Re: [Bioc-devel] Package "rmspc" failing on Bioconductor devel

[Jennifer Wokaty]

Hi Meriem,

.NET 6.0 was installed on lconway, so I removed it and replaced it with .NET 
5.0; however, I noticed that 5.0 is no longer supported by Microsoft, which now 
suggests .NET 6.0. The new version also supports Mac ARM64 whereas 5.0 does 
not. You may want to consider upgrading your package to work with .NET 6.0 in 
the future.

Jennifer Wokaty
they/them
Bioconductor Core Team
CUNY SPH


From: Bioc-devel  on behalf of Meriem Bahda 

Sent: Wednesday, September 28, 2022 11:48:47 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Package "rmspc" failing on Bioconductor devel

***ATTENTION: This email came from an external source. Do not open attachments 
or click on links from unknown senders or unexpected emails.***

Dear Community,

I have submitted the package rmspc to Bioconductor in July 2021. A
prerequisite for the rmspc package is .NET 5.0. Before installing the
rmspc package,
the program .NET 5.0. should already be installed on the user's computer.
The Bioconductor team added .NET to their builders and the package was
accepted in August 2021.

A few days ago, I received an email saying that the package didn't pass the
platform build check for the host *lconway*. I believe this error may have
occured because .NET isn't installed in  *lconway*.

Who should I contact regarding this issue?

Thank you!

--

*Meriem BAHDA*

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Re: [Bioc-devel] New maintainer for package - Updating a R package and pushing the commit

[Hervé Pagès]

Hi Tulip,

On 29/09/2022 13:52, Tulip Nandu wrote:


Hi Kern,

Anusha no longer is associated with the lab. So I will need to have access to 
the package. If you can create an account on GitCredentials that would be great.


If that means Anusha is no longer going to maintain the package, then 
their role in Authors@R would need to be switched from "cre" to "aut" or 
"ctb" or whatever is appropriate.


As Lori said, the Maintainer and Author fields should get removed, and 
your name and role moved to the Authors@R field.


Thanks,

H.



I do have a github account.  tulipnandu is the username.


https://github.com/tulipnandu
[https://avatars.githubusercontent.com/u/1099843?v=4?s=400]
tulipnandu - Overview
tulipnandu has 10 repositories available. Follow their code on GitHub.
github.com
Also I would need to push the changes in the src file to master on 
bioconductor/git. If I can get some help with that, it would be great too.

Regards,

Tulip.


From: Kern, Lori 
Sent: Thursday, September 29, 2022 6:52 AM
To: Tulip Nandu ; bioc-devel@r-project.org 
; Anusha Nagari 
Subject: Re: New maintainer for package - Updating a R package and pushing the 
commit


EXTERNAL MAIL

This message was sent securely using Zix�

a few points:

Normally only one person has maintainer access to a package this currently was Anusha 
Nagari .  Should they also retain maintainer 
access?

Anusha was assigned because that is who is listed with Authors@R.  You 
currently have a mixure of using Authors@R and Maintainer/Author field.  Please 
remove Author/Maintainer fields and only use Authors@R.

In a normal procedure the currently listed maintainer would request the switch 
or additional access.  Since I see you listed in the Maintainer field, we can 
ignore this step for this situation. I will need to create an account on our 
GitCredentials where you can manage your ssh keys for access.  We can link a 
github account for access.  Do you have a personal github account you would 
like associated with; if so please provide your github username?

Cheers,


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 Tulip Nandu 

Sent: Wednesday, September 28, 2022 5:15 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] New maintainer for package - Updating a R package and 
pushing the commit

Hi,

I'm the new maintainer of the groHMM package which is having issues in its 
build.

In that view I would like to update the package but it won't allow me since my 
email is not on file with the maintainer of bioconductor package.

Can you please list the steps to have me listed as a maintainer and update the 
package on bioconductor/git.

Let me know.

Regards,

Tulip.




UT Southwestern

Medical Center

The future of medicine, today.

 [[alternative HTML version deleted]]

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are hereby notified that any disclosure, copying, distribution, or use of this 
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--
Hervé Pagès

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Rd] Question about grid.group compositing operators in cairo

[Paul Murrell]

Hi

Some more thoughts ...

<1>
I said before that currently, dev->group() does this ...

[OVER] shape shape shape OP shape shape shape

... and one option would be an implicit group on 'src' and 'dst' like 
this ...


([OVER] shape shape shape) OP ([OVER] shape shape shape)

... but another approach could be just an implicit group on each shape, 
like this ...


[OVER] ([OVER] shape) ([OVER] shape) OP ([OVER] shape) ([OVER] shape)

That may be a better representation of what you are already doing with 
dsvg() ?  It may also better reflect what naturally occurs in some 
graphics systems.


