Re: [Rd] Rscript -e EXPR fails to launch if stdin is closed

[Dirk Eddelbuettel]

On 10 October 2022 at 09:34, Henrik Bengtsson wrote:
| Thank you Peter for the quick fix.  Will this make it into R-patched
| to become R 4.2.2 soon?

I checked when you posted this and didn't reply -- but this is also not an
issue for littler so if you need alternative there is one

  $ Rscript --vanilla -e 42 0<&- 
  Fatal error: creating temporary file for '-e' failed
  $
  $ r -p -e 42 0<&-  # -p to force print
  [1] 42
  $ 

Dirk

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[Rd] tools:: extracting pkg dependencies from DCF

[Jan Gorecki]

Dear R devs,

I would like to raise a request for a simple helper function.
Utility function to extract package dependencies from DESCRIPTION file.

I do think that tools package is better place, for such a fundamental
functionality, than community packages.

tools pkg seems perfect fit (having already great function write_PACKAGES).

Functionality I am asking for is already in R svn repository since 2016, in
a branch tools4pkgs. Function is called 'packages.dcf'.
Another one 'repos.dcf' would be a good functional complementary to it.

Those two simple helper functions really makes it easier for organizations
to glue together usage of their own R packages repos and CRAN repo in a
smooth way. That could possibly help to offload CRAN from new submissions.

gh mirror link for easy preview:
https://github.com/wch/r-source/blob/tools4pkgs/src/library/tools/R/packages.R#L419

Regards
Jan Gorecki

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Re: [Bioc-devel] Package checks with WARNING

[Hervé Pagès]

On 12/10/2022 13:42, Lapuente Santana, Oscar wrote:


Hi Hervé,

Thanks for your suggestion.

The package rstatix which I used and it's set as an import, calls the coin 
package but this one is defined as a suggests in the description file of 
rstatix package (https://github.com/kassambara/rstatix/blob/master/DESCRIPTION).

In particular, I am calling two two functions from this package: 
rstatix::wilcox_test and rstatix::wilcox_effsize. The later uses several 
functions from the coin package and one is called the same way which is 
coin::wilcox_test and then the warning arises.
  
Given this situation, I would feel more comfortable importing the full coin package. What are your thoughts?


I see. But still, you're only supposed to import what your code uses 
_directly_. In this case your code doesn't make any call to coin or 
doesn't use any symbol defined in coin. The code in rstatix does, but 
not your code.


One concern is that you want to make sure that coin is installed on the 
user machine, so it needs to be listed as a dependency. One way to 
achieve this is to move coin to Depends, and to not import anything from 
it. I just tried this but R CMD check now produces:


  * checking dependencies in R code ... NOTE
  Package in Depends field not imported from: ‘coin’
    These packages need to be imported from (in the NAMESPACE file)
    for when this namespace is loaded but not attached.

IMO this is actually a legitimate use of Depends, so I'd say it's ok. At 
least now you get a NOTE instead of a WARNING ;-)


A more hacky solution is to keep coin in Imports and to import an 
arbitrary symbol from it. Could be anything, except 'wilcox_test' of 
course, to avoid the clash with importFrom(rstatix,wilcox_test). That 
should produce a clean R CMD check.


Hope this helps,

H.




Cheers, Óscar

On 12/10/2022, 20:07, "Hervé Pagès"  wrote:

 Hi Óscar,

 On 12/10/2022 01:09, Lapuente Santana, Oscar via Bioc-devel wrote:

 > Dear Bioconductor developers/maintainers,
 >
 > My package ‘easier’ checks with WARNING in both the current 3.15 release 
and the devel version.
 > I am just checking in to see if that’s okay since this was also the case 
in the first submission (the warning stems from a dependency of a dependency)

 Sure but you can get rid of it by importing only what you need from the
 coin package. Right now you import the full coin namespace, by having
 import(coin) in your NAMESPACE file, and that introduces a clash with
 importFrom(rstatix,wilcox_test) that you also have in there.

 I'm actually not sure what you need coin for (I was not able to find a
 place in your code where you make any use of it). So maybe you could
 just drop that dependency entirely?

 Best,

 H.

