On 10/30/20 10:48, luke-tier...@uiowa.edu wrote:
> On Fri, 30 Oct 2020, Pages, Herve wrote:
>
>>
>> On 10/29/20 23:08, Pages, Herve wrote:
>> ...
>>>
>>> I can think of 2 ways to move forward:
>>>
>>> 1. Keep I()'s current impl
On 10/29/20 23:08, Pages, Herve wrote:
...
>
> I can think of 2 ways to move forward:
>
> 1. Keep I()'s current implementation but suppress the warning. We'll
> make the necessary adjustments to DataFrame() to repair columns supplied
> as I() objects. Note t
Hi Martin,
On 10/26/20 04:52, Martin Maechler wrote:
>>
>> Hi there,
>> Is that change in R-devel intentional?
>>
>> library(Matrix)
>> m <- as(matrix(c(0, 1)), "sparseMatrix")
>>
>> isS4(m)
>> # [1] TRUE
>>
>> x <- I(m)
>> # Warning message:
>> # In `class<-`(x, unique
Hi there,
Is that change in R-devel intentional?
library(Matrix)
m <- as(matrix(c(0, 1)), "sparseMatrix")
isS4(m)
# [1] TRUE
x <- I(m)
# Warning message:
# In `class<-`(x, unique.default(c("AsIs", oldClass(x :
# Setting class(x) to multiple strings ("AsIs", "dgCMat
Hi,
There are 2 bugs here. The proposed fix to Summary.data.frame() is fine
but it doesn't address the other problem reported by the OP that
as.matrix() on a zero-row data.frame doesn't respect the type of its
columns, like other column-combining operations do:
df <- data.frame(a=numeric(0)
Hello list,
In ?Reduce:
init: an R object of the same kind as the elements of ‘x’.
Seems like "the same kind" is an unnecessary and artificial restriction.
Furthermore, there is no notion of "same kind" for heterogeneous lists:
x <- list(letters, c(TRUE, FALSE))
Reduce(function(init
On 1/27/20 23:51, Martin Maechler wrote:
>>>>>> Pages, Herve
>>>>>> on Tue, 21 Jan 2020 17:33:01 + writes:
>
> > Dear Martin,
> > What's the ETA for _R_CLASS_MATRIX_ARRAY_=TRUE to become the new
> > unconditio
On 1/25/20 12:55, Gábor Csárdi wrote:
> R CMD build does not actually run any R code,
**unless** the package contains dynamic vignettes and/or dynamic man
pages (e.g. man pages that include \Sexpr macros), in which case 'R CMD
build' first installs the package in order to evaluate the dynamic st
t: a matrix is an array
> 2) Your package (or one you use) may be affected.
>
>
>>>>>> Martin Maechler
>>>>>> on Fri, 15 Nov 2019 17:31:15 +0100 writes:
>
>>>>>> Pages, Herve
>>>>>> on Thu, 14 N
On 1/9/20 06:56, Stepan wrote:
> On 09. 01. 20 15:41, lille stor wrote:
>
>> I believe this could be done without creating side effects (e.g.
>> crash) as we are just talking about changing values.
A crash would certainly be an annoying "side effect" ;-)
As Stepan explained, data.frame objects
On 1/7/20 06:13, brodie gaslam via R-devel wrote:
...
> Happy new decade.
*** caught segfault ***
conflicting decade boundaries
Traceback:
1: new_decade <- 2020:2029
2: previous_decade <- 2011:2020
3: previous_previous_decade <- 2001:2010
4: current_millenium <- 2001:3000
5: previous_
Happy New Year everybody!
The name (is.nana) doesn't make much sense to me. Can you explain it?
One alternative would be to add an extra argument (e.g. 'strict') to
is.na(). FALSE by default, and ignored (with or w/o a warning) when the
type of 'x' is not "numeric".
H.
On 12/31/19 22:16, Jan
The fact that strsplit() doesn't say anything about 'split' being longer
than 'x' adds to the confusion:
> strsplit(c("xAy", "xxByB", "xCyCCz"), split=c("A", "B", "C", "D"))
[[1]]
[1] "x" "y"
[[2]]
[1] "xx" "y"
[[3]]
[1] "x" "y" "" "z"
A warning (or error) would go a long
On 11/14/19 05:47, Hadley Wickham wrote:
> On Sun, Nov 10, 2019 at 2:37 AM Martin Maechler
> wrote:
>>
>>> Gabriel Becker
>>> on Sat, 2 Nov 2019 12:37:08 -0700 writes:
>>
>> > I agree that we can be careful and narrow and still see a
>> > nice improvement in behavior. Whil
On 11/12/19 14:03, Abby Spurdle wrote:
>> You can have your own rant about "user-defined binary operators being
>> over-used within the R community" without suggesting that my rant was
>> rude.
