[Rd] substitute inconsistent output

[Jan Gorecki]

Dear R-devel,

Is there anything that we can do to make output of those call more
consistent? So the first one will return `c(1L, 2L)` rather than
`1:2`. Note that it is not related to compact integer sequence
introduced by altrep, it is reproducible on R 3.1.0 as well.

substitute(v+x, list(x=c(1L,2L)))
#v + 1:2
substitute(v+x, list(x=c(0L,2L)))
#v + c(0L, 2L)

Thank you,
Jan Gorecki

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Re: [Rd] new bquote feature splice does not address a common LISP @ use case?

[Jan Gorecki]

Thank you Lionel for comprehensive explanation. I think that rotating
AST in base R is not a good way to go, it would probably complicate
the code heavily.

Best,
Jan Gorecki

On Tue, Mar 17, 2020 at 4:49 PM Lionel Henry  wrote:
>
> Hi Jan,
>
> In the lisp code you provide the operators are parsed as simple
> symbols in a pairlist. In the R snippet, they are parsed as
> left-associative binary operators of equal precedence. If you unquote
> a call in the right-hand side, you're artificially bypassing the
> left-associativity of these operators.
>
> To achieve what you're looking for in a general way, you'll need a
> more precise definition of the problem, and a solution that probably
> involves rotating the AST accordingly (see
> https://github.com/r-lib/rlang/blob/master/src/internal/expr-interp-rotate.c).
> Maybe it could be possible to formulate a definition where splicing in
> special calls like binary operators produces the same AST as the user
> would type by hand. It seems this would make splicing easier to use
> for end users, but make the metaprogramming model more complex for
> experts. This is an interesting perspective though. It also seems
> vaguely connected to the problem of splicing within model formulas.
>
> I see in your example that the new ..() operator in `bquote()` allows
> splicing calls, and seems to unquote them instead of splicing. In the
> first versions of rlang, splicing with !!! behaved just like this. We
> changed this behaviour last year and I would like to share the
> motivations behind this decision, as it might be helpful to inform the
> semantics of ..() in bquote() in R 4.0.
>
> The bottom line is that calls are now treated like scalars. This is a
> slight contortion of the syntax because calls are "language lists",
> and so they could be conceived as collections rather than scalars.
> However, R is vector-oriented rather than pairlist-oriented, and
> treating calls as scalars makes the metaprogramming model simpler.
>
> This is also how `bquote(splice = TRUE)` works. However `bquote()`
> and rlang do not treat scalars in the same way. In rlang scalars
> cannot be spliced, they must be unquoted.
>
> ```
> bquote(foo(..(function() NULL)), splice = TRUE)
> #> foo(function() NULL)
>
> bquote(foo(..(quote(bar))), splice = TRUE)
> #> foo(bar)
>
> expr(foo(!!!function() NULL))
> #> Error: Can't splice an object of type `closure` because it is not a vector.
>
> expr(foo(!!!quote(bar)))
> #> foo(bar)
> #> Warning message:
> #> Unquoting language objects with `!!!` is deprecated as of rlang 0.4.0.
> #> Please use `!!` instead.
> ```
>
> We decided to disallow splicing scalars (and thus calls) in rlang even
> though this is a legal operation in many lisps. In lisps, the splicing
> operation stands for unquoting in the CDR of a pairlist. By contrast
> the unquote operation unquotes in the CAR. For example `(1 ,@3) is
> legal in Common Lisp and stands for the cons cell (1 . 3). I think
> such semantics are not appealing in a language like R because it is
> vector-oriented rather than pairlist oriented. Pairlists are mostly an
> implicit data structure that users are not familiar with, and they are
> not even fully supported in all implementations of R (for instance
> TERR and Renjin do not allow non-NULL terminated pairlists, and while
> GNU R has vestigial print() support for these, they cause str() to crash).
>
> In general, it is much more useful to define a splice operation that
> also works for vectors:
>
> ```
> rlang::list2(1, !!!10:11, 3)
> #> [[1]]
> #> [1] 1
> #>
> #> [[2]]
> #> [1] 10
> #>
> #> [[3]]
> #> [1] 11
> #>
> #> [[4]]
> #> [1] 3
> ```
>
> Because vectors do not have any notion of CDR, the usual lisp
> interpretation of splicing scalars does not apply.
>
> One alternative to make it work is to devolve the splicing operation
> into a simple unquote operation, when supplied a scalar. This is how
> `bquote(splice = TRUE)` works. However I think this kind of
> overloading is more confusing in the long run, and makes it harder for
> users to form a correct mental model for programming with these
> operations. For this reason it seems preferable to force users to be
> explicit about the desired semantics with scalars and calls. In rlang
> they must either unquote the call, or explicitly transform it to a
> list prior to splicing:
>
> ```
> x <- quote(bar + baz)
>
> # Unquote instead of splicing
> expr(foo(!!x))
> #> foo(bar + baz)
>
> # Convert to list and then splice
> expr(add(!!!as.list(x[-1])))
> #> add(bar, baz)
> ```
>
> Unquoting could be consistent if all objects were truly vectors in R,
> i.e. if they were implicitly wrapped in a list. Then ..(quote(foo))
> would be very similar to ..(1). In the former case a list of size 1
> would be spliced, in the latter case a vector of size 1 is
> spliced. This would explain why .() and ..() have the same behaviour
> with scalars. While an interesting thought experiment, this is not
> how scalars work in R.
>
> It seems 

[Bioc-devel] Deploy a critical patch

[Julian Flesch]

Hi Bioc team,


I am the maintainer of the package /waddR/.

We have had built issues on the active branch recently, due a dependency
being unavailable. After pushing a patch, the issues were resolved on
the devel branch.

Is it possible to merge these critical changes (version 1.1.4) to the
active branch of Bioconductor?


Best,

Julian


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Re: [Bioc-devel] Push the updated package to Bioconductor

[Shepherd, Lori]

Please see the top portion of this page 
http://bioconductor.org/developers/how-to/troubleshoot-build-report/.  Updates 
are not instantaneous; it can take 24-48 hours to appear, and will only appear 
on the landing page if the build and check completed without Error.

Get Outlook for Android


From: Bioc-devel  on behalf of Ruijia Wang 

Sent: Tuesday, March 17, 2020 8:43:35 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Push the updated package to Bioconductor

Hi BioC-devel,

I am the author of the Bioconductor package APAlyzer (
https://bioconductor.org/packages/release/bioc/html/APAlyzer.html). We are
trying to push our updated package (version 1.1.1) to Bioconductor.
However, the git tutorial seems doesn't work in my case, here's what I've
done:

$ git remote -v
origin  https://github.com/RJWANGbioinfo/APAlyzer.git (fetch)
origin  https://github.com/RJWANGbioinfo/APAlyzer.git (push)
upstreamg...@git.bioconductor.org:packages/APAlyzer.git (fetch)
upstreamg...@git.bioconductor.org:packages/APAlyzer.git (push)

$ git checkout master
Already on 'master'
Your branch is up to date with 'origin/master'.

$ git push upstream master
Enumerating objects: 5, done.
Counting objects: 100% (5/5), done.
Delta compression using up to 4 threads
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 299 bytes | 74.00 KiB/s, done.
Total 3 (delta 2), reused 0 (delta 0)
To git.bioconductor.org:packages/APAlyzer.git
   4f098be..d2ad6cb  master -> master

I didn't get any notice and find any changes on the Bioconductor website
(both the development version and stable version). Did I miss anything?
Could you help me to figure out how to fix this?  Thank you in advance!

