mit of 16 menus. The limit is reached in
Bioconductor, as packages add vignettes.
R version 2.2.0, 2005-11-21, i386-pc-mingw32
attached base packages:
[1] "methods" "stats" "graphics" "grDevices" "utils" "datasets"
[7] &
A command
R CMD build
that fails, e.g., because of C code compilation errors, leaves a
directory %TMPDIR%/Rinst.xxx containing the file R.css. Although R
CMD INSTALL --build cleans up after itself, build does not. A fix is
below. Also, build.in references Rcmd.exe, which I thought was no
longer
Utils.pm (revision 36565)
+++ share/perl/R/Utils.pm (working copy)
@@ -75,7 +75,7 @@
$pat . $$ . sprintf("%05d", rand(10**5)));
my $n=0;
-while(-f $retval){
+while(-e $retval){
$retval = file_path($R::Vars::TMPDIR,
Here's my slow response; if there were other off-list replies it would
be great to have a summary.
Not exactly sure what you're looking for. You might adopt a parallel
program so that the 'master' node does something like
myprog.c:
MPI_Init(...)
/* parallel computations, e.g., of pi */
>> Duncan Murdoch
I would have expected numeric(0) as the result (numeric(0) is the
result from log(numeric(0)), etc).
Martin (Morgan)
Martin Maechler <[EMAIL PROTECTED]> writes:
>>>>>> "Ben" == Ben Bolker <[EMAIL PROTECTED]>
>
mean x == numeric(0),
n == 0 (0 copies of an empty set), x == ANY n == numeric(0) (an empty
set of ANYthing), x == numeric(0), n == numeric(0) ? For all of these,
x^n evaluates to numeric(0).
Martin (Morgan)
Duncan Murdoch <[EMAIL PROTECTED]> writes:
> On 1/9/2006 12:40 PM, Martin Morg
meric(0) + 1 ==> numeric(0)
>>> would give me pause.
>>> Gabor Grothendieck <[EMAIL PROTECTED]> writes:
>>> > The way to think about it is:
>>> >
>>> >prod(rep(x,n)) == x^n
>>> >
>>> > and that works for n=0 t
table 'release' branch, once every six months. This means that the
Bioconductor devel branch periodically (as recently and I suspect over
the next several days) contains considerable carnage that propagates to
CRAN devel builds, creating additional work for CRAN maintainers.
Martin Morg
tandard / best practice for merging branches
git checkout master
git merge ... a-pull-request
git push ...
Creating pull requests is a problem for the developer wanting to
contribute to R, not for the R-core developer. As we've seen in this
thread, R-core would not need to feel responsib
On 05/02/2018 03:21 PM, Joris Meys wrote:
Dear all,
I've noticed by trying to download gz files from here :
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811
At the bottom one can download GSM907811.CEL.gz . If I download this
manually and try
oligo::read.celfiles("GSM907811.CEL.g
On 05/03/2018 05:48 AM, Joris Meys wrote:
Dear all,
I've been diving a bit deeper into this per request of Tomas Kalibra, and
found the following :
- the lock on the file is only after trying to read it using oligo, so
that's not a R problem in itself. The problem is independent of extrenal
pa
nargs() provides the number of arguments without evaluating them
> f = function(x, ..., y) nargs()
> f()
[1] 0
> f(a=1, b=2)
[1] 2
> f(1, a=1, b=2)
[1] 3
> f(x=1, a=1, b=2)
[1] 3
> f(stop())
[1] 1
On 05/03/2018 11:01 AM, William Dunlap via R-devel wrote:
In R-3.5.0 you can use ...length():
vis builds of Bioconductor packages
https://stat.ethz.ch/pipermail/bioc-devel/2019-January/014506.html
and elsewhere
Martin Morgan
On 1/3/19, 7:05 PM, "R-devel on behalf of Duncan Murdoch"
wrote:
On 03/01/2019 3:37 p.m., Duncan Murdoch wrote:
> I see this too; by bisection, it see
g the version of the API, as advised in the
header file!)
Martin Morgan
On 5/6/20, 2:26 PM, "R-devel on behalf of Duncan Murdoch"
wrote:
On 06/05/2020 1:09 p.m., frede...@ofb.net wrote:
> Dear R Devel,
>
> Since Linux moved away from using a file-system interfac
ages I personally would implement a connection.
