[Rd] require(..., quietly=TRUE) does not suppress warning
Hi, The `quietly` argument of `require` is documented as follows: quietly: a logical. If ‘TRUE’, no message confirming package attaching is printed, and most often, no errors/warnings are printed if package attaching fails. However: > require(foo, quietly=TRUE) Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘foo’ Am I misreading the docs or is R misbehaving? > sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 10.12.1 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Dan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] wish list: generalized apply
Dear All,
I regularly want to "apply" some function to an array in a way that the
arguments to the user function depend on the index on which the apply is
working. A simple example is:
A <- array( runif(160), dim=c(5,4,8) )
x <- matrix( runif(32), nrow=4, ncol=8 )
b <- runif(8)
f1 <- function( A, x, b ) { sum( A %*% x ) + b }
result <- rep(0.0,8)
for (i in 1:8) {
result[i] <- f1( A[,,i], x[,i] , b[i] )
}
This works, but is slow. I'd like to be able to do something like:
generalized.apply( A, MARGIN=3, FUN=f1, list(x=x,MARGIN=2),
list(b=b,MARGIN=1) ), where the lists tell generalized.apply to pass x[,i] and
b[i] to FUN in addition to A[,,i].
Does such a generalized.apply already exist somewhere? While I can write a C
function to do a particular case, it would be nice if there was a fast, general
way to do this.
John
John P. Nolan
Math/Stat Dept., American University
Gray Hall, 4400 Massachusetts Ave, NW
Washington, DC 20016-8050
Phone: 202-885-3140
E-mail: jpno...@american.edu
Web: http://fs2.american.edu/jpnolan/www/
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Re: [Rd] require(..., quietly=TRUE) does not suppress warning
Well, it says "most often" no errors/warnings are given, so it is not contradicting the docs! It looks like the person/team that coded require( ) decided you should get an error when the package doesn't exist. If you want a silent loading, consider aaa <- try( library(foo,verbose=FALSE,quietly=TRUE),silent=TRUE) and then check to see if aaa is of class "try-error" and check for failure John …….. John P. Nolan Math/Stat Dept., American University Gray Hall, 4400 Massachusetts Ave, NW Washington, DC 20016-8050 Phone: 202-885-3140 E-mail: jpno...@american.edu Web: http://fs2.american.edu/jpnolan/www/ -Original Message From: R-devel [mailto:r-devel-boun...@r-project.org] On Behalf Of Dan Tenenbaum Sent: Thursday, December 8, 2016 2:43 PM To: R-devel Subject: [Rd] require(..., quietly=TRUE) does not suppress warning Hi, The `quietly` argument of `require` is documented as follows: quietly: a logical. If ‘TRUE’, no message confirming package attaching is printed, and most often, no errors/warnings are printed if package attaching fails. However: > require(foo, quietly=TRUE) Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘foo’ Am I misreading the docs or is R misbehaving? > sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 10.12.1 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Dan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] require(..., quietly=TRUE) does not suppress warning
Well, I'm getting a warning (not an error) when the package doesn't exist.
I interpreted "most often" to mean that suppressing warnings/errors is why
you'd most often use this argument, as most packages don't emit startup
messages.
And technically there isn't a problem with attaching the package, since we
don't even try to attach packages that don't exist.
So yes, very careful parsing of the docs suggests that the behavior is correct,
but it does seem to violate the 'spirit' of what a user might expect. I am
pretty sure I have used the 'if (!require("pkg")) install.packages("pkg")'
pattern before without seeing this warning, so I wondered if the behavior had
changed, and that's what prompted me to write.
I know I can squelch the warning by wrapping the require() in
suppressWarnings().
Dan
- Original Message -
> From: "John P. Nolan"
> To: "Dan Tenenbaum" , "R-devel"
>
> Sent: Thursday, December 8, 2016 12:37:02 PM
> Subject: RE: require(..., quietly=TRUE) does not suppress warning
> Well, it says "most often" no errors/warnings are given, so it is not
> contradicting the docs! It looks like the person/team that coded require( )
> decided you should get an error when the package doesn't exist.