Best,
Ray

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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 
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[Bioc-devel] Push the updated package to Bioconductor

[Ruijia Wang]

Hi BioC-devel,

I am the author of the Bioconductor package APAlyzer (
https://bioconductor.org/packages/release/bioc/html/APAlyzer.html). We are
trying to push our updated package (version 1.1.1) to Bioconductor.
However, the git tutorial seems doesn't work in my case, here's what I've
done:

$ git remote -v
origin  https://github.com/RJWANGbioinfo/APAlyzer.git (fetch)
origin  https://github.com/RJWANGbioinfo/APAlyzer.git (push)
upstreamg...@git.bioconductor.org:packages/APAlyzer.git (fetch)
upstreamg...@git.bioconductor.org:packages/APAlyzer.git (push)

$ git checkout master
Already on 'master'
Your branch is up to date with 'origin/master'.

$ git push upstream master
Enumerating objects: 5, done.
Counting objects: 100% (5/5), done.
Delta compression using up to 4 threads
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 299 bytes | 74.00 KiB/s, done.
Total 3 (delta 2), reused 0 (delta 0)
To git.bioconductor.org:packages/APAlyzer.git
   4f098be..d2ad6cb  master -> master

I didn't get any notice and find any changes on the Bioconductor website
(both the development version and stable version). Did I miss anything?
Could you help me to figure out how to fix this?  Thank you in advance!

Best,
Ray

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Re: [Bioc-devel] BiocParallel Variable Not Found

[Dario Strbenac]

Good day,

I am not sure how to fix my package properly, even with the good example. A 
link to the specific part of my function is 
https://github.com/DarioS/ClassifyR/blob/e35899caceb401691990136387a517f4c3b57d5e/R/runTests.R#L567
 and the example in the help page of runTestsEasyHard function triggers the 
error shown in Bioconductor's daily build.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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[Bioc-devel] regionReport error: leads to potential disk space issues for ImageMagick

[Leonardo Collado Torres]

Hi BioC-devel,

I spent some time yesterday getting my Windows laptop ready to debug a
Windows OS-only issue in regionReport (bioc-release 3.10), but
ultimately I couldn't reproduce it. Since the error seems to be some
type of cache, I bumped the version number but it still failed today
and it then also failed on bioc-devel (3.11) on Linux (as well as
Windows).

## Bioc-release (3.10) Windows is the only that fails

Quitting from lines 224-229 (basicExploration.Rmd)
Error: processing vignette 'regionReport.Rmd' failed with diagnostics:
R: unable to get registry ID `cache:hosts' @
error/registry.c/GetImageRegistry/202
--- failed re-building ‘regionReport.Rmd’

similarly

Quitting from lines 224-229 (basicExploration.Rmd)
Error in magick_image_trim(image, fuzz) :
  R: unable to get registry ID `cache:hosts' @
error/registry.c/GetImageRegistry/202
Calls: render ...  -> assert_image ->  ->
magick_image_trim


## Bioc-devel (3.11) Linux and Windows fails

http://bioconductor.org/checkResults/release/bioc-LATEST/regionReport/malbec1-buildsrc.html

However, I see at
http://bioconductor.org/checkResults/devel/bioc-LATEST/regionReport/malbec2-buildsrc.html
that the error appeared today also on the Linux bioc-devel builder.

## Google

Searching for the error message led me to
https://github.com/phw/peek/issues/112 which talks about disk space
running out for ImageMagick. Do you think that this is something that
is affecting the builders too? Do you have any suggestions I could
try?

Best,
Leo

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Re: [Bioc-devel] Change associated email/github

[Russell Bainer]

Thanks very much for the response. Can you recommend a way to do password
recovery? I no longer have access to the registered email address, and I'm
afraid that I registered long enough ago that I don't have the password
that I used.


On Tue, Mar 17, 2020 at 2:05 PM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi,
>
> There are a couple of things you'd have to do,
>
> 1. In the BiocCredentials app, you'd have to change your email address
> registered. And update your SSH keys if needed, add your personal Github ID
> as well.
>
> 2. In the DESCRIPTION file of the package, you'd have to change your email
> address to reflect where you'll be able to receive emails as a maintainer.
>
> 3. Update your email address on Bioc-devel mailing list if it is not
> already registered.
>
> Best,
>
> Nitesh
>
> > On Mar 17, 2020, at 1:34 PM, Russell Bainer 
> wrote:
> >
> > I'd like to change the email address associated with my
> > Bioconductor account, and also update the ownership of my packages to my
> > personal Github account (I originally registered both of these with my
> > employer, and I have since left the company). Could you please direct me
> to
> > documentation that will help me do this?
> >
> > Thanks very much
> >
> > -R
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> 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] Fw: Bioconductor package SIM

[Turaga, Nitesh]

You'll have to activate your account first, 

https://git.bioconductor.org/BiocCredentials/account_activation/



> On Mar 17, 2020, at 5:11 PM, ni41435_ca  wrote:
> 
> The SIM package is registered to mboetze...@hotmail.com.
> 
> You can change the email on BiocCredentials app yourself.
> 
> Best,
> 
> Nitesh 
> 
>> On Mar 17, 2020, at 11:52 AM, r.mene...@nki.nl wrote:
>> 
>> l.s.
>> 
>> 
>> I cannot seem to be able to activate my account on the bioconductor git. I 
>> get a message saying my email address (the same one on the package help 
>> file) is not associated with a maintainer of a Bioconductor package. The 
>> email address is write simply is
>> 
>> 
>> r.xavierdemene...@vumc.nl
>> 
>> 
>> as stated in the SIM package page.
>> 
>> 
>> I tried this on both firefox and chrome, and get the same error each time.
>> 
>> 
>> Is there anything I could be doing wrong?
>> 
>> 
>> Thanks in advance,
>> 
>> Renee
>> 
>> 
>> 
>> From: Shepherd, Lori 
>> Sent: 16 March 2020 15:47
>> To: Menezes, R. (Ren�e)
>> Cc: Ren�e Menezes
>> Subject: Re: Bioconductor package SIM
>> 
>> Please be aware your package is still failing.  This is very problematic.  
>> The
>> next Bioconductor release is scheduled for Tuesday April 28th. We appreciate
>> your quick response in this matter. If your package remains broken we will 
>> begin
>> the deprecation process to remove the package from Bioconductor.
>> 
>> 
>> 
>> Lori Shepherd
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Comprehensive Cancer Center
>> 
>> Department of Biostatistics & Bioinformatics
>> 
>> Elm & Carlton Streets
>> 
>> Buffalo, New York 14263
>> 
>> 
>> From: Shepherd, Lori 
>> Sent: Thursday, February 27, 2020 12:08 PM
>> To: Menezes, R. (Ren�e) 
>> Cc: r.mene...@nki.nl 
>> Subject: Re: Bioconductor package SIM
>> 
>> Thank you! Please remember to update your email address in the DESCRIPTION 
>> of the package when you make changes too.
>> 
>> Cheers,
>> 
>> 
>> Lori Shepherd
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Comprehensive Cancer Center
>> 
>> Department of Biostatistics & Bioinformatics
>> 
>> Elm & Carlton Streets
>> 
>> Buffalo, New York 14263
>> 
>> 
>> From: Menezes, R. (Ren�e) 
>> Sent: Thursday, February 27, 2020 12:07 PM
>> To: Shepherd, Lori 
>> Cc: r.mene...@nki.nl 
>> Subject: Re: Bioconductor package SIM
>> 
>> Dear Lori,
>> 
>> Thanks for your email. I saw the previous email but have not had the time to 
>> look at the problem. I have recently changed jobs (my new email address is 
>> in cc) and it has been really busy in the last few weeks.
>> 
>> I will look at the issue ASAP.
>> 
>> Kind regards,
>> Renee
>> 
>> Renee X. de Menezes
>> Lecturer, Dept. Epidemiology and Biostatistics, VUmc
>> r.mene...@vumc.nl
>> http://www.bigstatistics.nl/renee
>> 
>> 
>> 
>> 
>> 
>> Van: Shepherd, Lori 
>> Verzonden: donderdag 27 februari 2020 17:36
>> Aan: Menezes, R. (Ren�e) 
>> Onderwerp: Bioconductor package SIM
>> 
>> Dear Package Maintainer,
>> 
>> We would like to bring to your attention that your package is failing to 
>> build/check on our devel build machines:
>> 
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/SIM
>> 
>> Would you mind taking a look at this? Don't hesitate to ask on the 
>> bioc-devel mailing list if you have any question or need help.
>> 
>> While the development branch is a place to develop new features and we 
>> expect packages to occasionally break,  they should not remain broken for an 
>> extended period of time.   If no action is taken over the next few weeks we 
>> will begin the deprecation process for your package.  The package has been 
>> failing since at least 01/24/20.  Thank you for your time and effort.
>> 
>> We notified you of your package failure in a group message entitled 
>> "Bioconductor Package Needs Update"  back on 01/27/20.
>> 
>> Please see https://stat.ethz.ch/pipermail/bioc-devel/2020-January/016081.html
>> 
>> Information can also be found on the troubleshooting build page of the 
>> website:
>> http://bioconductor.org/developers/how-to/troubleshoot-build-report/
>> 
>> 
>> 
>> Lori Shepherd
>> 
>> 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 