<2>
Changing the Cairo implementation to work like that would I think 
produce the same result as your dsvg() for ...


grid.group(src, "in", dst)

... and it would make what constitutes more than one shape much less 
surprising ...


gList(rectGrob(), rectGrob())  ## multiple shapes (obviously)
rectGrob(width=1:2/2)  ## multiple shapes (less obvious)
rectGrob(gp=gpar(col=, fill=)) ## NOT multiple shapes (no surprise)

... and it should not break any pre-existing non-group behaviour.

<3>
One casualty from this third option would be that the following would no 
longer solve the overlapping fill and stroke problem ...


grid.group(overlapRect, "source")

... although the fact that that currently works is really a bit 
surprising AND that result could still be achieved by explicitly drawing 
separate shapes ...


grid.group(rectGrob(gp=gpar(col=rgb(1,0,0,.5), lwd=20, fill=NA)),
   "source",
   rectGrob(gp=gpar(col=NA, fill="green")))

<4>
I need to try some of this out and also check in with some other people 
who I think are working on implementing groups on different graphics 
devices.


<5>
In summary, don't go changing dsvg() too much just yet!

Paul

On 29/09/2022 1:30 pm, Paul Murrell wrote:

Hi

Would it work to explicitly record a filled-and-stroked shape as two 
separate elements (one only filled and one only stroked) ?


Then it should only be as hard to apply the active operator on both of 
those elements as it is to apply the active operator to more than one 
shape (?)


Paul

On 29/09/22 10:17, Panagiotis Skintzos wrote:

Thank you for the very thorough explanation Paul.

To answer your question on 11: The dsvg device, simply defines svg
elements with their attributes (rect with fill & stroke in my examples).
It does not do any internal image processing like cairo.

My concern is how to proceed with the implementation in dsvg.

If I leave it as it is now, they're will be cases where it will give
different results from cairo (and perhaps other devices that will
implement group compositing in similar way).

On the other hand It would be quite challenging in practice to simulate
the cairo implementation and apply first the fill and then the stroke
with the active operator, on the element itself.

Any suggestions? :-)

Panagiotis


On 28/9/22 02:56, Paul Murrell wrote:
 > Hi
 >
 > Thanks for the code (and for the previous attachments).
 >
 > Some thoughts so far (HTML version with images attached) ...
 >
 > <1>
 > As you have pointed out, the Cairo device draws a stroked-and-filled
 > shape with two separate drawing operations: the path is filled and
 > then the path is stroked.  I do not believe that there is any
 > alternative in Cairo graphics (apart from filling and stroking as an
 > isolated group and then drawing the group, which we will come back 
to).

 >
 > <2>
 > This fill-then-stroke approach is easy to demonstrate just with a 
thick

 > semitransparent border ...
 >
 > library(grid)
 > overlapRect <- rectGrob(width=.5, height=.5,
 >     gp=gpar(fill="green", lwd=20,
 >     col=rgb(1,0,0,.5)))
 > grid.newpage()
 > grid.draw(overlapRect)
 >
 > <3>
 > This fill-then-stroke approach is what happens on many (most?)
 > graphics devices, including, for example, the core windows() device,
 > the core quartz() device, the 'ragg' devices, and 'ggiraph'.  The
 > latter is true because this is actually the defined behaviour for 
SVG ...

 >
 > https://www.w3.org/TR/SVG2/render.html#Elements 

 > https://www.w3.org/TR/SVG2/render.html#PaintingShapesAndText 


 >
 > <4>
 > There are exceptions to the fill-then-stroke approach, including the
 > core pdf() device, but I think they are in the minority.  The PDF
 > language supports a "B" operator that only fills within the border (no
 > overlap between fill and border).  Demonstrating this is complicated
 > by the fact that not all PDF viewers support this correctly (e.g.,
 > evince and Firefox do not;  ghostscript and chrome do)!
 >
 > <5>
 > Forcing all R graphics devices to change the rendering of
 > filled-and-stroked shapes to match the PDF definition instead of
 > fill-then-stroke is unlikely to happen because it would impact a lot
 > of graphics devices, it would break existing 

Re: [R-pkg-devel] Found the following (possibly) invalid URLs:

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks!.  It tried it again,  got a 404,  then tried it again,  got the site.  
I will take it up with the people in charge.