>
> If you want a silent loading, consider
> aaa <- try( library(foo,verbose=FALSE,quietly=TRUE),silent=TRUE)
> and then check to see if aaa is of class "try-error" and check for failure
>
> John
> ……..
>
> John P. Nolan
> Math/Stat Dept., American University
> Gray Hall, 4400 Massachusetts Ave, NW
> Washington, DC 20016-8050
> Phone: 202-885-3140
> E-mail: jpno...@american.edu
> Web: http://fs2.american.edu/jpnolan/www/
>
>
>
> -Original Message
> From: R-devel [mailto:r-devel-boun...@r-project.org] On Behalf Of Dan
> Tenenbaum
> Sent: Thursday, December 8, 2016 2:43 PM
> To: R-devel
> Subject: [Rd] require(..., quietly=TRUE) does not suppress warning
>
> Hi,
>
> The `quietly` argument of `require` is documented as follows:
>
> quietly: a logical. If ‘TRUE’, no message confirming package
> attaching is printed, and most often, no errors/warnings are
> printed if package attaching fails.
>
> However:
>
>> require(foo, quietly=TRUE)
> Warning message:
> In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return =
> TRUE, :
> there is no package called ‘foo’
>
> Am I misreading the docs or is R misbehaving?
>
>> sessionInfo()
> R version 3.3.2 (2016-10-31)
> Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra
> 10.12.1
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> Dan
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
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Re: [Rd] require(..., quietly=TRUE) does not suppress warning
IMHO the strongest argument for suppressing the warning message here is the
fact that
requireNamespace("foo", quietly = TRUE)
does not emit any warning message when the package 'foo' does not exist.
On Thu, Dec 8, 2016 at 12:51 PM, Dan Tenenbaum
wrote:
> Well, I'm getting a warning (not an error) when the package doesn't exist.
> I interpreted "most often" to mean that suppressing warnings/errors is why
> you'd most often use this argument, as most packages don't emit startup
> messages.
>
> And technically there isn't a problem with attaching the package, since we
> don't even try to attach packages that don't exist.
>
> So yes, very careful parsing of the docs suggests that the behavior is
> correct, but it does seem to violate the 'spirit' of what a user might
> expect. I am pretty sure I have used the 'if (!require("pkg"))
> install.packages("pkg")' pattern before without seeing this warning, so I
> wondered if the behavior had changed, and that's what prompted me to write.
>
> I know I can squelch the warning by wrapping the require() in
> suppressWarnings().
>
> Dan
>
>
> - Original Message -
> > From: "John P. Nolan"
> > To: "Dan Tenenbaum" , "R-devel" <
> r-devel@r-project.org>
> > Sent: Thursday, December 8, 2016 12:37:02 PM
> > Subject: RE: require(..., quietly=TRUE) does not suppress warning
>
> > Well, it says "most often" no errors/warnings are given, so it is not
> > contradicting the docs! It looks like the person/team that coded
> require( )
> > decided you should get an error when the package doesn't exist.
> >
> > If you want a silent loading, consider
> > aaa <- try( library(foo,verbose=FALSE,quietly=TRUE),silent=TRUE)
> > and then check to see if aaa is of class "try-error" and check for
> failure
> >
> > John
> > ……..
> >
> > John P. Nolan
> > Math/Stat Dept., American University
> > Gray Hall, 4400 Massachusetts Ave, NW
> > Washington, DC 20016-8050
> > Phone: 202-885-3140
> > E-mail: jpno...@american.edu
> > Web: http://fs2.american.edu/jpnolan/www/
> >
> >
> >
> > -Original Message
> > From: R-devel [mailto:r-devel-boun...@r-project.org] On Behalf Of Dan
> Tenenbaum
> > Sent: Thursday, December 8, 2016 2:43 PM
> > To: R-devel
> > Subject: [Rd] require(..., quietly=TRUE) does not suppress warning
> >
> > Hi,
> >
> > The `quietly` argument of `require` is documented as follows:
> >
> > quietly: a logical. If ‘TRUE’, no message confirming package
> > attaching is printed, and most often, no errors/warnings are
> > printed if package attaching fails.