(I mistakenly thought this was a more specialized mailing list; I wouldn't have
posted to R-devel on this topic otherwise)
Martin Morgan
On 5/6/20, 4:12 PM, "Gábor Csárdi" wrote:
AFAIK that API is not allowed on CRAN. It triggers
;s DESCRIPTION file:
> Package: Test
> Type: Package
> Title: Testing format
> Version: 1.0
> Date: 2010-06-22
> Author: Dan Murphy
> Maintainer: Dan Murphy
> Depends: methods
> Description: Does format in a package work with S4 format me
", x=5:1)
An object of class "A"
Slot "x":
[1] 5 8 9 8 5
Martin
>
>
> I can't see what's wrong in my method definition. Can anyone help me =
> with this?
>
> J
>
> Dr James Foadi PhD
> Membrane Protein Laboratory (MPL)
> Diamond Lig
>
> Thanks,
> Dominick
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research
ple-darwin9.8.0
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> Best regards
> Christian
> _._._._._._._._._._._._._._._._._._
> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
> V.i.e.n.n.a A.u.s.t.
)
@674e88 09 CHARSXP g0c1 [MARK,gp=0x21] "x"
@728c38 09 CHARSXP g0c1 [MARK,gp=0x21] "y"
Martin
> a table of size 754KB seems still to be pretty large?
>
> Best regards
> Christian
>
>
> On 7/12/10 11:44 PM, Martin Morgan wrote:
>>
>
> What the people who do the CRAN package checks do get unhappy about are
> packages which fail running the R code in their vignettes, since this
> often indicates a problem in the package which is not exercised by the
> examples nor tests. This gives a warning, as you will see in
0, sep="")))
>> system.time(y4 <- x4[keys])
>user system elapsed
> 130.390 0.000 132.316
>
> And it's apparently worse than quadratic in time!
>
> I'm wondering why this subsetting by name is so slow since it
> seems it could be implemented with x4
On 07/15/2010 08:38 AM, Martin Morgan wrote:
> On 07/15/2010 01:12 AM, Hervé Pagès wrote:
>> Hi,
>>
>> I'm subsetting a named vector using character indices.
>> My vector of indices (or keys) is 10x longer than the vector
>> I'm subsetting. All my ke
always work?
> What are the additional rules?
callNextMethod() will cause additional problems; the idea that you'll
grab things from somewhere other than function arguments doesn't seem
like a robust design, even if it's used in some important parts of R.
Martin
>
> Man
On 09/03/2010 04:42 AM, Duncan Murdoch wrote:
> Philippe Grosjean wrote:
>> Hello,
>>
>> It's several days I try to track this bug, and even cannot cook a
>> reproducible example. Yet, it occurs consistently in a long-running
>> task after a variable period of time. Here is an example:
>>
>
> I
If I
f = function() {}
package.skeleton("PkgA", "f", path="/tmp")
and then edit man/PkgA-pacakge.Rd to read in part
\description{
More about what it does (maybe more than one line)
\Sexpr{1}
}
and then
R CMD build PkgA
I end up with
Saving output to ‘/tmp/PkgA/build/PkgA.pdf’ ...
Warning in
On 09/06/2010 10:00 PM, Dario Strbenac wrote:
> Hello,
>
> I've been attempting to make a generic method that dispatches on the first
> argument, which can be either an S3 or an S4 class. This is as far as I've
> gotten. Any suggestions about what to try next ?
>
> library(aroma.affymetrix)
> lib
On 10/06/2010 06:12 PM, Troy Robertson wrote:
> Hi all,
>
> After no replies to my previous message I thought I might show some code to
> demonstrate the change and again seek any explanation for the error now
> thrown by my code after upgrading from 2.10.1 to 2.11.1.
>
> Thanks
> Troy
> --
On 10/08/2010 01:25 PM, Dirk Eddelbuettel wrote:
>
> With several versions of R 2.12.0 I have been seeing this when running
>
> R CMD build Rcpp
>
> from the SVN sources:
>
> [...]
> Transcript written on Rd2.log.
> Saving output to '/home/edd/svn/rcpp/pkg/Rcpp/build/Rcpp.pdf' ...
