[R-pkg-devel] Error uploading file on CRAN

2022-11-07 Thread Jahajeeah, Havisha
Dear CRAN team,

The package 'Greymodels' has just been published on CRAN. After loading the
package on CRAN, when I try to upload file (xlsx or xls)
the following error appears:

Error: cannot open the connection

What could be the problem? Is it because of the working directory?

Please advise on how to fix this.

Many thanks,
Havisha Jahajeeah

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Re: [R-pkg-devel] Error uploading file on CRAN

2022-11-07 Thread Ivan Krylov
В Mon, 7 Nov 2022 12:30:35 +0400
"Jahajeeah, Havisha"  пишет:

> After loading the package on CRAN, when I try to upload file (xlsx or
> xls) the following error appears:
> 
> Error: cannot open the connection

Do you mean uploading files into your Shiny application, or somewhere
else?

Have you tried following this guide?
https://shiny.rstudio.com/articles/debugging.html

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] Error uploading file on CRAN

2022-11-07 Thread Jahajeeah, Havisha
Thank you for the reply.

Yes, uploading files into the Shiny app.

The Greymodels package loads data from spreadsheets and each model accepts
a set of data and outputs the  values. However, the package is unable to do
that because of the error: cannot open connection.

Regards,
Havisha

On Mon, Nov 7, 2022 at 2:13 PM Ivan Krylov  wrote:

> В Mon, 7 Nov 2022 12:30:35 +0400
> "Jahajeeah, Havisha"  пишет:
>
> > After loading the package on CRAN, when I try to upload file (xlsx or
> > xls) the following error appears:
> >
> > Error: cannot open the connection
>
> Do you mean uploading files into your Shiny application, or somewhere
> else?
>
> Have you tried following this guide?
> https://shiny.rstudio.com/articles/debugging.html
>
> --
> Best regards,
> Ivan
>

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Re: [R-pkg-devel] Error uploading file on CRAN

2022-11-07 Thread Ivan Krylov
В Mon, 7 Nov 2022 14:55:06 +0400
"Jahajeeah, Havisha"  пишет:

> The Greymodels package loads data from spreadsheets and each model
> accepts a set of data and outputs the  values. However, the package
> is unable to do that because of the error: cannot open connection.

Thank you for clarifying the problem!

The guide at https://shiny.rstudio.com/articles/debugging.html is full
of useful things to try when a Shiny app is misbehaving. I could try to
write an instruction for you to follow here, but it would end up being
a paraphrase of this guide. If you follow the guide, you should be able
to find out (1) which of your read_excel calls is failing, (2) what is
its argument and (3) what actually ends up at that path at the time of
the call. Once you know this information, the solution may become
obvious, or at least there may be something for us to give you more
pointers about.

While there is a chance that someone else will come along, run your
package on their machine and reproduce the problem, there's also a
significant chance that no one will do that. Meanwhile, these steps are
relatively simple and may help you solve the problem right away.

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] Error uploading file on CRAN

2022-11-07 Thread Jahajeeah, Havisha
Thank you for your help.

I will go through the guide.

Many thanks,
Havisha

On Mon, Nov 7, 2022 at 3:19 PM Ivan Krylov  wrote:

> В Mon, 7 Nov 2022 14:55:06 +0400
> "Jahajeeah, Havisha"  пишет:
>
> > The Greymodels package loads data from spreadsheets and each model
> > accepts a set of data and outputs the  values. However, the package
> > is unable to do that because of the error: cannot open connection.
>
> Thank you for clarifying the problem!
>
> The guide at https://shiny.rstudio.com/articles/debugging.html is full
> of useful things to try when a Shiny app is misbehaving. I could try to
> write an instruction for you to follow here, but it would end up being
> a paraphrase of this guide. If you follow the guide, you should be able
> to find out (1) which of your read_excel calls is failing, (2) what is
> its argument and (3) what actually ends up at that path at the time of
> the call. Once you know this information, the solution may become
> obvious, or at least there may be something for us to give you more
> pointers about.
>
> While there is a chance that someone else will come along, run your
> package on their machine and reproduce the problem, there's also a
> significant chance that no one will do that. Meanwhile, these steps are
> relatively simple and may help you solve the problem right away.
>
> --
> Best regards,
> Ivan
>

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Re: [R-pkg-devel] Examples with CPU time is greater than elapsed time.

