Re: [Rd] head.matrix can return 1000s of columns -- limit to n or add new argument?

[Jan Gorecki]

Gabriel,
My view is rather radical.

- head/tail should return object having same number of dimensions
- data.frame should be a special case
- matrix should be handled as 2D array

P.S. idea of accepting `n` argument as a vector of corresponding
dimensions is a brilliant one

On Wed, Oct 30, 2019 at 1:13 AM Gabriel Becker  wrote:
>
> Hi all,
>
> So I've started working on this and I ran into something that I didn't
> know, namely that for x a multi-dimensional (2+) array, head(x) and tail(x)
> ignore dimension completely, treat x as an atomic vector, and return an
> (unclassed) atomic vector:
>
> > x = array(100, c(4, 5, 5))
>
> > dim(x)
>
> [1] 4 5 5
>
> > head(x, 1)
>
> [1] 100
>
> > class(head(x))
>
> [1] "numeric"
>
>
> (For a 1d array, it does return another 1d array).
>
> When extending head/tail to understand multiple dimensions as discussed in
> this thread, then, should the behavior for 2+d arrays be explicitly
> retained, or should head and tail do the analogous thing (with a head(<2d
> array>) behaving the same as head(), which honestly is what I
> expected to already be happening)?
>
> Are people using/relying on this behavior in their code, and if so, why/for
> what?
>
> Even more generally, one way forward is to have the default methods check
> for dimensions, and use length if it is null:
>
> tail.default <- tail.data.frame <- function(x, n = 6L, ...)
> {
> if(any(n == 0))
> stop("n must be non-zero or unspecified for all dimensions")
> if(!is.null(dim(x)))
> dimsx <- dim(x)
> else
> dimsx <- length(x)
>
> ## this returns a list of vectors of indices in each
> ## dimension, regardless of length of the the n
> ## argument
> sel <- lapply(seq_along(dimsx), function(i) {
> dxi <- dimsx[i]
> ## select all indices (full dim) if not specified
> ni <- if(length(n) >= i) n[i] else dxi
> ## handle negative ns
> ni <- if (ni < 0L) max(dxi + ni, 0L) else min(ni, dxi)
> seq.int(to = dxi, length.out = ni)
> })
> args <- c(list(x), sel, drop = FALSE)
> do.call("[", args)
> }
>
>
> I think this precludes the need for a separate data.frame method at all,
> actually, though (I would think) tail.data.frame would still be defined and
> exported for backwards compatibility. (the matrix method has some extra
> bits so my current conception of it is still separate, though it might not
> NEED to be).
>
> The question then becomes, should head/tail always return something with
> the same dimensionally (number of dims) it got, or should data.frame and
> matrix be special cased in this regard, as they are now?
>
> What are people's thoughts?
> ~G
>
> [[alternative HTML version deleted]]
>
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Re: [R-pkg-devel] winbuilder fails for package depending on rJava

[Jeff Newmiller]

My understanding is that the failure of rJava in the winbuilder server is 
likely to be a system configuration error specific to that server, and is a 
sysadmin issue rather than a package maintainer issue. But the sysadmin may 
know different.

On October 29, 2019 4:23:24 PM PDT, David Winsemius  
wrote:
>
>On 10/29/19 2:12 PM, Jeff Newmiller wrote:
>> Once again, you can color me mystified. Are you reading logs not
>referred to in this email thread?
>
>Hi Jeff;
>
>I suppose am reading  else. I ran:
>
>maintainer("rJava")
>
>
>... and the result was Simon Urbanek's name (which wasn't surprising to
>
>me), and did not match the name of the OP.
>
>So I was (and am) puzzled that  Kevin was using win-builder on rJava.

-- 
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Re: [R-pkg-devel] winbuilder fails for package depending on rJava

[David Winsemius]

On 10/29/19 2:12 PM, Jeff Newmiller wrote:

Once again, you can color me mystified. Are you reading logs not referred to in 
this email thread?


Hi Jeff;

I suppose am reading  else. I ran:

maintainer("rJava")


... and the result was Simon Urbanek's name (which wasn't surprising to 
me), and did not match the name of the OP.


So I was (and am) puzzled that  Kevin was using win-builder on rJava.


--

David.



On October 29, 2019 12:28:59 PM PDT, David Winsemius  
wrote:

On 10/29/19 12:22 PM, Jeff Newmiller wrote:

I suspect David did not read the subject line. This is about

winbuilder [1]. I don't know who runs that service (Uwe?), but this
sounds like they need to investigate.


Correct on the first point, but when I go to that page it says:


Pleasedo notupload packages of other maintainers (particularly not
without changing the Maintainer field to your own e-mail address, if
you
have permissions to do that), because the maintainer indicated in the
maintainer field of the DESCRIPTION file get response from us. Pleasedo

notupload Bioconductor packages or CRAN packages.


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Re: [R-pkg-devel] winbuilder fails for package depending on rJava

[Jeff Newmiller]

Once again, you can color me mystified. Are you reading logs not referred to in 
this email thread?

