date:20200906

Re: [Rd] Error in ?lowess

2020-09-06 Thread Kurt Hornik

> Duncan Murdoch writes:

Thanks, fixed now.

Best
-k

> The lowess() help page refers to documentation in "src/appl/lowess.doc". 
>   This was moved to "src/library/stats/src/lowess.doc" in 2007.  This 
> patch fixes it:

> Index: src/library/stats/man/lowess.Rd
> ===
> --- src/library/stats/man/lowess.Rd   (revision 79137)
> +++ src/library/stats/man/lowess.Rd   (working copy)
> @@ -30,7 +30,7 @@
>   \details{
> \code{lowess} is defined by a complex algorithm, the Ratfor original
> of which (by W. S. Cleveland) can be found in the \R sources as file
> -  \file{src/appl/lowess.doc}.  Normally a local linear polynomial fit is
> +  \file{src/library/stats/src/lowess.doc}.  Normally a local linear 
> polynomial fit is
> used, but under some circumstances (see the file) a local constant fit
> can be used.  \sQuote{Local} is defined by the distance to the
> \code{floor(f*n)}th nearest neighbour, and tricubic weighting is used

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[Bioc-devel] BioCAsia Virtual Meeting, 15-18 October 2020

2020-09-06 Thread Matt Ritchie

BioCAsia is coming to a screen near you this October (15-18).

This will be the 6th annual Bioconductor Asia meeting that aims to bring 
together researchers with an interest in Bioconductor and R to exchange ideas 
and expertise. We're planning a fun and welcoming virtual meeting with talks 
and workshops to suit beginners through to more experienced users.

To learn about the amazing line-up of speakers, register for the event (it's 
free!) or submit an abstract (short and lightning talk slots available, 
abstracts due Friday September 25) please visit 
https://biocasia2020.bioconductor.org/.

Please help spread the word and we hope to e-see you there!

Best wishes,

Matt Ritchie, Qian Liu, Peter Hickey, Julie Zhu, Jin Gu, Rui Jiang and Xuegong 
Zhang (BioCAsia 2020 organising committee)

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You must not disclose, forward, print or use it without the permission of the 
sender.

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Nation as the traditional owners of the land where our campuses are located and
the continuing connection to country and community.
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Re: [R-pkg-devel] CRAN check error in Debian R only

2020-09-06 Thread Ben Bolker


  It's surprising that this is only an error on Debian ...
  In general "strong dependencies not in mainstream repositories" is a 
non-starter. Here is the relevant paragraph from the CRAN repository 
policies:


> Packages on which a CRAN package depends should be available from a 
mainstream repository ...  [where "depends" means 
"Depends/Imports/LinkingTo]


   In principle you could create a package that only "Suggests:" INLA 
(and uses it conditionally) but is effectively non-functional without it 
(i.e. in the absence of INLA, all examples or tests that depend on INLA 
are disabled).  This does seem to defeat the intention of the policy, 
though.  I don't know if the CRAN maintainers would reject it for 
violating the spirit of the policy ...


   cheers
Ben Bolker


On 9/6/20 3:48 PM, Edoardo Baldoni wrote:

Hi all,

I am trying to publish on CRAN a package that uses the INLA::inla function
from the INLA package. The INLA package is outside CRAN. After package
submission, CRAN gives me an error that seems to be related to the use of
this INLA::inla function on Debian R. The error says that the INLA package
is not available. Below the result of the CRAN check.