>
> I wasn't suggesting that you were rude.
> I was questioning a trend.
ok, well, I must ave misinterp
On 11/12/19 12:21, Abby Spurdle wrote:
>
>
>> x %inherits% "data.frame"
>
> IMHO, I think that user-defined binary operators are being over-used
> within the R community.
>
> I don't think that they're "cute" or stylish.
> I think their use should be limited to cases, where they significant
On 11/11/19 01:40, Martin Maechler wrote:
>> Duncan Murdoch
>> on Sun, 10 Nov 2019 11:48:26 -0500 writes:
>
> > On 10/11/2019 9:17 a.m., Bryan Hanson wrote:
> >>
> >>
> >>> On Nov 10, 2019, at 3:36 AM, Martin Maechler
> wrote:
> >>>
> Gabriel
stall.packages() internally, and so on.
>
> /Henrik
>
> PS. Although the idea of having update.packages() install missing
> packages is not bad, I don't think I'm a not a fan for the sole
> purpose of risking installation instructions starting using
> update.packages()
Actually there is one gotcha here: even if a package has not changed
(i.e. same exact hash), there are situations where you want to reinstall
it because one package it depends on has changed. This is because some
of the stuff that gets cached at installation time (e.g. method table)
can become
Hi Gabe,
Keeping track of where a package was installed from would be a nice
feature. However it wouldn't be as reliable as comparing hashes to
decide whether a package needs re-installation or not.
H.
On 11/8/19 12:37, Gabriel Becker wrote:
> Hi Josh,
>
> There are a few issues I can think o
Since we are on this topic, another area of improvement is when
install.packages() downloads hundreds of packages only to realize later
that many of them actually fail to install because one of the packages
they depend on (directly or indirectly) failed to install.
Cheers,
H.
On 11/8/19 11:55
I guess you would just use force=TRUE
H.
On 11/8/19 12:06, William Dunlap via R-devel wrote:
> While developing a package, I often run install.packages() on it many times
> in a session without updating its version number. How would your proposed
> change affect this workflow?
> Bill Dunlap
> TI
On 11/4/19 13:54, Duncan Murdoch wrote:
> On 04/11/2019 4:40 p.m., Pages, Herve wrote:
>> Hi Rolf,
>>
>> On 11/4/19 12:28, Rolf Turner wrote:
>>>
>>> On 5/11/19 3:41 AM, Hadley Wickham wrote:
>>>
>>>> For what it's worth, I do
Hi Rolf,
On 11/4/19 12:28, Rolf Turner wrote:
>
> On 5/11/19 3:41 AM, Hadley Wickham wrote:
>
>> For what it's worth, I don't think this strategy can work in general,
>> because a class might have attributes that depend on its data/contents
>> (e.g.
>> https://urldefense.proofpoint.com/v2/url?u
On 10/30/19 04:29, Martin Maechler wrote:
>> Gabriel Becker
>> on Tue, 29 Oct 2019 12:43:15 -0700 writes:
>
> > 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
>
Has someone looked into the image processing area for this? That sounds
a little bit too high-level for base R to me (and I would be surprised
if any mainstream programming language had this kind of functionality
built-in).
H.
On 10/11/19 03:44, Morgan Morgan wrote:
> Hi All,
>
> I was lookin
Hi,
Alternatively, how about a new glance() generic that would do something
like this:
> library(DelayedArray)
> glance <- DelayedArray:::show_compact_array
> M <- matrix(rnorm(1e6), nrow = 1000L, ncol = 2000L)
> glance(M)
<1000 x 2000> matrix object of type "double":
[,1]
On 8/19/19 16:23, Pages, Herve wrote:
...
> Note that this doesn't happen if A is defined as a VIRTUAL class.
To be precise, when A is a VIRTUAL class, it requires at least
one additional level of class extension to break class():
setClass("A", contains="VIRTU
Hi,
This is a long-standing bug where 'class(object)' does not
return the actual class of 'object' when used inside a validity
method. Instead it seems to return the class for which the validity
method is defined. For example:
setClass("A", slots=c(stuff="ANY"))
setValidity("A", function(o
On 7/7/19 17:41, Jialin Ma wrote:
> Hi Abby,
>
> Thanks a lot for your paraphrasing and your suggestion!