-Roy

> On Sep 29, 2022, at 1:55 PM, Ben Bolker  wrote:
> 
>  I get a 404.
> 
> On 2022-09-29 4:50 p.m., Roy Mendelssohn - NOAA Federal via R-package-devel 
> wrote:
>> In testing a new version of one of my package on win builder,   I get the 
>> following:
>> Found the following (possibly) invalid URLs:
>> .
>> .
>> .
>>   URL: 
>> https://www.integratedecosystemassessment.noaa.gov/regions/california-current-region/index.html
>> From: inst/doc/Using_rerddap.html
>> Status: 404
>> Message: Not Found
>> It is only in the vignette as a place to look up more about a project,  it 
>> is never actually accessed,  moreover at least from my home computer it is 
>> valid URL that I reach. I know I can include something about this in 
>> cran-comments,  but I would prefer not generating any notes so human 
>> intervention isn't needed.  Any suggestions?  Can others test the URL to see 
>> if they have problems reaching it.
>> Thanks,
>> -Roy
>> **
>> "The contents of this message do not reflect any position of the U.S. 
>> Government or NOAA."
>> **
>> Roy Mendelssohn
>> Supervisory Operations Research Analyst
>> NOAA/NMFS
>> Environmental Research Division
>> Southwest Fisheries Science Center
>> ***Note new street address***
>> 110 McAllister Way
>> Santa Cruz, CA 95060
>> Phone: (831)-420-3666
>> Fax: (831) 420-3980
>> e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/
>> "Old age and treachery will overcome youth and skill."
>> "From those who have been given much, much will be expected"
>> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 
> -- 
> Dr. Benjamin Bolker
> Professor, Mathematics & Statistics and Biology, McMaster University
> Director, School of Computational Science and Engineering
> (Acting) Graduate chair, Mathematics & Statistics
> > E-mail is sent at my convenience; I don't expect replies outside of working 
> > hours.
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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Re: [R-pkg-devel] Found the following (possibly) invalid URLs:

[Ben Bolker]

  I get a 404.

On 2022-09-29 4:50 p.m., Roy Mendelssohn - NOAA Federal via 
R-package-devel wrote:

In testing a new version of one of my package on win builder,   I get the 
following:

Found the following (possibly) invalid URLs:
.
.
.
   URL: 
https://www.integratedecosystemassessment.noaa.gov/regions/california-current-region/index.html
 From: inst/doc/Using_rerddap.html
 Status: 404
 Message: Not Found

It is only in the vignette as a place to look up more about a project,  it is 
never actually accessed,  moreover at least from my home computer it is valid 
URL that I reach. I know I can include something about this in cran-comments,  
but I would prefer not generating any notes so human intervention isn't needed. 
 Any suggestions?  Can others test the URL to see if they have problems 
reaching it.

Thanks,

-Roy


**
"The contents of this message do not reflect any position of the U.S. Government or 
NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

__
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--
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
(Acting) Graduate chair, Mathematics & Statistics
> E-mail is sent at my convenience; I don't expect replies outside of 
working hours.


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Re: [Bioc-devel] New maintainer for package - Updating a R package and pushing the commit

[Tulip Nandu]

Hi Kern,

Anusha no longer is associated with the lab. So I will need to have access to 
the package. If you can create an account on GitCredentials that would be great.

I do have a github account.  tulipnandu is the username.


https://github.com/tulipnandu
[https://avatars.githubusercontent.com/u/1099843?v=4?s=400]
tulipnandu - Overview
tulipnandu has 10 repositories available. Follow their code on GitHub.
github.com
Also I would need to push the changes in the src file to master on 
bioconductor/git. If I can get some help with that, it would be great too.

Regards,

Tulip.


From: Kern, Lori 
Sent: Thursday, September 29, 2022 6:52 AM
To: Tulip Nandu ; bioc-devel@r-project.org 
; Anusha Nagari 
Subject: Re: New maintainer for package - Updating a R package and pushing the 
commit


EXTERNAL MAIL

This message was sent securely using Zix�

a few points:

Normally only one person has maintainer access to a package this currently was 
Anusha Nagari .  Should they also retain 
maintainer access?

Anusha was assigned because that is who is listed with Authors@R.  You 
currently have a mixure of using Authors@R and Maintainer/Author field.  Please 
remove Author/Maintainer fields and only use Authors@R.

In a normal procedure the currently listed maintainer would request the switch 
or additional access.  Since I see you listed in the Maintainer field, we can 
ignore this step for this situation. I will need to create an account on our 
GitCredentials where you can manage your ssh keys for access.  We can link a 
github account for access.  Do you have a personal github account you would 
like associated with; if so please provide your github username?

Cheers,


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 Tulip Nandu 

Sent: Wednesday, September 28, 2022 5:15 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] New maintainer for package - Updating a R package and 
pushing the commit

Hi,

I'm the new maintainer of the groHMM package which is having issues in its 
build.