> >
> > However:
> >
> >> require(foo, quietly=TRUE)
> > Warning message:
> > In library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return =
> > TRUE, :
> > there is no package called ‘foo’
> >
> > Am I misreading the docs or is R misbehaving?
> >
> >> sessionInfo()
> > R version 3.3.2 (2016-10-31)
> > Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra
> 10.12.1
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
> >
> > Dan
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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Re: [Rd] wish list: generalized apply
> On Dec 8, 2016, at 12:09 PM, John P. Nolan wrote:
>
> Dear All,
>
> I regularly want to "apply" some function to an array in a way that the
> arguments to the user function depend on the index on which the apply is
> working. A simple example is:
>
> A <- array( runif(160), dim=c(5,4,8) )
> x <- matrix( runif(32), nrow=4, ncol=8 )
> b <- runif(8)
> f1 <- function( A, x, b ) { sum( A %*% x ) + b }
> result <- rep(0.0,8)
> for (i in 1:8) {
> result[i] <- f1( A[,,i], x[,i] , b[i] )
> }
>
> This works, but is slow. I'd like to be able to do something like:
>generalized.apply( A, MARGIN=3, FUN=f1, list(x=x,MARGIN=2),
> list(b=b,MARGIN=1) ), where the lists tell generalized.apply to pass x[,i]
> and b[i] to FUN in addition to A[,,i].
>
> Does such a generalized.apply already exist somewhere? While I can write a C
> function to do a particular case, it would be nice if there was a fast,
> general way to do this.
I would have thought that this would achieve the same result:
result <- sapply( seq_along(b) , function(i) { f1( A[,,i], x[,i] , b[i] )} )
Or:
result <- sapply( seq.int( dim(A)[3] ) , function(i) { f1( A[,,i], x[,i] , b[i]
)} )
(I doubt it will be any faster, but if 'i' is large, parallelism might help.
The inner function appears to be fairly efficient.)
--
David Winsemius
Alameda, CA, USA
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[Rd] methods(`|`) lists all functions?
Dear R-Devel,
I was attempting an exercise in Hadley Wickam's book "Advanced R". The
exercise is to find the generic with the greatest number of methods.
I found that 'methods(`|`)' produces a list of length 2506, in R
3.3.1. Similar behavior is found in 3.4.0. It seems to include all
functions and methods. I imagine something is being passed to "grep"
without being escaped.
I hope I didn't miss something in the documentation, and that I'm good
to report this as a bug. I can send it to Bugzilla if that's better.
By the way, how do I produce such a list of functions (or variables)
in a "normal" way? I used 'ls("package:base")' for the exercise,
because I saw this call used somewhere as an example, but I couldn't
find that "package:" syntax documented under ls()... Also found this
confusing:
> environmentName(globalenv())
[1] "R_GlobalEnv"
> ls("R_GlobalEnv")
Error in as.environment(pos) :
no item called "R_GlobalEnv" on the search list
So I'm not sure if "package:base" is naming an environment, or if
there are different ways to name environments and ls() is using one
form while environmentName is returning another ... It might be good
to add some clarifying examples under "?ls".
Thanks,
Frederick
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Re: [Rd] getGraphicsEvent() alternative for cairo graphics device?