 >
 > Thanks in advance,
 > Cheers, Óscar
 >
 >   [[alternative HTML version deleted]]
 >
 > ___
 > Bioc-devel@r-project.org mailing list
 > 
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 --
 Hervé Pagès

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



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

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Re: [R-pkg-devel] Problems with news in ‘NEWS’

[Spencer Graves]

On 10/13/22 4:34 AM, Ivan Krylov wrote:

В Wed, 12 Oct 2022 20:16:20 -0500
Spencer Graves  пишет:


I copied NEWS to NEWS.md and tried to format it as described in:


https://r-pkgs.org/other-markdown.html#news


  Sadly, I still get the same error.  It seems to be ignoring
my NEWS.md file and continuing to tell me I haven't fixed NEWS.


Does it help to remove the NEWS after you've created NEWS.md in the
root directory of your package? In theory, NEWS.md takes precedence
over everything except inst/NEWS.Rd, but maybe that's not the case when
checking the package.



Thanks.  I did that, and it worked.



For the record, both the plain text format R expects in the NEWS file
and the Markdown format for NEWS.md are described in help(news).



Thanks, I missed that reference but managed to find something that worked.


  Spencer

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Re: [Bioc-devel] change of maintainer for msqrob2

[Kern, Lori]

I will be sending log in information in a private email off list.


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: vandenbulcke stijn 
Sent: Thursday, October 13, 2022 9:00 AM
To: Kern, Lori 
Cc: lieven clement ; maintai...@bioconductor.org 
; bioc-devel@r-project.org 

Subject: Re: change of maintainer for msqrob2

Dear Bioconductor team,

Thank you, I would like to associate this account: 
https://github.com/StijnVandenbulcke

Best Regards
Vandenbulcke Stijn

Op do 13 okt. 2022 om 14:55 schreef Kern, Lori 
mailto:lori.sheph...@roswellpark.org>>:
I can take care of this request.

Stijn do you have a github account you would like associated with your 
Bioconductor GitCredentials account for auto upload of github ssh keys?

Cheers,


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: lieven clement 
mailto:lieven.clem...@telenet.be>>
Sent: Thursday, October 13, 2022 8:51 AM
To: maintai...@bioconductor.org 
mailto:maintai...@bioconductor.org>>; 
bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Cc: vandenbulcke.st...@gmail.com 
mailto:vandenbulcke.st...@gmail.com>>
Subject: change of maintainer for msqrob2

Dear bioconductor team,

We would like to change the maintainer of the msqrob2 package from me, Lieven 
Clement to the collaborator of the package Stijn Vandenbulcke 
(vandenbulcke.st...@gmail.com). I also 
included Stijn in cc to this mail.

Thank you for making these changes,
Best,

Lieven


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.

Op do 13 okt. 2022 om 14:55 schreef Kern, Lori 
mailto:lori.sheph...@roswellpark.org>>:
I can take care of this request.

Stijn do you have a github account you would like associated with your 
Bioconductor GitCredentials account for auto upload of github ssh keys?

Cheers,


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: lieven clement 
mailto:lieven.clem...@telenet.be>>
Sent: Thursday, October 13, 2022 8:51 AM
To: maintai...@bioconductor.org 
mailto:maintai...@bioconductor.org>>; 
bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Cc: vandenbulcke.st...@gmail.com 
mailto:vandenbulcke.st...@gmail.com>>
Subject: change of maintainer for msqrob2

Dear bioconductor team,

We would like to change the maintainer of the msqrob2 package from me, Lieven 
Clement to the collaborator of the package Stijn Vandenbulcke 
(vandenbulcke.st...@gmail.com). I also 
included Stijn in cc to this mail.

Thank you for making these changes,
Best,

Lieven


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 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 

Re: [Bioc-devel] change of maintainer for msqrob2

[vandenbulcke stijn]

Dear Bioconductor team,

Thank you, I would like to associate this account:
https://github.com/StijnVandenbulcke

Best Regards
Vandenbulcke Stijn

Op do 13 okt. 2022 om 14:55 schreef Kern, Lori <
lori.sheph...@roswellpark.org>:

> I can take care of this request.
>
> Stijn do you have a github account you would like associated with your
> Bioconductor GitCredentials account for auto upload of github ssh keys?
>
> Cheers,
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* lieven clement 
> *Sent:* Thursday, October 13, 2022 8:51 AM
> *To:* maintai...@bioconductor.org ;
> bioc-devel@r-project.org 
> *Cc:* vandenbulcke.st...@gmail.com 
> *Subject:* change of maintainer for msqrob2
>
> Dear bioconductor team,
>
> We would like to change the maintainer of the msqrob2 package from me,
> Lieven Clement to the collaborator of the package Stijn Vandenbulcke (
> vandenbulcke.st...@gmail.com). I also included Stijn in cc to this mail.
>
> Thank you for making these changes,
> Best,
>
> Lieven
>
>
> 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.
>

Op do 13 okt. 2022 om 14:55 schreef Kern, Lori <
lori.sheph...@roswellpark.org>:

> I can take care of this request.
>
> Stijn do you have a github account you would like associated with your
> Bioconductor GitCredentials account for auto upload of github ssh keys?
>
> Cheers,
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* lieven clement 
> *Sent:* Thursday, October 13, 2022 8:51 AM
> *To:* maintai...@bioconductor.org ;
> bioc-devel@r-project.org 
> *Cc:* vandenbulcke.st...@gmail.com 
> *Subject:* change of maintainer for msqrob2
>
> Dear bioconductor team,
>
> We would like to change the maintainer of the msqrob2 package from me,
> Lieven Clement to the collaborator of the package Stijn Vandenbulcke (
> vandenbulcke.st...@gmail.com). I also included Stijn in cc to this mail.
>
> Thank you for making these changes,
> Best,
>
> Lieven
>
>
> 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.
>

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[Bioc-devel] change of maintainer for msqrob2

[lieven clement]

Dear bioconductor team,

We would like to change the maintainer of the msqrob2 package from me, Lieven 
Clement to the collaborator of the package Stijn Vandenbulcke 
(vandenbulcke.st...@gmail.com ). I also 
included Stijn in cc to this mail. 

Thank you for making these changes, 
Best,

Lieven 
 
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Re: [Bioc-devel] change of maintainer for msqrob2

[Kern, Lori]

I can take care of this request.

Stijn do you have a github account you would like associated with your 
Bioconductor GitCredentials account for auto upload of github ssh keys?

Cheers,


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: lieven clement 
Sent: Thursday, October 13, 2022 8:51 AM
To: maintai...@bioconductor.org ; 
bioc-devel@r-project.org 
Cc: vandenbulcke.st...@gmail.com 
Subject: change of maintainer for msqrob2

Dear bioconductor team,

We would like to change the maintainer of the msqrob2 package from me, Lieven 
Clement to the collaborator of the package Stijn Vandenbulcke 
(vandenbulcke.st...@gmail.com). I also 
included Stijn in cc to this mail.

Thank you for making these changes,
Best,

Lieven



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.
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Re: [Bioc-devel] commit access

[Kern, Lori]

  I have add Anatoly Sorokin to those packages.  Let us know if there are any 
issues.




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 Oksana 
Sorokina 
Sent: Wednesday, October 12, 2022 10:11 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] commit access

Dear Bioc members,
I would like Anatoly Sorokin to have commit access for the synaptome.data and 
synaptome.db packages.
email: lpto...@gmail.com
github: lptolik.
Please let me know if you need more information.
Many thanks in advance!

All the best,
Oksana Sorokina
The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh 
Dh�deann, cl�ichte an Alba, �eamh cl�idh SC005336.

[[alternative HTML version deleted]]



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Re: [R-pkg-devel] Problems with news in ‘NEWS’

[Ivan Krylov]

В Wed, 12 Oct 2022 20:16:20 -0500
Spencer Graves  пишет:

> I copied NEWS to NEWS.md and tried to format it as described in:
> 
> 
> https://r-pkgs.org/other-markdown.html#news
> 
> 
> Sadly, I still get the same error.  It seems to be ignoring
> my NEWS.md file and continuing to tell me I haven't fixed NEWS.

Does it help to remove the NEWS after you've created NEWS.md in the
root directory of your package? In theory, NEWS.md takes precedence
over everything except inst/NEWS.Rd, but maybe that's not the case when
checking the package.

For the record, both the plain text format R expects in the NEWS file
and the Markdown format for NEWS.md are described in help(news).

-- 
Best regards,
Ivan

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