> W
On 10/12/2010 07:38 AM, lan gao wrote:
> Dear R Developers,
>
> I am developing a package to submit to bioconductor. Right now, a gene-set
> sample data is saved as a data frame. Each row contains a probe set and its
> corresponding gene-set name ( mutiple probe -set may map to a gene-set name)
>
On 10/19/2010 08:33 PM, Dario Strbenac wrote:
> Hello,
>
> I'm looking for a way to extract objects from what gets created when I Sweave
> with driver = weaver(). I found where the .Rdata objects are, but when I load
> one into R, I don't see anything that looks like the objects that were
> cre
On 10/20/2010 04:25 PM, Dominick Samperi wrote:
> Thanks David, but this doesn't work. Under R 2.12.0 the "Loading required
> packages"
> messages appear under R 2.12.0 when I use, for example:
>
> Rscript --vanilla -e "{ invisible(library(cxxPack)); cat(sqrt(2)) }"
?suppressPackageStartupMessage
If I try to build a package with a vignette
R CMD build Biobase
I see
* checking for file 'Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* creating vignettes ... OK
* cleaning src
On 10/25/2010 03:21 AM, Prof Brian Ripley wrote:
> Biobase is not self-contained so I cannot easily test it, but as far as
> I know this is now resolved.
Thank you it is. Martin
>
> On Sun, 24 Oct 2010, Martin Morgan wrote:
>
>> If I try to build a package with a vignet
On 10/26/2010 03:53 AM, Robin Hankin wrote:
> Hello.
>
> I am trying to write an S4 method for rbind(). I have a class of objects
> called 'mdm', and I want to be able to rbind() them to one another.
>
> I do not want the method for rbind() to coerce anything to an mdm object.
> I want rbind(x1,x
On 11/12/2010 02:31 PM, Patrick Leyshock wrote:
> Hello,
>
> I've created this class:
>
> setClass("example",
>representation (
> size = "numeric",
> id= "character"
>)
> )
>
> Suppose I create a new instance of this class:
>
>> x <- new("example", 4, "id_value"
alysis: Programming with R chapters
11 & 12,
Gentleman, 2008, R Programming for Bioinformatics chapter 6
might be helpful, but by the time they arrive you might find that you're
most of the way through the material covered...
I guess my opinion is that Rcpp would not be useful for u
On 11/15/2010 04:56 PM, Hadley Wickham wrote:
>> Well, that's what I thought too. But:
>>
>> parents <- function(x) {
>> if (identical(x, emptyenv())) return()
>> c(environmentName(x), parents(parent.env(x)))
>> }
>>> parents(as.environment("package:devtools"))
>> [1] "package:devtools" "package
On 11/22/2010 03:23 AM, evilphil wrote:
>
>
>
> anyone?
Hi evilphil --
Your method signature doesn't have 'missing' for its third argument, and
hence isn't the target of dispatch when the generic is invoked with a
missing argument. I guess you'd figured that out and are really asking
whether i
On 01/24/2011 08:37 AM, Kasper Daniel Hansen wrote:
> Johann,
>
> whether S4 is "better" than S3 is a heated subject. No-one (I think)
> disputes that S4 is in some sense more flexible (for some suitable
> definition of flexible), but it does incur some performance overhead
> (how much is debatab
On 01/26/2011 02:56 PM, wayne.zh...@barclayscapital.com wrote:
> Hi,
>
> I'd like to construct an R list object in C++, fill it with relevant data,
> and pass it to an R function which will return a different list object back.
> I have browsed through all the R manuals, and examples under tests
help too. I'm doing something very simple at the
moment, so I prefer not to bring in Rinside/Rcpp if possible.
Thanks again,
Wayne
-Original Message-
From: Martin Morgan [mailto:mtmor...@fhcrc.org]
Sent: Wednesday, January 26, 2011 10:04 PM
To: Zhang, Wayne: IT (NYK)
Cc: r-devel@r-proj
On 01/27/2011 08:51 PM, Paul Bailey wrote:
> Hi,
>
> I'm trying to make a new S4 object with a slot for a "link-glm" object. R
> doesn't like me have a slot of class "link-glm"
>
>> class(make.link("probit"))
> [1] "link-glm"
Tell the S4 system that you'd like to use this 'old' class
setOldCla
On 02/03/2011 09:29 AM, Paul Gilbert wrote:
> I am trying to extend an S3 method to work with an S4 object as well
> as the S3 objects it works with, but UseMethod does not seem to
> recognize the S4 class and dispatches to the default method. Is this
> to be expected or should I be looking for an
On 02/14/2011 11:54 PM, robin hankin wrote:
> Hello everybody
>
> [R-2.12.1]
>
> I am having difficulty dealing with Oarray objects.