Hi Paul, Thanks for your efforts. Do you have an idea when my patch(es) might be committed? Is there anything I can do to help move this along? Thanks, Frederick On Mon, Nov 14, 2016 at 08:55:20AM +1300, Paul Murrell wrote: > Hi > > The current status is that I am keen for people to contribute some testing > code (see https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16951) > > There were also some getGraphicsEvent() changes/fixes suggested by Richard > Bodewits (cc'ed), for which I am also seeking test code. > > Paul > > On 13/11/16 09:00, frede...@ofb.net wrote: > > Hi Paul, > > > > Just checking in to see what the status is. > > > > From my perspective it seems logical to split off X11 into a separate > > package, so development can proceed at a reasonable rate, but I > > haven't yet tried to see if that's even possible. > > > > Thanks, > > > > Frederick > > > > On Tue, Jul 26, 2016 at 09:23:35AM +1200, Paul Murrell wrote: > > > Hi > > > > > > Taking a look at those patches is now on my todo list, so I may be in > > > touch > > > with both of you at some point to request some testing. > > > > > > Paul > > > > > > On 26/07/16 07:17, frede...@ofb.net wrote: > > > > Dear Daniel Greenidge, > > > > > > > > To enable getGraphicsEvent on Cairo, you have two patches to choose > > > > from: > > > > > > > > https://bugs.r-project.org/bugzilla/show_bug.cgi?id=14364 > > > > https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16951 > > > > > > > > The second one is by me, and the first one is from five years ago by > > > > Hugo Mildenberger. > > > > > > > > Both patches are very simple, they move some lines enabling > > > > getGrahpicsEvent outside of a if(!cairo) statement. My patch also adds > > > > the ability to execute code (e.g. for animation) while the interface > > > > is idle. > > > > > > > > Top guy Duncan Murdoch has expressed that he doesn't have time to work > > > > on applying these patches, and I haven't had any responses from the > > > > rest of the R Core Team. I was thinking that perhaps your best bet is > > > > to try to create a package called e.g. "X11-fixes" which people can > > > > use to get a better X11 library (there is also a bug waiting to be > > > > fixed from 2001: > > > > https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16702). > > > > > > > > I don't know if CRAN would accept such a package, or if you'd have to > > > > distribute it via GitHub, but R has excellent tools to facilitate the > > > > distribution of code via packages. Whether the R kernel exports enough > > > > functions to allow a package to take over event handling, I'm not > > > > sure. I was intending to look more into the details of this > > > > possibility but haven't had time. > > > > > > > > Best wishes, > > > > > > > > Frederick > > > > > > > > On Mon, Jul 25, 2016 at 02:15:59PM -0400, Daniel Greenidge wrote: > > > > > Hi all, > > > > > > > > > > I'm writing an interactive plotting function for viewing fMRI > > > > > datasets. Currently, I get keypresses using > > > > > grDevices::getGraphicsEvent(). > > > > > > > > > > Unfortunately getGraphicsEvent() only supports the X11(type="Xlib") > > > > > graphics device on Unix systems. The Xlib device doesn't support > > > > > buffering (i.e. dev.hold() and dev.flush()), so redrawing the plots > > > > > causes lots of flickering. > > > > > > > > > > Is there a way to get keypresses while using the cairo graphics > > > > > device? Alternatively, is there a way to prevent flickering with the > > > > > Xlib graphics device? > > > > > > > > > > Best, > > > > > Daniel Greenidge > > > > > > > > > > __ > > > > > R-devel@r-project.org mailing list > > > > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > > > > > > > > > > __ > > > > R-devel@r-project.org mailing list > > > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > > > > > > > -- > > > Dr Paul Murrell > > > Department of Statistics > > > The University of Auckland > > > Private Bag 92019 > > > Auckland > > > New Zealand > > > 64 9 3737599 x85392 > > > p...@stat.auckland.ac.nz > > > http://www.stat.auckland.ac.nz/~paul/ > > > > > -- > Dr Paul Murrell > Department of Statistics > The University of Auckland > Private Bag 92019 > Auckland > New Zealand > 64 9 3737599 x85392 > p...@stat.auckland.ac.nz > http://www.stat.auckland.ac.nz/~paul/ > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] getGraphicsEvent() alternative for cairo graphics device?