Re: [Bioc-devel] Fw: Bioconductor package SIM

[Turaga, Nitesh]

The SIM package is registered to mboetze...@hotmail.com.

You can change the email on BiocCredentials app yourself.

Best,

Nitesh 

> On Mar 17, 2020, at 11:52 AM, r.mene...@nki.nl wrote:
> 
> l.s.
> 
> 
> I cannot seem to be able to activate my account on the bioconductor git. I 
> get a message saying my email address (the same one on the package help file) 
> is not associated with a maintainer of a Bioconductor package. The email 
> address is write simply is
> 
> 
> r.xavierdemene...@vumc.nl
> 
> 
> as stated in the SIM package page.
> 
> 
> I tried this on both firefox and chrome, and get the same error each time.
> 
> 
> Is there anything I could be doing wrong?
> 
> 
> Thanks in advance,
> 
> Renee
> 
> 
> 
> From: Shepherd, Lori 
> Sent: 16 March 2020 15:47
> To: Menezes, R. (Ren�e)
> Cc: Ren�e Menezes
> Subject: Re: Bioconductor package SIM
> 
> Please be aware your package is still failing.  This is very problematic.  The
> next Bioconductor release is scheduled for Tuesday April 28th. We appreciate
> your quick response in this matter. If your package remains broken we will 
> begin
> the deprecation process to remove the package from Bioconductor.
> 
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
> From: Shepherd, Lori 
> Sent: Thursday, February 27, 2020 12:08 PM
> To: Menezes, R. (Ren�e) 
> Cc: r.mene...@nki.nl 
> Subject: Re: Bioconductor package SIM
> 
> Thank you! Please remember to update your email address in the DESCRIPTION of 
> the package when you make changes too.
> 
> Cheers,
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
> From: Menezes, R. (Ren�e) 
> Sent: Thursday, February 27, 2020 12:07 PM
> To: Shepherd, Lori 
> Cc: r.mene...@nki.nl 
> Subject: Re: Bioconductor package SIM
> 
> Dear Lori,
> 
> Thanks for your email. I saw the previous email but have not had the time to 
> look at the problem. I have recently changed jobs (my new email address is in 
> cc) and it has been really busy in the last few weeks.
> 
> I will look at the issue ASAP.
> 
> Kind regards,
> Renee
> 
> Renee X. de Menezes
> Lecturer, Dept. Epidemiology and Biostatistics, VUmc
> r.mene...@vumc.nl
> http://www.bigstatistics.nl/renee
> 
> 
> 
> 
> 
> Van: Shepherd, Lori 
> Verzonden: donderdag 27 februari 2020 17:36
> Aan: Menezes, R. (Ren�e) 
> Onderwerp: Bioconductor package SIM
> 
> Dear Package Maintainer,
> 
> We would like to bring to your attention that your package is failing to 
> build/check on our devel build machines:
> 
> http://bioconductor.org/checkResults/devel/bioc-LATEST/SIM
> 
> Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel 
> mailing list if you have any question or need help.
> 
> While the development branch is a place to develop new features and we expect 
> packages to occasionally break,  they should not remain broken for an 
> extended period of time.   If no action is taken over the next few weeks we 
> will begin the deprecation process for your package.  The package has been 
> failing since at least 01/24/20.  Thank you for your time and effort.
> 
> We notified you of your package failure in a group message entitled 
> "Bioconductor Package Needs Update"  back on 01/27/20.
> 
> Please see https://stat.ethz.ch/pipermail/bioc-devel/2020-January/016081.html
> 
> Information can also be found on the troubleshooting build page of the 
> website:
> http://bioconductor.org/developers/how-to/troubleshoot-build-report/
> 
> 
> 
> Lori Shepherd
> 
> 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.
> __
> VUmc disclaimer : www.vumc.nl/disclaimer
> AMC disclaimer : www.amc.nl/disclaimer
> 
> This email message may contain legally privileged and/or confidential 
> information. If you are not the intended recipient(s), or the employee or 
> agent 

Re: [R-pkg-devel] note about mispelled words

[Ben Bolker]

  Interesting.  'Kruskal Wallis' gets 5.68M google hits, 'Kruskall
Wallis' gets 432K ...

 Within CRAN packages, sos::findFn("kruskal") gets 408 hits,
=sos::findFn("kruskall") gets 15 hits.  (Some of those may be like the
use of 'euclidian' in stats::dist() to intentionally match misspellings
... ?)

On 2020-03-17 2:09 p.m., Peter Dalgaard wrote:
> However, notice that if it is the guy from the Kruskal-Wallis test (William 
> K., 1919--2005), the "Kruskall" is in fact misspelt. It might be someone 
> else, of course...
> 
> -pd
> 
>> On 17 Mar 2020, at 18:24 , Duncan Murdoch  wrote:
>>
>> I believe it is also acceptable to explain in your submission message that 
>> the misspelled words are all proper names.  As far as I know, misspellings 
>> are not enough of a problem to cause an automatic rejection, so a human 
>> being will be making a judgment about the note.
>>
>> Duncan Murdoch
>>
>> On 17/03/2020 11:41 a.m., Henrik Bengtsson wrote:
>>> You can single quote them to avoid them being spell checked, e.g. ...
>>> using methods of 'Kruskall' and 'Brainerd'.  This is a common and
>>> accepted practice.
>>> This is hinted at in "Writing R Extensions" (e.g. help.start());
>>> The mandatory ‘Description’ field should give a comprehensive
>>> description of what the package does. One can use several (complete)
>>> sentences, but only one paragraph. It should be intelligible to all
>>> the intended readership (e.g. for a CRAN package to all CRAN users).
>>> It is good practice not to start with the package name, ‘This package’
>>> or similar. As with the ‘Title’ field, double quotes should be used
>>> for quotations (including titles of books and articles), and single
>>> quotes for non-English usage, including names of other packages and
>>> external software. This field should also be used for explaining the
>>> package name if necessary. URLs should be enclosed in angle brackets,
>>> e.g. ‘’: see also Specifying URLs.
>>> /Henrik
>>> On Tue, Mar 17, 2020 at 8:30 AM Gianmarco Alberti
>>>  wrote:

 Hello,
 I am checking a package of mine, and I got only 1 note regarding possibly 
 misspelled words in the DESCRIPTION.