Can I do anything about it? Can I still publish my package on CRAN?
Thanks
Edoardo

package AGPRIS_1.0.tar.gz does not pass the incoming checks automatically,
please see the following pre-tests:
Windows: <
https://win-builder.r-project.org/incoming_pretest/AGPRIS_1.0_20200906_195909/Windows/00check.log



Status: 1 WARNING, 2 NOTEs
Debian: <
https://win-builder.r-project.org/incoming_pretest/AGPRIS_1.0_20200906_195909/Debian/00check.log



Status: 1 ERROR, 1 WARNING

  * using log directory ‘/srv/hornik/tmp/CRAN/AGPRIS.Rcheck’

* using R Under development (unstable) (2020-09-04 r79137)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘AGPRIS/DESCRIPTION’ ... OK
* this is package ‘AGPRIS’ version ‘1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... WARNING
Maintainer: ‘Edoardo Baldoni ’

New submission

Strong dependencies not in mainstream repositories:
   INLA

Size of tarball: 13345524 bytes
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package required but not available: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR, 1 WARNING

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[R-pkg-devel] CRAN check error in Debian R only

2020-09-06 Thread Edoardo Baldoni

Hi all,

I am trying to publish on CRAN a package that uses the INLA::inla function
from the INLA package. The INLA package is outside CRAN. After package
submission, CRAN gives me an error that seems to be related to the use of
this INLA::inla function on Debian R. The error says that the INLA package
is not available. Below the result of the CRAN check.

Can I do anything about it? Can I still publish my package on CRAN?
Thanks
Edoardo

package AGPRIS_1.0.tar.gz does not pass the incoming checks automatically,
please see the following pre-tests:
Windows: <
https://win-builder.r-project.org/incoming_pretest/AGPRIS_1.0_20200906_195909/Windows/00check.log
>
Status: 1 WARNING, 2 NOTEs
Debian: <
https://win-builder.r-project.org/incoming_pretest/AGPRIS_1.0_20200906_195909/Debian/00check.log
>
Status: 1 ERROR, 1 WARNING

 * using log directory ‘/srv/hornik/tmp/CRAN/AGPRIS.Rcheck’

* using R Under development (unstable) (2020-09-04 r79137)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘AGPRIS/DESCRIPTION’ ... OK
* this is package ‘AGPRIS’ version ‘1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... WARNING
Maintainer: ‘Edoardo Baldoni ’

New submission

Strong dependencies not in mainstream repositories:
  INLA

Size of tarball: 13345524 bytes
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package required but not available: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR, 1 WARNING

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Re: [Bioc-devel] Pushing to Bioconductor repo gives errors

2020-09-06 Thread Alina Selega

Sorry, looks like the error got mangled. I pasted it in this gist:
https://gist.github.com/alinaselega/f5c4f724309211cc4a5bedd2a05bfd1e

Thanks,
Alina

On Sun, 6 Sep 2020 at 12:36, Alina Selega  wrote:

> Hi,
>
> I wanted to re-add a license file to my repository which got misplaced (no
> changes to code). I followed the instructions in this link (
> https://bioconductor.org/developers/how-to/git/pull-upstream-changes/) to
> pull upstream changes.
>
> I then followed these instructions (
> https://bioconductor.org/developers/how-to/git/push-to-github-bioc/). I
> successfully pushed the file to my Github repo, but when I reached step 6
> to push the changes to Bioconductor, I got the following errors:
>
> ```
> Counting objects: 3, done.
>   Delta compression using up to 8
> threads.
> Compressing objects: 100% (3/3), done.
> Writing objects: 100% (3/3), 12.11 KiB | 6.05
> MiB/s, done.  Total 3 (delta 1), reused 1
> (delta 0)
> remote: fatal: this operation must be run in a work tree
> remote: ERROR:root:Exception: Command '['git',
> 'rev-parse', '--show-toplevel']' returned non-zero exit status 128
> remote: ERROR:root:local variable 'package_name' referenced before
> assignment
> remote: Note: failed to update RSS feed;git repository updated
> successfully.To git.bioconductor.org:packages/BUMHMM.git
>   bbafa73..160b7a7  master -> master
> ```
>
> It appears that the upstream updated successfully but can you advise about
> the errors?
>
> Thank you,
> Alina
>
>

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[Bioc-devel] Pushing to Bioconductor repo gives errors

2020-09-06 Thread Alina Selega

Hi,

I wanted to re-add a license file to my repository which got misplaced (no
changes to code). I followed the instructions in this link (
https://bioconductor.org/developers/how-to/git/pull-upstream-changes/) to
pull upstream changes.