Hi Just taking a bit more of a look at this today (currently fixated on making sure I can build some good regression tests). The best thing you can do is to keep reminding me like this :) Paul On 09/12/16 11:19, frede...@ofb.net wrote: Hi Paul, Thanks for your efforts. Do you have an idea when my patch(es) might be committed? Is there anything I can do to help move this along? Thanks, Frederick On Mon, Nov 14, 2016 at 08:55:20AM +1300, Paul Murrell wrote: Hi The current status is that I am keen for people to contribute some testing code (see https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16951) There were also some getGraphicsEvent() changes/fixes suggested by Richard Bodewits (cc'ed), for which I am also seeking test code. Paul On 13/11/16 09:00, frede...@ofb.net wrote: Hi Paul, Just checking in to see what the status is. From my perspective it seems logical to split off X11 into a separate package, so development can proceed at a reasonable rate, but I haven't yet tried to see if that's even possible. Thanks, Frederick On Tue, Jul 26, 2016 at 09:23:35AM +1200, Paul Murrell wrote: Hi Taking a look at those patches is now on my todo list, so I may be in touch with both of you at some point to request some testing. Paul On 26/07/16 07:17, frede...@ofb.net wrote: Dear Daniel Greenidge, To enable getGraphicsEvent on Cairo, you have two patches to choose from: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=14364 https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16951 The second one is by me, and the first one is from five years ago by Hugo Mildenberger. Both patches are very simple, they move some lines enabling getGrahpicsEvent outside of a if(!cairo) statement. My patch also adds the ability to execute code (e.g. for animation) while the interface is idle. Top guy Duncan Murdoch has expressed that he doesn't have time to work on applying these patches, and I haven't had any responses from the rest of the R Core Team. I was thinking that perhaps your best bet is to try to create a package called e.g. "X11-fixes" which people can use to get a better X11 library (there is also a bug waiting to be fixed from 2001: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16702). I don't know if CRAN would accept such a package, or if you'd have to distribute it via GitHub, but R has excellent tools to facilitate the distribution of code via packages. Whether the R kernel exports enough functions to allow a package to take over event handling, I'm not sure. I was intending to look more into the details of this possibility but haven't had time. Best wishes, Frederick On Mon, Jul 25, 2016 at 02:15:59PM -0400, Daniel Greenidge wrote: Hi all, I'm writing an interactive plotting function for viewing fMRI datasets. Currently, I get keypresses using grDevices::getGraphicsEvent(). Unfortunately getGraphicsEvent() only supports the X11(type="Xlib") graphics device on Unix systems. The Xlib device doesn't support buffering (i.e. dev.hold() and dev.flush()), so redrawing the plots causes lots of flickering. Is there a way to get keypresses while using the cairo graphics device? Alternatively, is there a way to prevent flickering with the Xlib graphics device? Best, Daniel Greenidge __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] getGraphicsEvent() alternative for cairo graphics device?
Hi Paul, Thanks for keeping me posted and letting me know what I should do. Are there regression tests for other graphics functions in R? To me that sounds a bit unnecessary. I think you get more testing from people who use R; and having a good turnaround for applying patches (some have been waiting 5 years) would invite better participation. Thank you, Frederick On Fri, Dec 09, 2016 at 12:01:55PM +1300, Paul Murrell wrote: > Hi > > Just taking a bit more of a look at this today (currently fixated on making > sure I can build some good regression tests). > > The best thing you can do is to keep reminding me like this :) > > Paul > > On 09/12/16 11:19, frede...