> I have a generic function, call it foo(), and I wish
> to define a method for Oarray objects.
>
> I do not have or want a method for regular arrays [actually,
>
On 03/01/2011 03:19 PM, Benilton Carvalho wrote:
> Hi,
>
> I have a BioC infra-structure package that works fine (I can build,
> check and load it successfully) on revision r53950. The very same
> package fails on r54591 with the error below:
>
> Error in loadNamespace(package, c(which.lib.loc, l
On 03/10/2011 08:21 AM, ONKELINX, Thierry wrote:
> Dear all,
>
> I'm writing a package and I would like to reuse the residuals()
> function. When I use a function which calls the redefined residuals
> (for my custom class) I get an error (see below). It looks like the
> wrong method is used. The s
On 03/11/2011 02:07 AM, Andreas Borg wrote:
> Hi all,
>
> I have a function which makes use of missing() to determine which
> arguments are provided in the call - basically, there are two sets of
> arguments that map to different strategies the function uses to fulfill
> its task. After conversion
On 03/21/2011 07:22 PM, Simon Urbanek wrote:
On Mar 21, 2011, at 9:07 PM, Dan Tenenbaum wrote:
Hello,
I have come across two separate packages that have a Makefile in inst/doc
which use the R_HOME variable.
In both cases, the path to R_HOME gets munged in such a way that commands
that includ
ry, not on base::summary, so without the
Matrix::summary generic your object never sees the summary method for
lme4 objects.
So you need to Import: Matrix and importFrom(Matrix, summary).
Martin Morgan
exportMethods("coef","summary","show","print")
exportCla
R version 2.13.0 alpha (2011-03-27 r55091)
This error occurs when R CMD check'ing a Bioconductor package:
* checking for unstated dependencies in R code ... WARNING
Error in e[keep] : invalid subscript type 'list'
Execution halted
See the information on DESCRIPTION files in the chapter 'Creating
On 04/13/2011 11:34 AM, Dirk Eddelbuettel wrote:
On 13 April 2011 at 13:00, Terry Therneau wrote:
| I have a test directory for the survival suite, and dyn.load has ceased
| to work in it. Below shows the log:
|
| tmt1075% R --vanilla
|
| R version 2.12.2 (2011-02-25)
| Copyright (C) 2011 The R
On 04/15/2011 11:18 AM, Simon Urbanek wrote:
On Apr 14, 2011, at 11:00 PM, Dario Strbenac wrote:
I have a confusing error from R CMD check that I don't get when running the
example manually by hand.
In the \examples section of an Rd file, I create a GRanges object, then I call
a function wi
On 04/19/2011 05:00 PM, Dario Strbenac wrote:
Hello,
I've got a DESCRIPTION file with a the first line:
Package: Repitools
But, when I run R CMD INSTALL Repitools I get:
* installing *source* package Repitools ...
** R
** data
** inst
** preparing package for lazy loading
Warning in FUN(X[[1L
ly?
Martin
I guess I need to use there where argument. But how do I have this call outside
any S4 functions, but without having to load aroma.affymetrix when my package
loads ?
Original message
Date: Tue, 19 Apr 2011 19:23:20 -0700
From: Martin Morgan
Subject: Re: [Rd]
as.factor / as.ordered is not written as a generic. This differs from
as.numeric, as.matrix, and other as.*. The following seems to address
this and does not break make check-all.
FWIW, the patch is against r55563, because with r55564 I see
/home/mtmorgan/src/R-devel/src/main/dounzip.c:75:15:
On 04/20/2011 10:13 AM, William Dunlap wrote:
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Martin Morgan
Sent: Wednesday, April 20, 2011 9:56 AM
To: R-devel@r-project.org
Subject: [Rd] Make as.factor an S3 generic?
as.factor
.double.A instead of as.numeric.A) until factor.
Martin
On Wed, 20 Apr 2011, Martin Morgan wrote:
as.factor / as.ordered is not written as a generic. This differs from
as.numeric, as.matrix, and other as.*. The following seems to address
this and does not break make check-all.