I then followed these instructions (
https://bioconductor.org/developers/how-to/git/push-to-github-bioc/). I
successfully pushed the file to my Github repo, but when I reached step 6
to push the changes to Bioconductor, I got the following errors:

```
Counting objects: 3, done.
Delta compression using up to 8
threads.
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 12.11 KiB | 6.05
MiB/s, done.  Total 3 (delta 1), reused 1
(delta 0)
remote: fatal: this operation must be run in a work tree
remote: ERROR:root:Exception: Command '['git',
'rev-parse', '--show-toplevel']' returned non-zero exit status 128
remote: ERROR:root:local variable 'package_name' referenced before
assignment
remote: Note: failed to update RSS feed;git repository updated
successfully.To git.bioconductor.org:packages/BUMHMM.git
bbafa73..160b7a7  master -> master
```

It appears that the upstream updated successfully but can you advise about
the errors?

Thank you,
Alina

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Re: [R-pkg-devel] Submission to CRAN Contributed Documentation

2020-09-06 Thread Jakub Nowosad


Thanks, Stefan.

Yes, I have seen that. However I decided to ask here, as the next 
section of the Contributed Documentation website still encourages people 
to contribute. Thanks once more for clarifying it.


On 9/4/20 2:55 PM, Stefan Evert wrote:

Did you read the notice

Note: The CRAN area for contributed documentation is frozen and no 
longer actively maintained

at the top of that page?

Best,
Stefan



On 4 Sep 2020, at 14:43, Jakub Nowosad  wrote:

Dear all,

I have tried to submit a textbook to the CRAN Contributed Documentation
(https://cran.r-project.org/other-docs.html#nenglish).

However, the instruction on how to do that are vague. The Contributed
Documentation page states "To submit, follow the submission instructions
on the CRAN main page.", however, it is impossible to upload non-R
package using the standard way (https://cran.r-project.org/submit.html).
Therefore, I decided to follow another CRAN suggestion "If this fails,
upload toftp://CRAN.R-project.org/incoming/  and send an email to
cran-submissi...@r-project.org    following 
the policy.", uploaded the PDF to CRAN incoming FTP and wrote
an email several days ago. I did not get any answers back.

Could you suggest me a proper way how to add a document to the CRAN
Contributed Documentation?

Best,

Jakub Nowosad

--
https://nowosad.github.io/ | @jakub_nowosad | nowosad.ja...@gmail.com

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--
https://nowosad.github.io/ | @jakub_nowosad | nowosad.ja...@gmail.com

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[Rd] Error in ?lowess

2020-09-06 Thread Duncan Murdoch

The lowess() help page refers to documentation in "src/appl/lowess.doc". 
 This was moved to "src/library/stats/src/lowess.doc" in 2007.  This 
patch fixes it:


Index: src/library/stats/man/lowess.Rd
===
--- src/library/stats/man/lowess.Rd (revision 79137)
+++ src/library/stats/man/lowess.Rd (working copy)
@@ -30,7 +30,7 @@
 \details{
   \code{lowess} is defined by a complex algorithm, the Ratfor original
   of which (by W. S. Cleveland) can be found in the \R sources as file
-  \file{src/appl/lowess.doc}.  Normally a local linear polynomial fit is
+  \file{src/library/stats/src/lowess.doc}.  Normally a local linear 
polynomial fit is

   used, but under some circumstances (see the file) a local constant fit
   can be used.  \sQuote{Local} is defined by the distance to the
   \code{floor(f*n)}th nearest neighbour, and tricubic weighting is used

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Re: [Rd] Error in ?lowess

[Bioc-devel] BioCAsia Virtual Meeting, 15-18 October 2020

Re: [R-pkg-devel] CRAN check error in Debian R only

[R-pkg-devel] CRAN check error in Debian R only

Re: [Bioc-devel] Pushing to Bioconductor repo gives errors

[Bioc-devel] Pushing to Bioconductor repo gives errors

Re: [R-pkg-devel] Submission to CRAN Contributed Documentation

[Rd] Error in ?lowess

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