@ofb.net wrote: > > Hi Paul, > > > > Thanks for your efforts. Do you have an idea when my patch(es) might > > be committed? Is there anything I can do to help move this along? > > > > Thanks, > > > > Frederick > > > > On Mon, Nov 14, 2016 at 08:55:20AM +1300, Paul Murrell wrote: > > > Hi > > > > > > The current status is that I am keen for people to contribute some testing > > > code (see https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16951) > > > > > > There were also some getGraphicsEvent() changes/fixes suggested by Richard > > > Bodewits (cc'ed), for which I am also seeking test code. > > > > > > Paul > > > > > > On 13/11/16 09:00, frede...@ofb.net wrote: > > > > Hi Paul, > > > > > > > > Just checking in to see what the status is. > > > > > > > > From my perspective it seems logical to split off X11 into a separate > > > > package, so development can proceed at a reasonable rate, but I > > > > haven't yet tried to see if that's even possible. > > > > > > > > Thanks, > > > > > > > > Frederick > > > > > > > > On Tue, Jul 26, 2016 at 09:23:35AM +1200, Paul Murrell wrote: > > > > > Hi > > > > > > > > > > Taking a look at those patches is now on my todo list, so I may be in > > > > > touch > > > > > with both of you at some point to request some testing. > > > > > > > > > > Paul > > > > > > > > > > On 26/07/16 07:17, frede...@ofb.net wrote: > > > > > > Dear Daniel Greenidge, > > > > > > > > > > > > To enable getGraphicsEvent on Cairo, you have two patches to choose > > > > > > from: > > > > > > > > > > > > https://bugs.r-project.org/bugzilla/show_bug.cgi?id=14364 > > > > > > https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16951 > > > > > > > > > > > > The second one is by me, and the first one is from five years ago by > > > > > > Hugo Mildenberger. > > > > > > > > > > > > Both patches are very simple, they move some lines enabling > > > > > > getGrahpicsEvent outside of a if(!cairo) statement. My patch also > > > > > > adds > > > > > > the ability to execute code (e.g. for animation) while the interface > > > > > > is idle. > > > > > > > > > > > > Top guy Duncan Murdoch has expressed that he doesn't have time to > > > > > > work > > > > > > on applying these patches, and I haven't had any responses from the > > > > > > rest of the R Core Team. I was thinking that perhaps your best bet > > > > > > is > > > > > > to try to create a package called e.g. "X11-fixes" which people can > > > > > > use to get a better X11 library (there is also a bug waiting to be > > > > > > fixed from 2001: > > > > > > https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16702). > > > > > > > > > > > > I don't know if CRAN would accept such a package, or if you'd have > > > > > > to > > > > > > distribute it via GitHub, but R has excellent tools to facilitate > > > > > > the > > > > > > distribution of code via packages. Whether the R kernel exports > > > > > > enough > > > > > > functions to allow a package to take over event handling, I'm not > > > > > > sure. I was intending to look more into the details of this > > > > > > possibility but haven't had time. > > > > > > > > > > > > Best wishes, > > > > > > > > > > > > Frederick > > > > > > > > > > > > On Mon, Jul 25, 2016 at 02:15:59PM -0400, Daniel Greenidge wrote: > > > > > > > Hi all, > > > > > > > > > > > > > > I'm writing an interactive plotting function for viewing fMRI > > > > > > > datasets. Currently, I get keypresses using > > > > > > > grDevices::getGraphicsEvent(). > > > > > > > > > > > > > > Unfortunately getGraphicsEvent() only supports the > > > > > > > X11(type="Xlib") > > > > > > > graphics device on Unix systems. The Xlib device doesn't support > > > > > > > buffering (i.e. dev.hold() and dev.flush()), so redrawing the > > > > > > > plots > > > > > > > causes lots of flickering. > > > > > > > > > > > > > > Is there a way to get keypresses while using the cairo graphics > > > > > > > device? Alternatively, is there a way to prevent flickering with > > > > > > > the > > > > > > > Xlib graphics device? > > > > > > > > > > > > > > Best, > > > > > > > Daniel Greenidge > > > > > > > > > > > > > > __ > > > > > > > R-devel@r-project.org mailing list > > > > > > > https://stat.ethz.ch/mailman/listinfo/r-devel > > >
Re: [Rd] getGraphicsEvent() alternative for cairo graphics device?