 The issue I am facing is that those 6 words are not actually misspelled, 
 being either first or last names of individuals (actually, statistician; 
 e.g., Kruskall, Brainerd).

 Shall I have to do something (removing those; which does not make sense), 
 or upon submitting my new version of the package there is a way to make 
 clear that that note can be ignored?

 By the way, those names were already there in earlier versions of the 
 package and no note cropped out in those occasions.

 Thank you
 Best
 GmA

 
 Dr Gianmarco Alberti (PhD Udine)
 Lecturer in Spatial Forensics
 Coordinator of the BA course in Criminology
 Department of Criminology
 Faculty for Social Wellbeing
 Room 332, Humanities B (FEMA)
 University of Malta, Msida, Malta (Europe) - MSD 2080
 tel +356 2340 3718

 Academic profiles
 https://www.researchgate.net/profile/Gianmarco_Alberti4
 https://malta.academia.edu/GianmarcoAlberti

 Google Scholar profile
 https://scholar.google.com/citations?user=tFrJKQ0J=en

 Correspondence Analysis website
 http://cainarchaeology.weebly.com/

 R packages on CRAN:
 CAinterprTools
 https://cran.r-project.org/web/packages/CAinterprTools/index.html

 GmAMisc
 https://cran.r-project.org/package=GmAMisc

 movecost
 https://cran.r-project.org/web/packages/movecost/index.html
 

 [[alternative HTML version deleted]]

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 R-package-devel@r-project.org mailing list
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>>> __
>>> R-package-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
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Re: [Bioc-devel] Change associated email/github

[Turaga, Nitesh]

Hi,

There are a couple of things you'd have to do,

1. In the BiocCredentials app, you'd have to change your email address 
registered. And update your SSH keys if needed, add your personal Github ID as 
well.

2. In the DESCRIPTION file of the package, you'd have to change your email 
address to reflect where you'll be able to receive emails as a maintainer. 

3. Update your email address on Bioc-devel mailing list if it is not already 
registered. 

Best,

Nitesh 

> On Mar 17, 2020, at 1:34 PM, Russell Bainer  wrote:
> 
> I'd like to change the email address associated with my
> Bioconductor account, and also update the ownership of my packages to my
> personal Github account (I originally registered both of these with my
> employer, and I have since left the company). Could you please direct me to
> documentation that will help me do this?
> 
> Thanks very much
> 
> -R
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-pkg-devel] note about dependency on archived package

[Gianmarco Alberti]

Further to my earlier email,

I understand that my package has been archived since my last version on CRAN 
(1.1.0) had among its dependencies a package that has been archived.

Now my question:
How can I bring my package (actually the new version 1.1.1 that I’m trying to 
check) back to life (i.e., CRAN) again?

Best
Gm


Dr Gianmarco Alberti (PhD Udine)
Lecturer in Spatial Forensics
Coordinator of the BA course in Criminology
Department of Criminology
Faculty for Social Wellbeing
Room 332, Humanities B (FEMA)
University of Malta, Msida, Malta (Europe) - MSD 2080
tel +356 2340 3718

Academic profiles
https://www.researchgate.net/profile/Gianmarco_Alberti4
https://malta.academia.edu/GianmarcoAlberti

Google Scholar profile
https://scholar.google.com/citations?user=tFrJKQ0J=en

Correspondence Analysis website
http://cainarchaeology.weebly.com/

R packages on CRAN:
CAinterprTools
https://cran.r-project.org/web/packages/CAinterprTools/index.html

GmAMisc
https://cran.r-project.org/package=GmAMisc

movecost
https://cran.r-project.org/web/packages/movecost/index.html

On 17 Mar 2020, 21:22 +0100, Gianmarco Alberti , 
wrote:
> Hello,
>
> After checking my package with win builder, I got 1 note that I seem to not 
> fully understand:
>
> CRAN repository db overrides:
>  X-CRAN-Comment: Archived on 2020-03-17 as depends on archived package
>'spatialEco'.
>
> Do you have any suggestion?
> There is not reference to that package in my NAMESPACE, nor it is listed 
> among the dependencies.
>
> Full log here:
> https://win-builder.r-project.org/98x9zsbaHsp1/00check.log
>
> Best
> Gm
>
> 
> Dr Gianmarco Alberti (PhD Udine)
> Lecturer in Spatial Forensics
> Coordinator of the BA course in Criminology
> Department of Criminology
> Faculty for Social Wellbeing
> Room 332, Humanities B (FEMA)
> University of Malta, Msida, Malta (Europe) - MSD 2080
> tel +356 2340 3718
>
> Academic profiles
> https://www.researchgate.net/profile/Gianmarco_Alberti4
> https://malta.academia.edu/GianmarcoAlberti
>
> Google Scholar profile
> https://scholar.google.com/citations?user=tFrJKQ0J=en
>
> Correspondence Analysis website
> http://cainarchaeology.weebly.com/
>
> R packages on CRAN:
> CAinterprTools
> https://cran.r-project.org/web/packages/CAinterprTools/index.html
>
> GmAMisc
> https://cran.r-project.org/package=GmAMisc
>
> movecost
> https://cran.r-project.org/web/packages/movecost/index.html
> 

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[R-pkg-devel] note about dependency on archived package

[Gianmarco Alberti]

Hello,

After checking my package with win builder, I got 1 note that I seem to not 
fully understand:

CRAN repository db overrides:
 X-CRAN-Comment: Archived on 2020-03-17 as depends on archived package
   'spatialEco'.

Do you have any suggestion?
There is not reference to that package in my NAMESPACE, nor it is listed among 
the dependencies.

Full log here:
https://win-builder.r-project.org/98x9zsbaHsp1/00check.log

Best
Gm


Dr Gianmarco Alberti (PhD Udine)
Lecturer in Spatial Forensics
Coordinator of the BA course in Criminology
Department of Criminology
Faculty for Social Wellbeing
Room 332, Humanities B (FEMA)
University of Malta, Msida, Malta (Europe) - MSD 2080
tel +356 2340 3718

Academic profiles
https://www.researchgate.net/profile/Gianmarco_Alberti4
https://malta.academia.edu/GianmarcoAlberti

Google Scholar profile
https://scholar.google.com/citations?user=tFrJKQ0J=en

Correspondence Analysis website
http://cainarchaeology.weebly.com/

R packages on CRAN:
CAinterprTools
https://cran.r-project.org/web/packages/CAinterprTools/index.html

GmAMisc
https://cran.r-project.org/package=GmAMisc

movecost
https://cran.r-project.org/web/packages/movecost/index.html


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Re: [Bioc-devel] BiocParallel Variable Not Found

[Martin Morgan]

The question is a bit abstract for me to understand and it might be better to 
point to actual code in a git repository or similar... 

Inside a package, something like

fun = function(x, y, ...) {
c(x, y, length(as.list(...)))
}

user_visible <- function(x, ...) {
y = 1
internal_function(x, y, ...)
}

internal_function <- function(x, y, ...) {
bplapply(1:5, fun, x, y, ...)
}

I think would 'work'.