On October 29, 2019 12:28:59 PM PDT, David Winsemius  
wrote:
>
>On 10/29/19 12:22 PM, Jeff Newmiller wrote:
>> I suspect David did not read the subject line. This is about
>winbuilder [1]. I don't know who runs that service (Uwe?), but this
>sounds like they need to investigate.
>
>
>Correct on the first point, but when I go to that page it says:
>
>
>Pleasedo notupload packages of other maintainers (particularly not 
>without changing the Maintainer field to your own e-mail address, if
>you 
>have permissions to do that), because the maintainer indicated in the 
>maintainer field of the DESCRIPTION file get response from us. Pleasedo
>
>notupload Bioconductor packages or CRAN packages.

-- 
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[Bioc-devel] Access to Bioc git server resumed

[Shepherd, Lori]

Dear Bioconductor developers,

Access to Bioconductor git server is now active again.

Maintainers will now have access to RELEASE_3_10 and master branch.

Make sure you sync your packages with the latest release changes before making 
any updates 
(http://bioconductor.org/developers/how-to/git/sync-existing-repositories/).

Thank you,

Nitesh Turaga


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 
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Re: [Rd] head.matrix can return 1000s of columns -- limit to n or add new argument?

[Gabriel Becker]

Hi all,

So I've started working on this and I ran into something that I didn't
know, namely that for x a multi-dimensional (2+) array, head(x) and tail(x)
ignore dimension completely, treat x as an atomic vector, and return an
(unclassed) atomic vector:

> x = array(100, c(4, 5, 5))

> dim(x)

[1] 4 5 5

> head(x, 1)

[1] 100

> class(head(x))

[1] "numeric"


(For a 1d array, it does return another 1d array).

When extending head/tail to understand multiple dimensions as discussed in
this thread, then, should the behavior for 2+d arrays be explicitly
retained, or should head and tail do the analogous thing (with a head(<2d
array>) behaving the same as head(), which honestly is what I
expected to already be happening)?

Are people using/relying on this behavior in their code, and if so, why/for
what?

Even more generally, one way forward is to have the default methods check
for dimensions, and use length if it is null:

tail.default <- tail.data.frame <- function(x, n = 6L, ...)
{
if(any(n == 0))
stop("n must be non-zero or unspecified for all dimensions")
if(!is.null(dim(x)))
dimsx <- dim(x)
else
dimsx <- length(x)

## this returns a list of vectors of indices in each
## dimension, regardless of length of the the n
## argument
sel <- lapply(seq_along(dimsx), function(i) {
dxi <- dimsx[i]
## select all indices (full dim) if not specified
ni <- if(length(n) >= i) n[i] else dxi
## handle negative ns
ni <- if (ni < 0L) max(dxi + ni, 0L) else min(ni, dxi)
seq.int(to = dxi, length.out = ni)
})
args <- c(list(x), sel, drop = FALSE)
do.call("[", args)
}


I think this precludes the need for a separate data.frame method at all,
actually, though (I would think) tail.data.frame would still be defined and
exported for backwards compatibility. (the matrix method has some extra
bits so my current conception of it is still separate, though it might not
NEED to be).

The question then becomes, should head/tail always return something with
the same dimensionally (number of dims) it got, or should data.frame and
matrix be special cased in this regard, as they are now?

What are people's thoughts?
~G

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Re: [R-pkg-devel] winbuilder fails for package depending on rJava

[David Winsemius]

On 10/29/19 12:22 PM, Jeff Newmiller wrote:
> I suspect David did not read the subject line. This is about winbuilder [1]. 
> I don't know who runs that service (Uwe?), but this sounds like they need to 
> investigate.


Correct on the first point, but when I go to that page it says:


Pleasedo notupload packages of other maintainers (particularly not 
without changing the Maintainer field to your own e-mail address, if you 
have permissions to do that), because the maintainer indicated in the 
maintainer field of the DESCRIPTION file get response from us. Pleasedo 
notupload Bioconductor packages or CRAN packages.


-- 

David.

>
> [1] https://win-builder.r-project.org/
>
> On October 29, 2019 9:28:23 AM PDT, David Winsemius  
> wrote:
>> On 10/29/19 4:48 AM, Kevin Kuo wrote:
>>> Seems like all rev deps of rJava are failing Windows checks with the
>> same
>>> error. Might be a Java architecture mismatch issue?
>> Copied from the rJava GitHub page:
>>
>> ==
>>
>>
>>   Bug reports
>>
>> Please userJava GitHub issues page
>> 
>>
>> to report bugs.
>>
>>
>> (Seems likely that Simon would be aware of such a problem.)
>>
>> 
>>
>>
>> I get no errors in Ubuntu 18.04 with:
>>
>>
>> |install.packages("rJava",,"http://rforge.net;) |
>>
>> You are supposed to offer your OS and other version details with a bug
>> report.

