Re: [R-pkg-devel] Spelling of PDB in Package Description

2023-09-14 Thread Uwe Ligges




On 14.09.2023 23:35, Leonard Mada wrote:

Dear Uwe,


I found out what is going on. There is an example:

## Write the pdb object in file "Rpdb.pdb" into the current directory
write.pdb(pdb, file = "Rpdb.pdb")



In examples, you should write to tempdir(), if at all.

Best,
Uwe Ligges






The example was present in the previous version as well. So I did not 
thought about it. I do not know how to handle this: although the example 
should probably remain.



Sincerely,


Leonard


On 9/15/2023 12:27 AM, Uwe Ligges wrote:

The spellng is fine and not a problem.

For
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘Rpdb.pdb’
You need to move this to ./inst or a subdirectory or, if data, 
consider ./extdata See Writing R Extensions.


Best,
Uwe Ligges


On 14.09.2023 22:06, Avraham Adler wrote:
Regarding PDB, in Rd format it’s best to wrap that in an \acronym{} 
tag. See section 2.3 of 
https://cran.r-project.org/doc/manuals/R-exts.html#Marking-text


Avi

Sent from my iPhone

On Sep 14, 2023, at 3:40 PM, Leonard Mada via R-package-devel 
 wrote:


Dear List Members,

After resubmitting the updated version of the Rpdb package (2.3.1), 
the following Notes were generated:


1.) Spelling PDB
https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Windows/00check.log
https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Debian/00check.log

The PDB stands for Protein Data Bank:
http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html

It should be the correct spelling (and was the same in the previous 
versions of the package).


2.)  Small Sample PDB Files
* checking for non-standard things in the check directory ...
NOTE Found the following files/directories: ‘Rpdb.pdb’

There is a directory with 3 very small sample pdb-files. The 
directory was also present in the previous version.


How should I proceed? Or did I miss something?


Sincerely,


Leonard

__
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Re: [R-pkg-devel] Spelling of PDB in Package Description

2023-09-14 Thread Leonard Mada via R-package-devel

Dear Uwe,


I found out what is going on. There is an example:

## Write the pdb object in file "Rpdb.pdb" into the current directory
write.pdb(pdb, file = "Rpdb.pdb")


The example was present in the previous version as well. So I did not 
thought about it. I do not know how to handle this: although the example 
should probably remain.



Sincerely,


Leonard


On 9/15/2023 12:27 AM, Uwe Ligges wrote:

The spellng is fine and not a problem.

For
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘Rpdb.pdb’
You need to move this to ./inst or a subdirectory or, if data, 
consider ./extdata See Writing R Extensions.


Best,
Uwe Ligges


On 14.09.2023 22:06, Avraham Adler wrote:
Regarding PDB, in Rd format it’s best to wrap that in an \acronym{} 
tag. See section 2.3 of 
https://cran.r-project.org/doc/manuals/R-exts.html#Marking-text


Avi

Sent from my iPhone

On Sep 14, 2023, at 3:40 PM, Leonard Mada via R-package-devel 
 wrote:


Dear List Members,

After resubmitting the updated version of the Rpdb package (2.3.1), 
the following Notes were generated:


1.) Spelling PDB
https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Windows/00check.log 

https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Debian/00check.log 



The PDB stands for Protein Data Bank:
http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html 



It should be the correct spelling (and was the same in the previous 
versions of the package).


2.)  Small Sample PDB Files
* checking for non-standard things in the check directory ...
NOTE Found the following files/directories: ‘Rpdb.pdb’

There is a directory with 3 very small sample pdb-files. The 
directory was also present in the previous version.


How should I proceed? Or did I miss something?


Sincerely,


Leonard

__
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] Spelling of PDB in Package Description

2023-09-14 Thread Uwe Ligges

The spellng is fine and not a problem.

For
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘Rpdb.pdb’
You need to move this to ./inst or a subdirectory or, if data, consider 
./extdata See Writing R Extensions.


Best,
Uwe Ligges


On 14.09.2023 22:06, Avraham Adler wrote:

Regarding PDB, in Rd format it’s best to wrap that in an \acronym{} tag. See 
section 2.3 of https://cran.r-project.org/doc/manuals/R-exts.html#Marking-text

Avi

Sent from my iPhone


On Sep 14, 2023, at 3:40 PM, Leonard Mada via R-package-devel 
 wrote:

Dear List Members,

After resubmitting the updated version of the Rpdb package (2.3.1), the 
following Notes were generated:

1.) Spelling PDB
https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Windows/00check.log
https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Debian/00check.log

The PDB stands for Protein Data Bank:
http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html

It should be the correct spelling (and was the same in the previous versions of 
the package).