Hi Yes, we have regression tests for graphics. In general, but especially for core R code, I would rather have confidence that a fix has not broken existing behaviour before I commit it. I cannot argue with the point that we could respond to some bug reports faster. Paul On 09/12/16 12:58, frede...@ofb.net wrote: Hi Paul, Thanks for keeping me posted and letting me know what I should do. Are there regression tests for other graphics functions in R? To me that sounds a bit unnecessary. I think you get more testing from people who use R; and having a good turnaround for applying patches (some have been waiting 5 years) would invite better participation. Thank you, Frederick On Fri, Dec 09, 2016 at 12:01:55PM +1300, Paul Murrell wrote: Hi Just taking a bit more of a look at this today (currently fixated on making sure I can build some good regression tests). The best thing you can do is to keep reminding me like this :) Paul On 09/12/16 11:19, frede...@ofb.net wrote: Hi Paul, Thanks for your efforts. Do you have an idea when my patch(es) might be committed? Is there anything I can do to help move this along? Thanks, Frederick On Mon, Nov 14, 2016 at 08:55:20AM +1300, Paul Murrell wrote: Hi The current status is that I am keen for people to contribute some testing code (see https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16951) There were also some getGraphicsEvent() changes/fixes suggested by Richard Bodewits (cc'ed), for which I am also seeking test code. Paul On 13/11/16 09:00, frede...@ofb.net wrote: Hi Paul, Just checking in to see what the status is. From my perspective it seems logical to split off X11 into a separate package, so development can proceed at a reasonable rate, but I haven't yet tried to see if that's even possible. Thanks, Frederick On Tue, Jul 26, 2016 at 09:23:35AM +1200, Paul Murrell wrote: Hi Taking a look at those patches is now on my todo list, so I may be in touch with both of you at some point to request some testing. Paul On 26/07/16 07:17, frede...@ofb.net wrote: Dear Daniel Greenidge, To enable getGraphicsEvent on Cairo, you have two patches to choose from: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=14364 https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16951 The second one is by me, and the first one is from five years ago by Hugo Mildenberger. Both patches are very simple, they move some lines enabling getGrahpicsEvent outside of a if(!cairo) statement. My patch also adds the ability to execute code (e.g. for animation) while the interface is idle. Top guy Duncan Murdoch has expressed that he doesn't have time to work on applying these patches, and I haven't had any responses from the rest of the R Core Team. I was thinking that perhaps your best bet is to try to create a package called e.g. "X11-fixes" which people can use to get a better X11 library (there is also a bug waiting to be fixed from 2001: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16702). I don't know if CRAN would accept such a package, or if you'd have to distribute it via GitHub, but R has excellent tools to facilitate the distribution of code via packages. Whether the R kernel exports enough functions to allow a package to take over event handling, I'm not sure. I was intending to look more into the details of this possibility but haven't had time. Best wishes, Frederick On Mon, Jul 25, 2016 at 02:15:59PM -0400, Daniel Greenidge wrote: Hi all, I'm writing an interactive plotting function for viewing fMRI datasets. Currently, I get keypresses using grDevices::getGraphicsEvent(). Unfortunately getGraphicsEvent() only supports the X11(type="Xlib") graphics device on Unix systems. The Xlib device doesn't support buffering (i.e. dev.hold() and dev.flush()), so redrawing the plots causes lots of flickering. Is there a way to get keypresses while using the cairo graphics device? Alternatively, is there a way to prevent flickering with the Xlib graphics device? Best, Daniel Greenidge __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 37375
Re: [Rd] wish list: generalized apply
-Original Message-
From: David Winsemius [mailto:dwinsem...@comcast.net]
Sent: Thursday, December 8, 2016 4:59 PM
To: John P. Nolan
Cc: Charles C. Berry
Subject: Re: [Rd] wish list: generalized apply
> On Dec 8, 2016, at 12:09 PM, John P. Nolan wrote:
>
> Dear All,
>
> I regularly want to "apply" some function to an array in a way that the
> arguments to the user function depend on the index on which the apply is
> working. A simple example is:
>
> A <- array( runif(160), dim=c(5,4,8) ) x <- matrix( runif(32), nrow=4,
> ncol=8 ) b <- runif(8)
> f1 <- function( A, x, b ) { sum( A %*% x ) + b } result <- rep(0.0,8)
> for (i in 1:8) { result[i] <- f1( A[,,i], x[,i] , b[i] ) }
>
> This works, but is slow. I'd like to be able to do something like:
>generalized.apply( A, MARGIN=3, FUN=f1, list(x=x,MARGIN=2),
> list(b=b,MARGIN=1) ), where the lists tell generalized.apply to pass x[,i]
> and b[i] to FUN in addition to A[,,i].
>
> Does such a generalized.apply already exist somewhere? While I can write a C
> function to do a particular case, it would be nice if there was a fast,
> general way to do this.