2022-11-07 Thread Uwe Ligges




On 05.11.2022 15:41, Jiaming Yuan wrote:

Hi all,

I tried to submit an update to the xgboost package but didn't pass the 
pre-tests with the following note (solved the other one, but this one is 
a bit confusing):


```
Flavor: r-devel-linux-x86_64-debian-gcc
Check: examples, Result: NOTE
   Examples with CPU time > 2.5 times elapsed time
    user system elapsed ratio
   cb.gblinear.history 1.454  0.017    0.49 3.002

```


as ratio is > 2.5 it looks like you are using multiple threads or 
processes. And CRAN only allows for two nodes when runnign parallel code.


Best,
Uwe Ligges


I can't reproduce the note on win-builder: 
https://win-builder.r-project.org/ as it's running on Windows but the 
note appears on debian tests. I'm not able to reproduce it on my local 
machine either with Ubuntu 22.04. I'm wondering what the note is trying 
to tell me and how can I resolve it with confidence.



The full log is here: 
https://win-builder.r-project.org/incoming_pretest/xgboost_1.7.1.1_20221104_194252/Debian/00check.log .



Many thanks!

Jiaming

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[R-pkg-devel] cross-ref possible ext.pkg's --not mentioned in DESCRIPTION file-- in non-code sections in .Rd files

2022-11-07 Thread Peter Ruckdeschel
Hi,

triggered by some new NOTEs uncovering infallacities in my packages on CRAN, I 
stumbled upon

Result: NOTE Undeclared packages ‘distrMod’, ‘RobAStBase’ in Rd xrefs

which is issued in R-devel-linux-x86_64-fedora-clang (but not otherwise).

Digging into it, this comes from a text in a \seealso section where through 
something like

\code{\{link}[]{}

we want to link to a method provided in some extension package  for a 
generic
 documented in Rd-file of the current package.

In this case, we intentionally do not have  in any of the entries 
"Depends", "Suggests",
"Imports", "Enhances" in the DESCRIPTION file, as  is neither needed 
visible for the
user, nor for the code in the current package nor for testing code nor for 
example code and vignettes
of the current package, and because having it in "Suggests" would produce a 
circular dependence
as  has the current package in its "Imports" section.

Of course, in "Writing R extesions" we find that

"Packages referred to by these ‘other forms’ should be declared in the 
DESCRIPTION file, in
   the ‘Depends’, ‘Imports’, ‘Suggests’ or ‘Enhances’ fields. "

so I am aware that this is my fault, as I use these 'other forms'  without 
declaration in the DESCRIPTION file.
Now I guess I could wrap my conditional cross-ref into some R-code, testing 
whether  is available,
i.e., something like

\Sexpr[eval=TRUE,stage=render,results=text]{if("" %in% 
installed.packages()[,1] )
  cat("\\code{\\{link}[]{}") else cat(" from package 
\\pkg{})

and so produce the link only if  is installed at rendering time, but I 
would guess such a
conditional linkage would be something which could be of interest to a broader 
scope of R-package
developers and hence could and should be implemented in a less cumbersome, and 
more
efficient way.

Any suggestions welcome,
best, Peter

--
%**
% Prof. Dr. Peter Ruckdeschel
% Institut fuer Mathematik, Fakultaet V - Mathematik und Naturwissenschaften
% Carl von Ossietzky Universitaet Oldenburg,
% Postfach 5634,  26111 Oldenburg
% Office: Wechloy W1 02-227 Tel: +49 (0)441 798-3240  Fax: +49 (0)441 798-193240
%peter.ruckdesc...@uni-oldenburg.de
%http://www.uni-oldenburg.de/peter-ruckdeschel
%**

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[R-pkg-devel] CRAN index replaces ampersand in BugReports URL with HTML entity

2022-11-07 Thread Mikael Jagan

Hello,

It was raised on the Matrix bug tracker [1] that the BugReports URL
on the CRAN index [2] is broken.  The URL in our DESCRIPTION file [3]
is fine, but contains an ampersand, which is improperly replaced with
the corresponding HTML entity in the HTML sources of the index.