Martin

On 3/17/20, 4:00 PM, "Bioc-devel on behalf of Dario Strbenac" 
 
wrote:

Good day,

Thanks for the examples which demonstrate the issue. Do you have other 
recommendations if, inside the loop, another function in the package is being 
called and the variable being passed is the ellipsis? There are only a couple 
of variables which might be provided by the user collected in the ellipsis, so 
the functional approach might still be the best in that case.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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Re: [Bioc-devel] BiocParallel Variable Not Found

[Dario Strbenac]

Good day,

Thanks for the examples which demonstrate the issue. Do you have other 
recommendations if, inside the loop, another function in the package is being 
called and the variable being passed is the ellipsis? There are only a couple 
of variables which might be provided by the user collected in the ellipsis, so 
the functional approach might still be the best in that case.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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[Rd] configure --with-pcre1 fails with latest R 4.0 on Ubuntu 14.04

[Hervé Pagès]

Using --with-pcre1 to configure the latest R 4.0 (revision 77988) on an 
Ubuntu 14.04.5 LTS system gives me the following error:


...
checking if lzma version >= 5.0.3... yes
checking for pcre2-config... no
checking for pcre_fullinfo in -lpcre... yes
checking pcre.h usability... yes
checking pcre.h presence... yes
checking for pcre.h... yes
checking pcre/pcre.h usability... no
checking pcre/pcre.h presence... no
checking for pcre/pcre.h... no
checking if PCRE1 version >= 8.32 and has UTF-8 support... no
checking whether PCRE support suffices... configure: error: pcre2 
library and headers are required, or use --with-pcre1


Maybe the real problem is that the PCRE version on this OS is 8.31?

The error message is not particularly helpful.

Thanks,
H.

--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [R-pkg-devel] note about mispelled words

[Peter Dalgaard]

However, notice that if it is the guy from the Kruskal-Wallis test (William K., 
1919--2005), the "Kruskall" is in fact misspelt. It might be someone else, of 
course...

-pd

> On 17 Mar 2020, at 18:24 , Duncan Murdoch  wrote:
> 
> I believe it is also acceptable to explain in your submission message that 
> the misspelled words are all proper names.  As far as I know, misspellings 
> are not enough of a problem to cause an automatic rejection, so a human being 
> will be making a judgment about the note.
> 
> Duncan Murdoch
> 
> On 17/03/2020 11:41 a.m., Henrik Bengtsson wrote:
>> You can single quote them to avoid them being spell checked, e.g. ...
>> using methods of 'Kruskall' and 'Brainerd'.  This is a common and
>> accepted practice.
>> This is hinted at in "Writing R Extensions" (e.g. help.start());
>> The mandatory ‘Description’ field should give a comprehensive
>> description of what the package does. One can use several (complete)
>> sentences, but only one paragraph. It should be intelligible to all
>> the intended readership (e.g. for a CRAN package to all CRAN users).
>> It is good practice not to start with the package name, ‘This package’
>> or similar. As with the ‘Title’ field, double quotes should be used
>> for quotations (including titles of books and articles), and single
>> quotes for non-English usage, including names of other packages and
>> external software. This field should also be used for explaining the
>> package name if necessary. URLs should be enclosed in angle brackets,
>> e.g. ‘’: see also Specifying URLs.
>> /Henrik
>> On Tue, Mar 17, 2020 at 8:30 AM Gianmarco Alberti
>>  wrote:
>>> 
>>> Hello,
>>> I am checking a package of mine, and I got only 1 note regarding possibly 
>>> misspelled words in the DESCRIPTION.
>>> 
>>> The issue I am facing is that those 6 words are not actually misspelled, 
>>> being either first or last names of individuals (actually, statistician; 
>>> e.g., Kruskall, Brainerd).
>>> 
>>> Shall I have to do something (removing those; which does not make sense), 
>>> or upon submitting my new version of the package there is a way to make 
>>> clear that that note can be ignored?
>>> 
>>> By the way, those names were already there in earlier versions of the 
>>> package and no note cropped out in those occasions.
>>> 
>>> Thank you
>>> Best
>>> GmA
>>> 
>>> 
>>> Dr Gianmarco Alberti (PhD Udine)
>>> Lecturer in Spatial Forensics
>>> Coordinator of the BA course in Criminology
>>> Department of Criminology
>>> Faculty for Social Wellbeing
>>> Room 332, Humanities B (FEMA)
>>> University of Malta, Msida, Malta (Europe) - MSD 2080
>>> tel +356 2340 3718
>>> 
>>> Academic profiles
>>> https://www.researchgate.net/profile/Gianmarco_Alberti4
>>> https://malta.academia.edu/GianmarcoAlberti
>>> 
>>> Google Scholar profile
>>> https://scholar.google.com/citations?user=tFrJKQ0J=en
>>> 
>>> Correspondence Analysis website
>>> http://cainarchaeology.weebly.com/
>>> 
>>> R packages on CRAN:
>>> CAinterprTools
>>> https://cran.r-project.org/web/packages/CAinterprTools/index.html
>>> 
>>> GmAMisc
>>> https://cran.r-project.org/package=GmAMisc
>>> 
>>> movecost
>>> https://cran.r-project.org/web/packages/movecost/index.html
>>> 
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> __
>>> R-package-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> __
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>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> 
> 
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [Rd] pipe(): input to, and output from, a single process

[Greg Minshall]

Dirk,

> Octave had this already in the 1990s, see documentation for 'popen2' here:

thanks.  unix that had since the 1970s... :)

cheers, Greg

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[Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

[Charles Warden]

Hi,

I recently received error messages for 2 packages.  As a worst-case-scenario, 
it is acceptable if the sRAP package had to be removed.  However, I need to 
resolve the issue for the COHCAP package.

This is odd because I don’t think I have updated either package in the last 
year or so.  In fact, if I check the CHANGES file in the COHCAP package, the 
last change I manually noted was v1.29.3, which I can see was added to the 
GitHub version of the code on 3/2/2019:

https://github.com/cwarden45/COHCAP/commits/master/CHANGES

I can successfully install the package, with either the GitHub or Bioconductor 
instructions.  However, I want to correct the error because I don’t want the 
Bioconductor package to be removed.

I had some dependency issues on some systems related to the PDF generation 
(which I would usually ignore).  However, if I run “R CMD build” on an Ubuntu 
system where I have all dependencies installed, I don’t get any error message:

$ R CMD build COHCAP
* checking for file ‘COHCAP/DESCRIPTION’ ... OK
* preparing ‘COHCAP’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
Warning: ‘inst/doc’ files
‘COHCAP.Rnw’, ‘COHCAP.pdf’, ‘COHCAP.R’
  ignored as vignettes have been rebuilt.
  Run R CMD build with --no-build-vignettes to prevent rebuilding.
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘COHCAP_1.33.0.tar.gz’

I am using the development version, which I thought should match what was being 
tested for the BioC 3.11 error message.

Can you please either tell me what I need to do to reproduce (and then correct) 
this error, or confirm that it is OK to ignore the e-mails that I have received 
recently?

Thank You,
Charles

Charles Warden, Bioinformatics Specialist
Integrative Genomics Core
City of Hope National Medical Center
Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA, 91016)
Room 1086
Internal Ext: 80375 | Direct: 626-218-0375
Work-From-Home Cell: 404-316-0012

--

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[Bioc-devel] Change associated email/github

[Russell Bainer]

I'd like to change the email address associated with my
Bioconductor account, and also update the ownership of my packages to my
personal Github account (I originally registered both of these with my
employer, and I have since left the company). Could you please direct me to
documentation that will help me do this?