2.)  Small Sample PDB Files
* checking for non-standard things in the check directory ...
NOTE Found the following files/directories: ‘Rpdb.pdb’

There is a directory with 3 very small sample pdb-files. The directory was also 
present in the previous version.

How should I proceed? Or did I miss something?


Sincerely,


Leonard

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


[[alternative HTML version deleted]]

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Re: [R-pkg-devel] Spelling of PDB in Package Description

2023-09-14 Thread Avraham Adler
Regarding PDB, in Rd format it’s best to wrap that in an \acronym{} tag. See 
section 2.3 of https://cran.r-project.org/doc/manuals/R-exts.html#Marking-text

Avi

Sent from my iPhone

> On Sep 14, 2023, at 3:40 PM, Leonard Mada via R-package-devel 
>  wrote:
> 
> Dear List Members,
> 
> After resubmitting the updated version of the Rpdb package (2.3.1), the 
> following Notes were generated:
> 
> 1.) Spelling PDB
> https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Windows/00check.log
> https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Debian/00check.log
> 
> The PDB stands for Protein Data Bank:
> http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html
> 
> It should be the correct spelling (and was the same in the previous versions 
> of the package).
> 
> 2.)  Small Sample PDB Files
> * checking for non-standard things in the check directory ...
> NOTE Found the following files/directories: ‘Rpdb.pdb’
> 
> There is a directory with 3 very small sample pdb-files. The directory was 
> also present in the previous version.
> 
> How should I proceed? Or did I miss something?
> 
> 
> Sincerely,
> 
> 
> Leonard
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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[R-pkg-devel] Spelling of PDB in Package Description

2023-09-14 Thread Leonard Mada via R-package-devel

Dear List Members,

After resubmitting the updated version of the Rpdb package (2.3.1), the 
following Notes were generated:


1.) Spelling PDB
https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Windows/00check.log
https://win-builder.r-project.org/incoming_pretest/Rpdb_2.3.1_20230914_173458/Debian/00check.log

The PDB stands for Protein Data Bank:
http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html

It should be the correct spelling (and was the same in the previous 
versions of the package).


2.)  Small Sample PDB Files
* checking for non-standard things in the check directory ...
NOTE Found the following files/directories: ‘Rpdb.pdb’

There is a directory with 3 very small sample pdb-files. The directory 
was also present in the previous version.


How should I proceed? Or did I miss something?


Sincerely,


Leonard

__
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Re: [Bioc-devel] Deprecated Packages for Bioc 3.18

2023-09-14 Thread Kern, Lori via Bioc-devel
Yes I will undeprecate now that the build report is clear. Thank you .


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Jean-Philippe 
Fortin 
Sent: Thursday, September 14, 2023 11:15 AM
To: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Deprecated Packages for Bioc 3.18

Hi Lori,

shinyMethyl is now building -- could you undeprecate the package please?

Thank you,
JP

On Tue, Sep 5, 2023 at 10:50 AM Kern, Lori via Bioc-devel <
bioc-devel@r-project.org> wrote:

> The Bioconductor Team is continuing to identify packages that will be
> deprecated in the next release to allow for the Bioconductor community to
> respond accordingly.
>
> Please see the current list at
> https://secure-web.cisco.com/1_b7-3BJUqbWpcljNgxwTqQej1fRAwTnfvD1X3nXP1BIUEMu8i3w7cAUCiqYSojwILSsfD4zGb7YFx1E-Tm3Ufa3_SHwMOTw53moeDJUQ0vK9NzQxSBT2J7MIoP3flsOYDBOJAxo_Rw4bECt5KdLQHDV1Xe42bvlqlbaCmNnhOEbqYR5REy8LEiIilAh0M2BL_9nE-146XLT4Vmg9UI_lbkV2KzxohQ_q5AloWwjBXQcOrlt82Ggo9eNB5ZYxB9a2YtTnZ1Y7L2om0YbLixPCJDZHrhRYbdVic_j3JXk5ix1wuQ4iH1uC-eUHWcBelpPm/https%3A%2F%2Fsupport.bioconductor.org%2Fp%2F9152979%2F
>
>
>
> It should be noted, we did try to reach out to these package maintainers
> multiple times and they were either unresponsive or had emails bounce. We
> encourage anyone that is familiar with a package maintainer on this list to
> reach out to them and notify them directly. Packages can be un-deprecated
> if a maintainer fixes the package to build/check cleanly before the next
> release and requests un-deprecation on the bioc-devel@r-project.org
> mailing list
>
>
>
> Please do not undeprecate a package yourself. You must request
> undeprecation from the Bioconductor core team at bioc-devel@r-project.org.
>
>
> Thank you
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
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Re: [Bioc-devel] Deprecated Packages for Bioc 3.18

2023-09-14 Thread Jean-Philippe Fortin
Hi Lori,

shinyMethyl is now building -- could you undeprecate the package please?