I would have thought that this would achieve the same result:
result <- sapply( seq_along(b) , function(i) { f1( A[,,i], x[,i] , b[i] )} )
Or:
result <- sapply( seq.int( dim(A)[3] ) , function(i) { f1( A[,,i], x[,i] , b[i]
)} )
(I doubt it will be any faster, but if 'i' is large, parallelism might help.
The inner function appears to be fairly efficient.)
--
David Winsemius
Alameda, CA, USA
Thanks for the response. I gave a toy example with 8 iterations to illustrate
the point, so I thought I would bump it up to make my point about speed. But
to my surprise, using a 'for' loop is FASTER than using 'sapply' as David
suggest or even 'apply' on a bit simpler problem. Here is the example:
n <- 80; m <- 10; k <- 10
A <- array( 1:(m*n*k), dim=c(m,k,n) )
y <- matrix( 1:(k*n), nrow=k, ncol=n )
b <- 1:n
f1 <- function( A, y, b ) { sum( A %*% y ) + b }
# use a for loop
time1 <- system.time( {
result <- rep(0.0,n)
for (i in 1:n) {
result[i] <- f1( A[,,i], y[,i] , b[i] )
}
result } )
# use sapply
time2 <- system.time( result2 <- sapply( seq.int( dim(A)[3] ) , function(i) {
f1( A[,,i], y[,i] , b[i] )} ))
# fix y and b, and use standard apply
time3 <- system.time( result3 <- apply( A, MARGIN=3, FUN=f1, y=y[,1], b=b[1] )
)
# user times, then ratios of user times
c( time1[1], time2[1],time3[1]); c( time2[1]/time1[1], time3[1]/time1[1] )
# 4.84 5.22 5.32
# 1.078512 1.099174
So using a for loop saves 8-10% of the execution time as compared to sapply and
apply!? Years ago I experimented and found out I could speed things up
noticeably by replacing loops with apply. This is no longer the case, at least
in this simple experiment. Is this a result of byte code? Can someone tell us
when a for loop is going to be slower than using apply? A more complicated
loop that computes multiple quantities?
John
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Re: [Rd] methods(`|`) lists all functions?
On 12/08/2016 05:16 PM, frede...@ofb.net wrote:
Dear R-Devel,
I was attempting an exercise in Hadley Wickam's book "Advanced R". The
exercise is to find the generic with the greatest number of methods.
I found that 'methods(`|`)' produces a list of length 2506, in R
3.3.1. Similar behavior is found in 3.4.0. It seems to include all
functions and methods. I imagine something is being passed to "grep"
without being escaped.
Exactly; I've fixed this in r71763 (R-devel).
Martin Morgan
I hope I didn't miss something in the documentation, and that I'm good
to report this as a bug. I can send it to Bugzilla if that's better.
By the way, how do I produce such a list of functions (or variables)
in a "normal" way? I used 'ls("package:base")' for the exercise,
because I saw this call used somewhere as an example, but I couldn't
find that "package:" syntax documented under ls()... Also found this
confusing:
> environmentName(globalenv())
[1] "R_GlobalEnv"
> ls("R_GlobalEnv")
Error in as.environment(pos) :
no item called "R_GlobalEnv" on the search list
So I'm not sure if "package:base" is naming an environment, or if
there are different ways to name environments and ls() is using one
form while environmentName is returning another ... It might be good
to add some clarifying examples under "?ls".
Thanks,
Frederick
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Re: [Rd] methods(`|`) lists all functions?
On Thu, Dec 08, 2016 at 09:37:59PM -0500, Martin Morgan wrote: > On 12/08/2016 05:16 PM, frede...@ofb.net wrote: > > Dear R-Devel, > > > > I was attempting an exercise in Hadley Wickam's book "Advanced R". The > > exercise is to find the generic with the greatest number of methods. > > > > I found that 'methods(`|`)' produces a list of length 2506, in R > > 3.3.1. Similar behavior is found in 3.4.0. It seems to include all > > functions and methods. I imagine something is being passed to "grep" > > without being escaped. > > Exactly; I've fixed this in r71763 (R-devel). > > Martin Morgan Thank you. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