>
> The problem of wrapping the list into a S3/S4 object, i.e. subclassing array
> or matrix, is that one also has to define a bunch of methods for subsetting,
> joining, etc, in order to make
On 5/31/19 08:41, Toby Hocking wrote:...
> In my opinion install.packages should stop with an error (instead of a
> warning) if this happens.
Totally agree with that.
Best,
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Cen
Also note that this can lead to people not being able to load the
package if the set of .Call entry points has changed between the old
and new versions of the package. We strongly suspect that this is what
happened to this Bioconductor user:
https://support.bioconductor.org/p/121228/
Note that
On 5/16/19 17:48, Gabriel Becker wrote:
Hi Herve,
Inline.
On Thu, May 16, 2019 at 4:45 PM Pages, Herve
mailto:hpa...@fredhutch.org>> wrote:
Hi Gabe,
ncol(data.frame(aa=c("a", "b", "c"), AA=c("A", "B", "C")))
# [1] 2
Hi Gabe,
ncol(data.frame(aa=c("a", "b", "c"), AA=c("A", "B", "C")))
# [1] 2
ncol(data.frame(aa="a", AA="A"))
# [1] 2
ncol(data.frame(aa=character(0), AA=character(0)))
# [1] 2
ncol(cbind(aa=c("a", "b", "c"), AA=c("A", "B", "C")))
# [1] 2
ncol(cbind(aa="a", AA="A"))
On 4/25/19 07:50, Tomas Kalibera wrote:
> On 4/20/19 10:39 PM, Pages, Herve wrote:
>> Hi,
>>
>> I was trying to update packages today on one of our MacOS servers, and
>> got this:
>>
>> > update.packages(ask=FALSE)
>>
>> There i
On 4/25/19 04:57, Tomas Kalibera wrote:
> On 4/25/19 3:11 AM, Pages, Herve wrote:
>> Hi,
>>
>> I was playing around with inotifywait (great tool!) to see the new
>> staged installation of source packages in action. In one terminal I'm
>> monitorin
Hi,
I was playing around with inotifywait (great tool!) to see the new
staged installation of source packages in action. In one terminal I'm
monitoring the create/delete/move events of the installation library with:
inotifywait -m --timefmt '%F %T' --format '%T -- %w %e %f' -e create
-e del
Hi,
FWIW I also noticed this problem and reported it on R’s Bugzilla 4 years
ago:
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16223
I actually had to report it twice because my first report
(https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16153) was closed
after a few days and tag
Hi,
I was trying to update packages today on one of our MacOS servers, and
got this:
> update.packages(ask=FALSE)
There is a binary version available but the source version is later:
binary source needs_compilation
gsl 1.9-10.3 2.1-6 TRUE
Do you want to ins
trix",
na.rm = "logical", dims = "numeric"’
But maybe it uses selectMethod() behind the seen so will work once
selectMethod() gets fixed?
Thanks,
H.
On 3/21/19 22:05, Michael Lawrence wrote:
Agreed but I'm not sure we want users accessing documentation with thos
ure we want to mess with it.
Michael
On Thu, Mar 21, 2019 at 8:14 PM Pages, Herve
mailto:hpa...@fredhutch.org>> wrote:
Hi Michael,
Thanks for looking into this. I suspect that truncation of ANY suffixes from
method signatures is also the culprit behind the sudden breakage of aliases of
th
ion of ANY suffixes from method
signatures. I've hacked selectMethod() to be robust to that and will commit
soon. Thanks for the report.
Michael
On Thu, Mar 14, 2019 at 9:32 AM Pages, Herve
mailto:hpa...@fredhutch.org>> wrote:
Here is an example:
setGeneric("foo", func
Here is an example:
setGeneric("foo", function(x, y) standardGeneric("foo"))
setMethod("foo", c("numeric", "ANY"),
function(x, y) cat("I'm the foo#numeric#ANY method\n")
)
Dispatch works as expected but selectMethod() fails to find the method:
> foo(1, TRUE)
I'm the foo#numeric#
Hi,
It's unfortunate that with recent revisions of R 2.13 (this
appeared in revision 54640, March 2), 'R CMD build' now removes
empty dirs in the package. People might have good reasons for
having empty dirs in their packages. For example, in Bioconductor,
we have some tools to automatically gener
Hi,
[hpages@localhost pkgreviews]$ R-2.13 CMD check qrqc_0.99.2.tar.gz
* using log directory ‘/home/hpages/pkgreviews/qrqc.Rcheck’
* using R version 2.13.0 alpha (2011-03-24 r55004)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘
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