Thank you,
JP

On Tue, Sep 5, 2023 at 10:50 AM Kern, Lori via Bioc-devel <
bioc-devel@r-project.org> wrote:

> The Bioconductor Team is continuing to identify packages that will be
> deprecated in the next release to allow for the Bioconductor community to
> respond accordingly.
>
> Please see the current list at
> https://support.bioconductor.org/p/9152979/
>
>
>
> It should be noted, we did try to reach out to these package maintainers
> multiple times and they were either unresponsive or had emails bounce. We
> encourage anyone that is familiar with a package maintainer on this list to
> reach out to them and notify them directly. Packages can be un-deprecated
> if a maintainer fixes the package to build/check cleanly before the next
> release and requests un-deprecation on the bioc-devel@r-project.org
> mailing list
>
>
>
> Please do not undeprecate a package yourself. You must request
> undeprecation from the Bioconductor core team at bioc-devel@r-project.org.
>
>
> Thank you
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
> ___
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Re: [Rd] R packages to send plottable data to external apps

2023-09-14 Thread Mike Marchywka
I put this up on github in current form where it sort of
works and I can use it for my needs but if anyone 
thinks it fills a niche I guess I could clean it up.

https://github.com/mmarchywka/mjmdatascope

Definitely not ready for users but maybe a deverloper.
In terms of the "Trend" package you mentioned 
maybe one interface would be to emulate that action
too as that was my original interest circa 2007 lol. 

fwiw.
Thanks. 


 Mike Marchywka 
44 Crosscreek Trail
Jasper GA 30143
was 306 Charles Cox Drive  Canton, GA 30115
470-758-0799
404-788-1216 





From: Iñaki Ucar 
Sent: Sunday, August 27, 2023 7:12 PM
To: Mike Marchywka
Cc: r-devel; R Package Development
Subject: Re: [Rd] R packages to send plottable data to external apps

I think r-package-devel is a better place for this. CC'ing there.

On Sun, 27 Aug 2023 at 23:50, Mike Marchywka  wrote:
>
> I was curious what R packages, or indeed any other applications, exist
> to plot streamed data from arbitrary data generators. It need not
> be publication quality plotting but it should be easy to use  like
> an oscilloscope.

The last time I checked, there wasn't any R package suitable for
plotting high-throughput streaming data.

There's a nice command-line utility called trend [1] that I
extensively used in the past as an oscilloscope to visualize the
output from a DAQ card. I don't see any new development there, but it
does exactly what it promises; it's easy to use, quite configurable
and very fast. Old but gold.

I also explored VisPy, which is much more ambitious, but at that time
the API had a limitation that didn't allow me to achieve what I
required, and I haven't looked at it ever since, but the project seems
in good shape.

[1] https://www.thregr.org/wavexx/software/trend/
[2] https://vispy.org/

Hope it helps,
Iñaki

> I was working on something called datascope that I
> am using for 1D finite difference monitoring and recently interfaced it
> to freefem. I also created an R package. If there is any interest in something
> like this I guess I could put it up somewhere when it is more usable
> or if you can suggest some similar popular packages that would be good
> too. Is there something I could drop-in to the attached code and get
> something like the attached output that could also be switched to other
> data sources?  This right now works via linux fifo and somewhat by UDP.
> It can queue data and stop making it if no one seems to be  consuming
> it depending on the channel.
>
> Thanks.
>
>  Mike Marchywka
> 44 Crosscreek Trail
> Jasper GA 30143
> was 306 Charles Cox Drive  Canton, GA 30115
> 470-758-0799
> 404-788-1216
>
>
> __
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Re: [R-pkg-devel] Cadence of macOS builds at CRAN

2023-09-14 Thread Aron Atkins
Dirk,

Providing a partial answer: Simon replied earlier today to my related
question; macOS builds had been blocked, but are starting to flow again.