Thanks very much

-R

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Re: [R-pkg-devel] note about mispelled words

[Duncan Murdoch]

I believe it is also acceptable to explain in your submission message 
that the misspelled words are all proper names.  As far as I know, 
misspellings are not enough of a problem to cause an automatic 
rejection, so a human being will be making a judgment about the note.


Duncan Murdoch

On 17/03/2020 11:41 a.m., Henrik Bengtsson wrote:

You can single quote them to avoid them being spell checked, e.g. ...
using methods of 'Kruskall' and 'Brainerd'.  This is a common and
accepted practice.

This is hinted at in "Writing R Extensions" (e.g. help.start());

The mandatory ‘Description’ field should give a comprehensive
description of what the package does. One can use several (complete)
sentences, but only one paragraph. It should be intelligible to all
the intended readership (e.g. for a CRAN package to all CRAN users).
It is good practice not to start with the package name, ‘This package’
or similar. As with the ‘Title’ field, double quotes should be used
for quotations (including titles of books and articles), and single
quotes for non-English usage, including names of other packages and
external software. This field should also be used for explaining the
package name if necessary. URLs should be enclosed in angle brackets,
e.g. ‘’: see also Specifying URLs.

/Henrik

On Tue, Mar 17, 2020 at 8:30 AM Gianmarco Alberti
 wrote:


Hello,
I am checking a package of mine, and I got only 1 note regarding possibly 
misspelled words in the DESCRIPTION.

The issue I am facing is that those 6 words are not actually misspelled, being 
either first or last names of individuals (actually, statistician; e.g., 
Kruskall, Brainerd).

Shall I have to do something (removing those; which does not make sense), or 
upon submitting my new version of the package there is a way to make clear that 
that note can be ignored?

By the way, those names were already there in earlier versions of the package 
and no note cropped out in those occasions.

Thank you
Best
GmA


Dr Gianmarco Alberti (PhD Udine)
Lecturer in Spatial Forensics
Coordinator of the BA course in Criminology
Department of Criminology
Faculty for Social Wellbeing
Room 332, Humanities B (FEMA)
University of Malta, Msida, Malta (Europe) - MSD 2080
tel +356 2340 3718

Academic profiles
https://www.researchgate.net/profile/Gianmarco_Alberti4
https://malta.academia.edu/GianmarcoAlberti

Google Scholar profile
https://scholar.google.com/citations?user=tFrJKQ0J=en

Correspondence Analysis website
http://cainarchaeology.weebly.com/

R packages on CRAN:
CAinterprTools
https://cran.r-project.org/web/packages/CAinterprTools/index.html

GmAMisc
https://cran.r-project.org/package=GmAMisc

movecost
https://cran.r-project.org/web/packages/movecost/index.html


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Re: [Rd] pipe(): input to, and output from, a single process

[Greg Minshall]

Simon,

> FWIW if you're on unix, you can use named pipes (fifos) for that:

i've always wondered what named pipes actually were.  thanks!

cheers, Greg

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Re: [Rd] pipe(): input to, and output from, a single process

[Greg Minshall]

Gabor, thanks.  yes, managing the two-way communication is always a bit
error-prone, as it depends on the input/output characteristics of the
two ends -- they either match, or deadlock.  it's too bad if polling is
always *required* -- i'd think sometimes a programmer would be happy
blocking, though other times one wants better control over when to
block.  cheers, Greg

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[Bioc-devel] Fw: Bioconductor package SIM

[r.menezes]

l.s.


I cannot seem to be able to activate my account on the bioconductor git. I get 
a message saying my email address (the same one on the package help file) is 
not associated with a maintainer of a Bioconductor package. The email address 
is write simply is


r.xavierdemene...@vumc.nl


as stated in the SIM package page.


I tried this on both firefox and chrome, and get the same error each time.


Is there anything I could be doing wrong?


Thanks in advance,

Renee



From: Shepherd, Lori 
Sent: 16 March 2020 15:47
To: Menezes, R. (Ren�e)
Cc: Ren�e Menezes
Subject: Re: Bioconductor package SIM

Please be aware your package is still failing.  This is very problematic.  The
next Bioconductor release is scheduled for Tuesday April 28th. We appreciate
your quick response in this matter. If your package remains broken we will begin
the deprecation process to remove the package from Bioconductor.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Shepherd, Lori 
Sent: Thursday, February 27, 2020 12:08 PM
To: Menezes, R. (Ren�e) 
Cc: r.mene...@nki.nl 
Subject: Re: Bioconductor package SIM

Thank you! Please remember to update your email address in the DESCRIPTION of 
the package when you make changes too.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Menezes, R. (Ren�e) 
Sent: Thursday, February 27, 2020 12:07 PM
To: Shepherd, Lori 
Cc: r.mene...@nki.nl 
Subject: Re: Bioconductor package SIM

Dear Lori,

Thanks for your email. I saw the previous email but have not had the time to 
look at the problem. I have recently changed jobs (my new email address is in 
cc) and it has been really busy in the last few weeks.

I will look at the issue ASAP.

Kind regards,
Renee

Renee X. de Menezes
Lecturer, Dept. Epidemiology and Biostatistics, VUmc
r.mene...@vumc.nl
http://www.bigstatistics.nl/renee





Van: Shepherd, Lori 
Verzonden: donderdag 27 februari 2020 17:36
Aan: Menezes, R. (Ren�e) 
Onderwerp: Bioconductor package SIM

Dear Package Maintainer,

We would like to bring to your attention that your package is failing to 
build/check on our devel build machines:

http://bioconductor.org/checkResults/devel/bioc-LATEST/SIM

Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel 
mailing list if you have any question or need help.

While the development branch is a place to develop new features and we expect 
packages to occasionally break,  they should not remain broken for an extended 
period of time.   If no action is taken over the next few weeks we will begin 
the deprecation process for your package.  The package has been failing since 
at least 01/24/20.  Thank you for your time and effort.

We notified you of your package failure in a group message entitled 
"Bioconductor Package Needs Update"  back on 01/27/20.

Please see https://stat.ethz.ch/pipermail/bioc-devel/2020-January/016081.html

Information can also be found on the troubleshooting build page of the website:
http://bioconductor.org/developers/how-to/troubleshoot-build-report/



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

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Re: [R-pkg-devel] note about mispelled words

[Henrik Bengtsson]

You can single quote them to avoid them being spell checked, e.g. ...
using methods of 'Kruskall' and 'Brainerd'.  This is a common and
accepted practice.

This is hinted at in "Writing R Extensions" (e.g. help.start());

The mandatory ‘Description’ field should give a comprehensive
description of what the package does. One can use several (complete)
sentences, but only one paragraph. It should be intelligible to all
the intended readership (e.g. for a CRAN package to all CRAN users).
It is good practice not to start with the package name, ‘This package’
or similar. As with the ‘Title’ field, double quotes should be used
for quotations (including titles of books and articles), and single
quotes for non-English usage, including names of other packages and
external software. This field should also be used for explaining the
package name if necessary. URLs should be enclosed in angle brackets,
e.g. ‘’: see also Specifying URLs.