Hence this does not affect bug.report(package="Matrix"), but _does_
make our bug tracker inaccessible to people accustomed to visiting
the CRAN page for links.

Can this be repaired?

Mikael

[1] 
https://r-forge.r-project.org/tracker/?func=detail&aid=6787&group_id=61&atid=294
[2] https://cran.r-project.org/package=Matrix
[3] https://r-forge.r-project.org/tracker/?atid=294&group_id=61

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Re: [R-pkg-devel] cross-ref possible ext.pkg's --not mentioned in DESCRIPTION file-- in non-code sections in .Rd files

2022-11-07 Thread Andrew Simmons
Packages in Suggests and Enhances do not create a circular dependency, only
the packages in the Depends and Imports need to be installed at INSTALL and
loaded at load time. Packages in Suggests and Enhances are only needed at
check time, and even then it's more of a desire to be loaded than actually
needing to be loaded.

I would just put them in Suggests or Enhances

On Mon, Nov 7, 2022, 11:10 Peter Ruckdeschel 
wrote:

> Hi,
>
> triggered by some new NOTEs uncovering infallacities in my packages on
> CRAN, I stumbled upon
>
> Result: NOTE Undeclared packages ‘distrMod’, ‘RobAStBase’ in Rd xrefs
>
> which is issued in R-devel-linux-x86_64-fedora-clang (but not otherwise).
>
> Digging into it, this comes from a text in a \seealso section where
> through something like
>
> \code{\{link}[]{}
>
> we want to link to a method provided in some extension package 
> for a generic
>  documented in Rd-file of the current package.
>
> In this case, we intentionally do not have  in any of the entries
> "Depends", "Suggests",
> "Imports", "Enhances" in the DESCRIPTION file, as  is neither
> needed visible for the
> user, nor for the code in the current package nor for testing code nor for
> example code and vignettes
> of the current package, and because having it in "Suggests" would produce
> a circular dependence
> as  has the current package in its "Imports" section.
>
> Of course, in "Writing R extesions" we find that
>
> "Packages referred to by these ‘other forms’ should be declared in the
> DESCRIPTION file, in
>the ‘Depends’, ‘Imports’, ‘Suggests’ or ‘Enhances’ fields. "
>
> so I am aware that this is my fault, as I use these 'other forms'  without
> declaration in the DESCRIPTION file.
> Now I guess I could wrap my conditional cross-ref into some R-code,
> testing whether  is available,
> i.e., something like
>
> \Sexpr[eval=TRUE,stage=render,results=text]{if("" %in%
> installed.packages()[,1] )
>   cat("\\code{\\{link}[]{}") else cat(" from
> package \\pkg{})
>
> and so produce the link only if  is installed at rendering time,
> but I would guess such a
> conditional linkage would be something which could be of interest to a
> broader scope of R-package
> developers and hence could and should be implemented in a less cumbersome,
> and more
> efficient way.
>
> Any suggestions welcome,
> best, Peter
>
> --
> %**
> % Prof. Dr. Peter Ruckdeschel
> % Institut fuer Mathematik, Fakultaet V - Mathematik und
> Naturwissenschaften
> % Carl von Ossietzky Universitaet Oldenburg,
> % Postfach 5634,  26111 Oldenburg
> % Office: Wechloy W1 02-227 Tel: +49 (0)441 798-3240  Fax: +49 (0)441
> 798-193240
> %peter.ruckdesc...@uni-oldenburg.de
> %http://www.uni-oldenburg.de/peter-ruckdeschel
> %**
>
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>
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