> one package managed to spawn a separate process that was blocking the
build process (long story) and I was on the other side of the world. It
should be fixed now, but it may take up to a day before the backlog is
processed.

https://stat.ethz.ch/pipermail/r-package-devel/2023q3/009562.html

Aron

On Thu, Sep 14, 2023 at 9:09 AM Dirk Eddelbuettel  wrote:

>
> Simon,
>
> A new package of mine [1] appeared on CRAN on Sep 5. Respecting the one
> week gap,
> I made a small update on Sep 12.
>
> Today is Sep 14. There are still no builds for
>   macOS r-release (arm64)
>   macOS r-oldrel (arm64)
>   macOS r-release (x86_64)
> but we do have two oldrel releases. Weirder still we have results for
> macOS r-release (x86_64) even when the binary is not listed.
>
> There is nothing tricky in the package or it dependencies.  Could you
> provide
> an update of what should and can be expected in the macOS provision? Is
> this
> a matter of intra-CRAN syncing between your builder(s) and the Vienna site?
>
> Thanks as always,  Dirk
>
> [1] https://cran.r-project.org/package=RcppInt64
>
> --
> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>
> __
> R-package-devel@r-project.org mailing list
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>


-- 
email: aron.atk...@gmail.com
home: http://gweep.net/~aron/

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[R-pkg-devel] Cadence of macOS builds at CRAN

2023-09-14 Thread Dirk Eddelbuettel


Simon,

A new package of mine [1] appeared on CRAN on Sep 5. Respecting the one week 
gap,
I made a small update on Sep 12.

Today is Sep 14. There are still no builds for
  macOS r-release (arm64)
  macOS r-oldrel (arm64)
  macOS r-release (x86_64)
but we do have two oldrel releases. Weirder still we have results for
macOS r-release (x86_64) even when the binary is not listed.

There is nothing tricky in the package or it dependencies.  Could you provide
an update of what should and can be expected in the macOS provision? Is this
a matter of intra-CRAN syncing between your builder(s) and the Vienna site?

Thanks as always,  Dirk

[1] https://cran.r-project.org/package=RcppInt64

-- 
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[Bioc-devel] Reminder: BioCAsia2023 Abstract Submission Closes Tomorrow!

2023-09-14 Thread Maria . Doyle
Dear Bioconductor Developers,

A quick reminder that the deadline for BioCAsia2023 abstract submissions is 
tomorrow, September 15. If you've been considering presenting a short or 
lightning talk, now's your chance!

Submit Your Abstract 
Here

Don't miss this opportunity to share your work with the community.

Warm regards,
Maria

Maria Doyle, PhD
Bioconductor Community Manager

From: Maria.Doyle 
Date: Friday, 1 September 2023 at 11:49
To: bioc-devel@r-project.org 
Subject: News: BioCAsia2023 Abstract Submission & Registration Now Open!
Dear Bioconductor Developers,

We're excited to announce that the BioCAsia2023 symposium is scheduled to be 
held in Hong Kong on October 16-17.
BioCAsia2023 Event Details

Registration is free!

We invite you to submit your abstracts by September 15 for:

  *   Short talk (15 min)
  *   Lightning talk (3 min)

Submit Your Abstract 
Here

Thank you for your continued contributions to the Bioconductor community.

Warm regards,
Maria

Maria Doyle, PhD
Bioconductor Community Manager

School of Medicine,
University of Limerick, Limerick, V94 T9PX
Email: maria.do...@ul.ie
Phone (office): +353 61 234 768
[I work flexible hours across several time zones. I don't expect you to read or 
respond to my emails outside of your normal working hours]


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Re: [R-pkg-devel] published packages not showing updated macOS results

2023-09-14 Thread Simon Urbanek
Aron,

one package managed to spawn a separate process that was blocking the build 
process (long story) and I was on the other side of the world. It should be 
fixed now, but it may take up to a day before the backlog is processed. In the 
future for faster response, please contact me directly - see "CRAN Binary 
Package Maintenance" on the CRAN Team webpage.

Cheers,
Simon


> On Sep 13, 2023, at 2:10 AM, Aron Atkins  wrote:
> 
> Hi.
> 
> It looks like macOS package publishing may have stalled. One of my
> packages, rsconnect 1.1.0, arrived on CRAN about a week ago. It is built
> almost everywhere, but r-release-macos* and r-release-macos-arm64 are still
> showing results from the previous release.
> 
> Recent releases did see check failures on the r-release-macos-x86_64 host
> (because its Pandoc installation was older than supported by one of our
> dependencies). The rsconnect 1.1.0 release should address these failures,
> but I am still waiting to see builds flow through.
> 
> https://cran.r-project.org/web/packages/rsconnect/index.html
> https://cran.r-project.org/web/checks/check_results_rsconnect.html
> 
> Is someone able to look into this or otherwise offer advice?
> 
> Thanks,
> Aron
> -- 
> email: aron.atk...@gmail.com
> home: http://gweep.net/~aron/
> 
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