project.org/package=BiocManager

Vignettes are a part of the package and their code is automatically
checked together with your examples. For the users of your package,
this will help keep the tutorial available (even if the website moves
in the future) and compatible with the current version of the package
(even if the package evolves and the tutorial website evolves together
with it).

R has built-in support for PDF vignettes via LaTeX using Sweave [*].
HTML vignettes can be much more accessible than PDF files, but there is
no built-in HTML vignette engine in R [**]. The 'markdown' package is
reasonably lightweight and has an HTML vignette engine. Markdown tries
to be a superset of HTML, so it should be possible to keep most of your
original HTML, including the styling, while rewriting the tutorial as
an executable vignette.

-- 
Best regards,
Ivan

[*]
https://cran.r-project.org/doc/manuals/R-exts.html#Writing-package-vignettes

[**]
It's possible to write a crude HTML vignette engine in ~100 lines of R
code, but we cannot expect every package author to do that.

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