In that view I would like to update the package but it won't allow me since my 
email is not on file with the maintainer of bioconductor package.

Can you please list the steps to have me listed as a maintainer and update the 
package on bioconductor/git.

Let me know.

Regards,

Tulip.




UT Southwestern

Medical Center

The future of medicine, today.

[[alternative HTML version deleted]]

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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.

This message was secured by Zix�.

CAUTION: This email originated from outside UTSW. Please be cautious of links 
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[R-pkg-devel] Found the following (possibly) invalid URLs:

[Roy Mendelssohn - NOAA Federal via R-package-devel]

In testing a new version of one of my package on win builder,   I get the 
following:

Found the following (possibly) invalid URLs:
.
.
.
  URL: 
https://www.integratedecosystemassessment.noaa.gov/regions/california-current-region/index.html
From: inst/doc/Using_rerddap.html
Status: 404
Message: Not Found

It is only in the vignette as a place to look up more about a project,  it is 
never actually accessed,  moreover at least from my home computer it is valid 
URL that I reach. I know I can include something about this in cran-comments,  
but I would prefer not generating any notes so human intervention isn't needed. 
 Any suggestions?  Can others test the URL to see if they have problems 
reaching it.

Thanks,

-Roy


**
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

__
R-package-devel@r-project.org mailing list
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Re: [Bioc-devel] broken DOI link for SINGLe package

[Rocio Espada via Bioc-devel]

Hi Jennifer,
Thank you for taking care.

Have a nice day,
Rocio

On 2022-09-28 18:45, Jennifer Wokaty wrote:

Hi Rocio,

Thanks for bringing this to our attention. I've fixed the DOI for 
SINGLe.


Jennifer Wokaty
they/them
Bioconductor Core Team
CUNY SPH


From: Bioc-devel  on behalf of Rocio
Espada via Bioc-devel 
Sent: Wednesday, September 28, 2022 7:51 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] broken DOI link for SINGLe package

***ATTENTION: This email came from an external source. Do not open
attachments or click on links from unknown senders or unexpected
emails.***

Hi,

The DOI link for the package SINGLe (which I uploaded to bioconductor)
is not working. Do you know how I can fix this?
This is the link to the package (that does work):
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_packages_release_bioc_html_single.html=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=7FmOGwG3w09AwysDnb8Mkoe_nOk8KtlEkHCXFNrJMN4s-f0d4JllRph-pHuaRrJm=LcpRgSrxEqBnuWyGR3u5fnNwC1rP1Jc5_LkPoFIlWRQ=
and this is the DOI's link included there, that does not work:
https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_doi-3A10.18129_B9.bioc.single=DwICAg=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=7FmOGwG3w09AwysDnb8Mkoe_nOk8KtlEkHCXFNrJMN4s-f0d4JllRph-pHuaRrJm=rGiIvVYCzEeKC19nlsEiMeiUG6regDYdLlnGssZaAUk=

Thanks in advance,
Rocio

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Re: [Bioc-devel] New maintainer for package - Updating a R package and pushing the commit

[Kern, Lori]

a few points:

Normally only one person has maintainer access to a package this currently was 
Anusha Nagari .  Should they also retain 
maintainer access?

Anusha was assigned because that is who is listed with Authors@R.  You 
currently have a mixure of using Authors@R and Maintainer/Author field.  Please 
remove Author/Maintainer fields and only use Authors@R.

In a normal procedure the currently listed maintainer would request the switch 
or additional access.  Since I see you listed in the Maintainer field, we can 
ignore this step for this situation. I will need to create an account on our 
GitCredentials where you can manage your ssh keys for access.  We can link a 
github account for access.  Do you have a personal github account you would 
like associated with; if so please provide your github username?

Cheers,


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 Tulip Nandu 

Sent: Wednesday, September 28, 2022 5:15 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] New maintainer for package - Updating a R package and 
pushing the commit

Hi,

I'm the new maintainer of the groHMM package which is having issues in its 
build.

In that view I would like to update the package but it won't allow me since my 
email is not on file with the maintainer of bioconductor package.

Can you please list the steps to have me listed as a maintainer and update the 
package on bioconductor/git.

Let me know.

Regards,

Tulip.




UT Southwestern

Medical Center

The future of medicine, today.

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Re: [R-pkg-devel] no incoming checks

[Uwe Ligges]

On 28.09.2022 17:33, Uwe Ligges wrote:

Dear developers,

currently CRAN incoming checks are offline due to network issues at my 
university. I hope this will be resolved early tomorrow.


Best,
Uwe Ligges



This has been resolved last night (by a reboot of the central switch of 
the university) and is currently catching up with submissions.


Best,
Uwe Ligges

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