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Re: [Bioc-devel] MISTAKES IN DESCRIPTION FILES

[EDUARDO ILLUECA FERNANDEZ]

  Dear Lori Sepherd,

The package is ready. Thanks very much for your attention.

Yours sincerely,

Eduardo Illueca

"Shepherd, Lori"  escribió:

> Please make the correction and notify me when the package is ready.   
> As this is an annotation package the process of pushing changes is  
> slightly different (although we are hoping to make more consistent  
> in the next 6 months release cycle).   
>    
>    
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> -
>FROM: EDUARDO ILLUECA FERNANDEZ 
> SENT: Tuesday, October 29, 2019 2:53 PM
> TO: Shepherd, Lori ;  
> bioc-devel@r-project.org 
> SUBJECT: MISTAKES IN DESCRIPTION FILES    
>
>
> Dear Lori Sepherd,
>
> There is a little mistake in the description section of the  
> DESCRIPTION file and a small error in the name of a directory that  
> has prevented the generation of the vignette. Is it possible to  
> correct it before the release of version 3.10? Should I make these  
> changes in my repository? I also see that version 1.0.22 appears on  
> the provisional page, should I also change it? Thanks very much for  
> your attention.
>
> Yours sincerely,
>
> Eduardo Illueca

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Re: [R-pkg-devel] winbuilder fails for package depending on rJava

[Jeff Newmiller]

I suspect David did not read the subject line. This is about winbuilder [1]. I 
don't know who runs that service (Uwe?), but this sounds like they need to 
investigate.

[1] https://win-builder.r-project.org/

On October 29, 2019 9:28:23 AM PDT, David Winsemius  
wrote:
>
>On 10/29/19 4:48 AM, Kevin Kuo wrote:
>> Seems like all rev deps of rJava are failing Windows checks with the
>same
>> error. Might be a Java architecture mismatch issue?
>
>Copied from the rJava GitHub page:
>
>==
>
>
>  Bug reports
>
>Please userJava GitHub issues page 
>
>
>to report bugs.
>
>
>(Seems likely that Simon would be aware of such a problem.)
>
>
>
>
>I get no errors in Ubuntu 18.04 with:
>
>
>|install.packages("rJava",,"http://rforge.net;) |
>
>You are supposed to offer your OS and other version details with a bug 
>report.

-- 
Sent from my phone. Please excuse my brevity.

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Re: [Bioc-devel] MISTAKES IN DESCRIPTION FILES

[Shepherd, Lori]

Please make the correction and notify me when the package is ready.  As this is 
an annotation package the process of pushing changes is slightly different 
(although we are hoping to make more consistent in the next 6 months release 
cycle).



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: EDUARDO ILLUECA FERNANDEZ 
Sent: Tuesday, October 29, 2019 2:53 PM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: MISTAKES IN DESCRIPTION FILES


Dear Lori Sepherd,

There is a little mistake in the description section of the DESCRIPTION file 
and a small error in the name of a directory that has prevented the generation 
of the vignette. Is it possible to correct it before the release of version 
3.10? Should I make these changes in my repository? I also see that version 
1.0.22 appears on the provisional page, should I also change it? Thanks very 
much for your attention.

Yours sincerely,

Eduardo Illueca


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] MISTAKES IN DESCRIPTION FILES

[EDUARDO ILLUECA FERNANDEZ]

Dear Lori Sepherd,

There is a little mistake in the description section of the  
DESCRIPTION file and a small error in the name of a directory that has  
prevented the generation of the vignette. Is it possible to correct it  
before the release of version 3.10? Should I make these changes in my  
repository? I also see that version 1.0.22 appears on the provisional  
page, should I also change it? Thanks very much for your attention.

Yours sincerely,

Eduardo Illueca

[[alternative HTML version deleted]]

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Re: [R-pkg-devel] winbuilder fails for package depending on rJava

[David Winsemius]

On 10/29/19 4:48 AM, Kevin Kuo wrote:

Seems like all rev deps of rJava are failing Windows checks with the same
error. Might be a Java architecture mismatch issue?


Copied from the rJava GitHub page:

==


 Bug reports

Please userJava GitHub issues page 
 
to report bugs.



(Seems likely that Simon would be aware of such a problem.)




I get no errors in Ubuntu 18.04 with:


|install.packages("rJava",,"http://rforge.net;) |

You are supposed to offer your OS and other version details with a bug 
report.



--

David.



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[Bioc-devel] Disabling push access 11 am EST TODAY!

[Shepherd, Lori]

Dear Bioconductor developers,

Today we'll be creating the Bioconductor 3.10 branch (RELEASE_3_10) starting at 
11am EST. All push access to git.bioconductor.org will be blocked for a few 
hours starting at 11AM. We'll post back when push access is restored and you 
can resume commits.

Thanks.

Nitesh Turaga

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 
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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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Re: [R-pkg-devel] winbuilder fails for package depending on rJava

[Kevin Kuo]

Seems like all rev deps of rJava are failing Windows checks with the same
error. Might be a Java architecture mismatch issue?

[[alternative HTML version deleted]]

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