/Henrik

On Tue, Mar 17, 2020 at 8:30 AM Gianmarco Alberti
 wrote:
>
> Hello,
> I am checking a package of mine, and I got only 1 note regarding possibly 
> misspelled words in the DESCRIPTION.
>
> The issue I am facing is that those 6 words are not actually misspelled, 
> being either first or last names of individuals (actually, statistician; 
> e.g., Kruskall, Brainerd).
>
> Shall I have to do something (removing those; which does not make sense), or 
> upon submitting my new version of the package there is a way to make clear 
> that that note can be ignored?
>
> By the way, those names were already there in earlier versions of the package 
> and no note cropped out in those occasions.
>
> Thank you
> Best
> GmA
>
> 
> Dr Gianmarco Alberti (PhD Udine)
> Lecturer in Spatial Forensics
> Coordinator of the BA course in Criminology
> Department of Criminology
> Faculty for Social Wellbeing
> Room 332, Humanities B (FEMA)
> University of Malta, Msida, Malta (Europe) - MSD 2080
> tel +356 2340 3718
>
> Academic profiles
> https://www.researchgate.net/profile/Gianmarco_Alberti4
> https://malta.academia.edu/GianmarcoAlberti
>
> Google Scholar profile
> https://scholar.google.com/citations?user=tFrJKQ0J=en
>
> Correspondence Analysis website
> http://cainarchaeology.weebly.com/
>
> R packages on CRAN:
> CAinterprTools
> https://cran.r-project.org/web/packages/CAinterprTools/index.html
>
> GmAMisc
> https://cran.r-project.org/package=GmAMisc
>
> movecost
> https://cran.r-project.org/web/packages/movecost/index.html
> 
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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Re: [Rd] strange bahaviour of predict.lm

[Rui Barradas]

Hello,

I'm glad that it worked.
Two things:

1. Please, click reply all to keep this threaded.
2. The question should have belonged to r-h...@r-project.org, not to 
r-devel@r-project.org.


Rui Barradas

Às 07:10 de 17/03/20, Moshe Olshansky escreveu:

It works, thank you!

On Tuesday, 17 March 2020, 5:47:05 pm AEDT, Rui Barradas 
 wrote:



Hello,

The problem seems to be that A is a matrix. The following solves the error.

# create A and b as in your code then run
A <- as.data.frame(A)
df1 <- cbind(A, b)
reg <- lm(b ~ ., df1)

# etc


Hope this helps,

Rui Barradas

Às 04:36 de 17/03/20, Moshe Olshansky via R-devel escreveu:
 > Hello,
 > Below is my code:
 >> A <- matrix(rnorm(10*3),ncol=3)
 >> b <- runif(10)
 >> reg <- lm(b ~ A)
 >> A1 <- matrix(rnorm(5*3),ncol=3)
 >> A1 <- as.data.frame(A1)
 >> b1 <- predict(reg,A1)
 > Warning message:
 > 'newdata' had 5 rows but variables found have 10 rows
 >
 >    And instead of being an array of length 5, b1 is of length 10 and 
is identical to reg$fitted.values

 > I think that it should not be like this.
 > Let me note that for lm I do not care about this as much since I can 
use reg$coefficients, but unfortunately this behaviour is "inherited" by 
other methods. When I am trying to fit a regression tree, predicting 
from the object without using 'predict' method is less trivial.

 > Thank you,Moshe.
 > P.S. just in case:> sessionInfo()
 > R version 3.6.2 (2019-12-12)
 > Platform: x86_64-pc-linux-gnu (64-bit)
 > Running under: Linux Mint 19.1
 >
 > Matrix products: default
 > BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
 > LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
 >
 > locale:
 > [1] C
 >
 > attached base packages:
 > [1] stats graphics  grDevices utils datasets  methods   base
 >
 > loaded via a namespace (and not attached):
 > [1] compiler_3.6.2 tools_3.6.2

 >
 >
 >
 >
 >
 >     [[alternative HTML version deleted]]
 >
 > __
 > R-devel@r-project.org  mailing list
 > https://stat.ethz.ch/mailman/listinfo/r-devel

 >


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[R-pkg-devel] note about mispelled words

[Gianmarco Alberti]

Hello,
I am checking a package of mine, and I got only 1 note regarding possibly 
misspelled words in the DESCRIPTION.

The issue I am facing is that those 6 words are not actually misspelled, being 
either first or last names of individuals (actually, statistician; e.g., 
Kruskall, Brainerd).

Shall I have to do something (removing those; which does not make sense), or 
upon submitting my new version of the package there is a way to make clear that 
that note can be ignored?

By the way, those names were already there in earlier versions of the package 
and no note cropped out in those occasions.

Thank you
Best
GmA


Dr Gianmarco Alberti (PhD Udine)
Lecturer in Spatial Forensics
Coordinator of the BA course in Criminology
Department of Criminology
Faculty for Social Wellbeing
Room 332, Humanities B (FEMA)
University of Malta, Msida, Malta (Europe) - MSD 2080
tel +356 2340 3718

Academic profiles
https://www.researchgate.net/profile/Gianmarco_Alberti4
https://malta.academia.edu/GianmarcoAlberti

Google Scholar profile
https://scholar.google.com/citations?user=tFrJKQ0J=en

Correspondence Analysis website
http://cainarchaeology.weebly.com/

R packages on CRAN:
CAinterprTools
https://cran.r-project.org/web/packages/CAinterprTools/index.html

GmAMisc
https://cran.r-project.org/package=GmAMisc

movecost
https://cran.r-project.org/web/packages/movecost/index.html


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[R-pkg-devel] Dependency problem

[Schultheis, Hendrik]

Hi r-package-devel,

CRAN asked me to correct some errors so I'm currently in the process of 
updating/ resubmitting my package and ran into an error connected to one of my 
dependencies.
The thing is that the problem only occurs during the r-devel checks because of 
a newer package version of said depdendency but due to it being on Bioconductor 
I cannot exclude this version. Furthermore the problem seems to be fixed in 
their github so it will be solved with the next update cycle.

Should I tell CRAN that this error will resolve itself and can be ignored? Or 
should I wait until it is resolved and risk the package being archived?

Best Hendrik

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Re: [Bioc-devel] BiocParallel Variable Not Found

[Martin Morgan]

Windows uses separate processes that do not share memory (SnowParam()), whereas 
linux / mac by default use forked processes that share the original memory 
(MulticoreParam()). So

> y = 1
> param = MulticoreParam()
> res = bplapply(1:2, function(x) y, BPPARAM=param)

works because the function can 'see' y, whereas

> param = SnowParam()
> res = bplapply(1:2, function(x) y, BPPARAM=param)
Error: BiocParallel errors
  element index: 1, 2
  first error: object 'y' not found

fails because the new processes cannot see y. The robust way to implement this 
makes the FUN in bplapply truly functional, depending only on variables 
received as arguments

> res = bplapply(1:2, function(x, y) y, y = 1, BPPARAM=param)
>

The situation is more complicated in package code in particular and in general, 
because R sends not just FUN to the workers, but also the environment (up to 
but not including the global environment) in which the function applies. So

doit <- function() {
y = 1
bplapply(1:2, function(x) y, BPPARAM = SnowParam(2))
}

also works

> res = doit()
>

Note that

fun = function(x) y

doit = function() {
y = 1
bplapply(1:2, fun, BPPARAM = SnowParam(2))
}

fails, because y is not defined in the environment in which fun is defined 
(it's defined in the calling environment, which is different).

The most robust advice is to develop you code with the most conservative 
assumptions (e.g., register(SnowParam())) and to write functional functions 
where all variables are passed as arguments.

Martin

On 3/17/20, 6:00 AM, "Bioc-devel on behalf of Dario Strbenac" 
 
wrote:

Good day,

I have a loop in a function of my R package which by default uses bpparam() 
to set the framework used for parallelisation. On Windows, I see the error

Error: BiocParallel errors
  element index: 1, 2, 3, 4, 5, 6, ...
  first error: object 'selParams' not found

This error does not happen on the Linux or MacOS operating systems. It 
happens using both R 3.6 and the upcoming version 4. The error can be 
reproduced running the examples of runTests function in ClassifyR.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

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Re: [Rd] new bquote feature splice does not address a common LISP @ use case?