FWIW, the pat
ls without installing RepitoolsExamples.
"if (require(RepitoolsExamples))" in an example on a man page is much
preferred to \dontrun{}, as Simon mentions.
Martin Morgan
For more info: this is covered in the "Writing R Extensions," but is
also described here:
http
Several Bioconductor packages were expecting Windows Rzlib.dll to
provide gzopen / gzread / gzseek / gzgets / gzrewind / gzclose. Are
these gone for good, viz., r55624 ?
Martin
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
On 05/01/2011 03:09 PM, John Chambers wrote:
Yes, as presented on that site it makes a little more sense:
"While experimenting with the new reference classes in R I noticed some
odd behaviour if you use the "[[ ]]" notation for methods
(X[["doSomething"]] instead of X$doSomething). This notation
This change has significant consequences for Windows packages using R's
zlib, including packages providing core Bioconductor functionality. Are
the changes in r55624 meant to be long-term?
Martin
On 04/29/2011 03:13 PM, Martin Morgan wrote:
Several Bioconductor packages were expe
An .Rnw file in the vignettes/ directory might reasonably \usepackage or
\include .sty, .bib, or other (e.g., image) files in the same directory
or a sub-directory. The .Rnw file is copied to inst/doc and hence
installed, but the additional files are not. This means that the
installed .Rnw file
also seems like a poor choice. What other strategies are recommended?
Martin
On 05/06/2011 09:58 AM, Martin Morgan wrote:
This change has significant consequences for Windows packages using R's
zlib, including packages providing core Bioconductor functionality. Are
the changes in r55624 meant
On 05/27/2011 06:13 AM, Janko Thyson wrote:
Dear list,
is it possible that method dispatch checks for superclasses/virtual
classes before checking "ANY"?
I'd like to build a generic initialization method for all my Reference
Class (say "MyDataFrame") objects by having them inherit from class, s
On 05/30/2011 08:54 AM, Janko Thyson wrote:
Dear List,
when I first started to use S4 classes, I used the function
'completeClassDef()' in order to see the super- and subclasses of a
certain class:
Hi Janko -- I think 'complete' is meant as an adverb here; what you
might want is names(getClas
On 06/03/2011 02:03 PM, mcguirebc wrote:
Is there a simple way to assign values to S4 slots from within a function?
Doing this doesn't work:
assign_slot<-function(x){
assign("OBJECT@slot",x,envir=parent.env(environment())
}
assign_slot(x)
All I get from this is a new object with the nam
On 06/04/2011 03:07 AM, soeren.vo...@uzh.ch wrote:
Hello, an S4 class "Foo" is defined with a setter, $. For several reasons, the
setter calls a function, .foo.update(). However, bypassing the argument names of the
setter does not work. Question 1: Why not and how can I fix this? Question 2: Wh
On 06/09/2011 10:11 AM, John Chambers wrote:
Good catch.
Here's the problem. To save space and time, reference methods are not
all copied to every object in the class. Instead, the methods are copied
in when first accessed. Methods are functions which use the object as
their environment. So that
On 06/10/2011 04:04 PM, Kornelius Rohmeyer wrote:
I'm sorry for sending a wrongly formated mail before. This is the missing text:
Dear all,
for a CRAN-package that depends on another Bioconductor-package I find
two things annoying and would like to know whether there are some
workarounds:
1) I
On 06/10/2011 05:46 PM, Kornelius Rohmeyer wrote:
Dear Martin,
thanks for your response.
The superclass graphBase is introduced in graph 1.30. In my
understanding the problem is that our package gMCP is build on CRAN
for R 2.12 with the package graph in version 1.30. Unfortunately
biocLite ins
On 07/04/2011 05:08 AM, Prof Brian Ripley wrote:
There was an R-core meeting the week before last, and various planned
changes will appear in R-devel over the next few weeks.
These are changes planned for R 2.14.0 scheduled for Oct 31. As we are
sick of people referring to R-devel as '2.14' or '
It would be convenient if, under R-devel r56422, packages that require
re-installation because they do not have a NAMESPACE were marked as
old.packages, so their lack of functionality can be discovered more easily.