[Lionel Henry]

Hi Jan,

In the lisp code you provide the operators are parsed as simple
symbols in a pairlist. In the R snippet, they are parsed as
left-associative binary operators of equal precedence. If you unquote
a call in the right-hand side, you're artificially bypassing the
left-associativity of these operators.

To achieve what you're looking for in a general way, you'll need a
more precise definition of the problem, and a solution that probably
involves rotating the AST accordingly (see
https://github.com/r-lib/rlang/blob/master/src/internal/expr-interp-rotate.c).
Maybe it could be possible to formulate a definition where splicing in
special calls like binary operators produces the same AST as the user
would type by hand. It seems this would make splicing easier to use
for end users, but make the metaprogramming model more complex for
experts. This is an interesting perspective though. It also seems
vaguely connected to the problem of splicing within model formulas.

I see in your example that the new ..() operator in `bquote()` allows
splicing calls, and seems to unquote them instead of splicing. In the
first versions of rlang, splicing with !!! behaved just like this. We
changed this behaviour last year and I would like to share the
motivations behind this decision, as it might be helpful to inform the
semantics of ..() in bquote() in R 4.0.

The bottom line is that calls are now treated like scalars. This is a
slight contortion of the syntax because calls are "language lists",
and so they could be conceived as collections rather than scalars.
However, R is vector-oriented rather than pairlist-oriented, and
treating calls as scalars makes the metaprogramming model simpler.

This is also how `bquote(splice = TRUE)` works. However `bquote()`
and rlang do not treat scalars in the same way. In rlang scalars
cannot be spliced, they must be unquoted.

```
bquote(foo(..(function() NULL)), splice = TRUE)
#> foo(function() NULL)

bquote(foo(..(quote(bar))), splice = TRUE)
#> foo(bar)

expr(foo(!!!function() NULL))
#> Error: Can't splice an object of type `closure` because it is not a vector.

expr(foo(!!!quote(bar)))
#> foo(bar)
#> Warning message:
#> Unquoting language objects with `!!!` is deprecated as of rlang 0.4.0.
#> Please use `!!` instead.
```

We decided to disallow splicing scalars (and thus calls) in rlang even
though this is a legal operation in many lisps. In lisps, the splicing
operation stands for unquoting in the CDR of a pairlist. By contrast
the unquote operation unquotes in the CAR. For example `(1 ,@3) is
legal in Common Lisp and stands for the cons cell (1 . 3). I think
such semantics are not appealing in a language like R because it is
vector-oriented rather than pairlist oriented. Pairlists are mostly an
implicit data structure that users are not familiar with, and they are
not even fully supported in all implementations of R (for instance
TERR and Renjin do not allow non-NULL terminated pairlists, and while
GNU R has vestigial print() support for these, they cause str() to crash).

In general, it is much more useful to define a splice operation that
also works for vectors:

```
rlang::list2(1, !!!10:11, 3)
#> [[1]]
#> [1] 1
#>
#> [[2]]
#> [1] 10
#>
#> [[3]]
#> [1] 11
#>
#> [[4]]
#> [1] 3
```

Because vectors do not have any notion of CDR, the usual lisp
interpretation of splicing scalars does not apply.

One alternative to make it work is to devolve the splicing operation
into a simple unquote operation, when supplied a scalar. This is how
`bquote(splice = TRUE)` works. However I think this kind of
overloading is more confusing in the long run, and makes it harder for
users to form a correct mental model for programming with these
operations. For this reason it seems preferable to force users to be
explicit about the desired semantics with scalars and calls. In rlang
they must either unquote the call, or explicitly transform it to a
list prior to splicing:

```
x <- quote(bar + baz)

# Unquote instead of splicing
expr(foo(!!x))
#> foo(bar + baz)

# Convert to list and then splice
expr(add(!!!as.list(x[-1])))
#> add(bar, baz)
```

Unquoting could be consistent if all objects were truly vectors in R,
i.e. if they were implicitly wrapped in a list. Then ..(quote(foo))
would be very similar to ..(1). In the former case a list of size 1
would be spliced, in the latter case a vector of size 1 is
spliced. This would explain why .() and ..() have the same behaviour
with scalars. While an interesting thought experiment, this is not
how scalars work in R.

It seems relevant that Clojure is a lisp that does not allow splicing
scalars. Like rlang, Clojure defines the splicing operation in other
contexts than pairlists, such as vectors. I suspect the rationale of
making scalar-splicing an error in Clojure, even in pairlist context,
is to avoid overloading the semantics of this fundamental operation.

Best,
Lionel


On 3/17/20, Jan Gorecki  wrote:
> Dear R-devel,
>
> There is a new feature in R-devel, 

[Bioc-devel] BiocParallel Variable Not Found

[Dario Strbenac]

Good day,

I have a loop in a function of my R package which by default uses bpparam() to 
set the framework used for parallelisation. On Windows, I see the error

Error: BiocParallel errors
  element index: 1, 2, 3, 4, 5, 6, ...
  first error: object 'selParams' not found

This error does not happen on the Linux or MacOS operating systems. It happens 
using both R 3.6 and the upcoming version 4. The error can be reproduced 
running the examples of runTests function in ClassifyR.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

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Re: [Rd] ":::" operator doesn't work with data object Ecdat:::Crime

[Abby Spurdle]

Crime?
(Macavity, Macavity, ..., and when you reach the scene of crime
Macavity's not there...)

I suspect your data objects are like Macavity, they're not there.

I found this in the R Internals 1.17.

Lazy-load databases are loaded into the exports for a package, but not
into the namespace environment itself. Thus they are visible when the
package is attached, and also via the :: operator. This was a
deliberate design decision...

The manual is not explicit about the converse, but implies (I think)
that the converse is true.
(i.e. Non-lazyloaded datasets are not supposed to available via this mechanism).

I didn't check your examples.

Are your examples lazyloaded?
And are they any different from other similar packages/datasets?


>A different but related issue is that "plm::Crime" says "Error:
> 'Crime' is not an exported object from 'namespace:plm'", even though
> "library(plm); data(Crime); Crime" works.  I would naively think a user
> should be able to compare "Crime" objects documented in different
> packages using the "::" and ":::" operators, even if a package
> maintainer chooses not to "export" data objects.
>What do you think?

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Re: [Rd] strange bahaviour of predict.lm

[Rui Barradas]

Hello,

The problem seems to be that A is a matrix. The following solves the error.

# create A and b as in your code then run
A <- as.data.frame(A)
df1 <- cbind(A, b)
reg <- lm(b ~ ., df1)

# etc


Hope this helps,

Rui Barradas

Às 04:36 de 17/03/20, Moshe Olshansky via R-devel escreveu:

Hello,
Below is my code:

A <- matrix(rnorm(10*3),ncol=3)
b <- runif(10)
reg <- lm(b ~ A)
A1 <- matrix(rnorm(5*3),ncol=3)
A1 <- as.data.frame(A1)
b1 <- predict(reg,A1)

Warning message:
'newdata' had 5 rows but variables found have 10 rows

   And instead of being an array of length 5, b1 is of length 10 and is 
identical to reg$fitted.values
I think that it should not be like this.
Let me note that for lm I do not care about this as much since I can use 
reg$coefficients, but unfortunately this behaviour is "inherited" by other 
methods. When I am trying to fit a regression tree, predicting from the object without 
using 'predict' method is less trivial.
Thank you,Moshe.
P.S. just in case:> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19.1

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
[1] C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.6.2 tools_3.6.2





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