> "snow" %in% row.names(old.packages())
[1] FALSE
> library(snow)
Error in libra
With this set-up
options(warn = 1)
tf <- tempfile()
finalizer <- function(obj) {
message("finalizer")
close(obj$f)
}
this code works
ev <- new.env()
ev$f <- file(tf, "w")
reg.finalizer(ev, finalizer)
rm(ev)
gc()
whereas this (reversing the order of file() and reg.finalizer())
ev <- ne
On 08/23/2011 03:02 PM, Janko Thyson wrote:
Dear list,
I was wondering how to best implement some sort of a "plugin" paradigm
using R methods and the dispatcher:
Say we have a function/method ('foo') that does something useful, but
that should be open for extension in ONE specific area by OTHERS
On 08/26/2011 04:44 AM, Gavin Simpson wrote:
Dear List,
This may be related to this email thread initiated by Ben Bolker last
month: https://stat.ethz.ch/pipermail/r-devel/2011-July/061630.html
In answering this Question on StackOverflow
http://stackoverflow.com/q/7195628/429846 I noticed that
On 08/29/2011 05:36 PM, Simon Urbanek wrote:
On Aug 29, 2011, at 7:48 PM, Alireza Mahani wrote:
I am trying to parallelize part of a C function that is called from
R (via .C) using OpenMP's "parallel for" pragma. I get mixed
results: some runs finish with no problem, but some lead to R
crashin
On 09/23/2011 01:46 PM, Hervé Pagès wrote:
Hi,
cbind() doesn't seem to like raw vectors:
> df <- cbind(a=integer(4000), b=raw(4000))
> df
*** glibc detected *** /home/hpages/R-2.13.1/bin/exec/R: malloc():
memory corruption: 0x02d73ca0 ***
For what it's worth, under valgrind
R -d va
On windows under current R-devel (r57066), R CMD INSTALL, for instance,
invokes gcc with -I"$(R_HOME)/include" prior to any user-defined include
paths. This means that a package cannot specify an alternative zlib.h,
as a (reduced) version of this is in $(R_HOME)/include.
One way around this is
Allocating many small objects triggers numerous garbage collections as R
grows its memory, seriously degrading performance. The specific use case
is in creating a STRSXP of several 1,000,000's of elements of 60-100
characters each; a simplified illustration understating the effects
(because the
On 10/05/2011 02:36 AM, Mark Cowley wrote:
Dear list,
I'm trying to suppress/redirect/squash the output from commands like
install.packages, or download.file. The problem is that none of:
sink(..., type="message"), sink(..., type="output"), capture.output,
suppressMessages are quite doing the
ttern)
grep(pattern, slotNames(x), value = TRUE)
Instead of setOldClass, define a $ method on A
setMethod("$", "A", function(x, name) slot(x, name))
And then
a = new("A")
a$
d = new("D")
d$
I don't know about the setOldClass problem; it se
ts
"plot.prcomp" "plot.princomp" "plot.profile.nls"
graphicsstatsstats
"plot.raster" "plot.spec" "plot.stepfun"
stats graphics
t; > there's anything we can do to help please let me know; Elliot
> > Waingold (CC'd here) can provide access to the VM we used for
> > testing if that's of any help.
> >
>
> Thanks!
>
> I have just been looking at this issue with Martin Mo
On 08/25/2015 12:54 PM, Kevin Ushey wrote:
Hi all,
The following fails for me (on OS X, although I imagine it's the same
on other platforms using libcurl):
options(download.file.method = "libcurl")
options(repos = c(CRAN = "https://cran.rstudio.com/";, CRANextra =
"http://www.stats.ox
than from read.dcf on
error page...
Martin
Thanks, and sorry for the noise.
Kevin
On Tue, Aug 25, 2015, 13:11 Martin Morgan mailto:mtmor...@fredhutch.org>> wrote:
On 08/25/2015 12:54 PM, Kevin Ushey wrote:
> Hi all,
>
> The following fails for me (on OS X
On 08/27/2015 08:16 AM, Martin Maechler wrote:
"DM" == Duncan Murdoch
on Wed, 26 Aug 2015 19:07:23 -0400 writes:
DM> On 26/08/2015 6:04 PM, Jeroen Ooms wrote:
>> On Tue, Aug 25, 2015 at 10:33 PM, Martin Morgan
wrote:
>>>
>>> act
R-devel r69197 returns appropriate errors for the cases below; I know of a few
rough edges
- ftp error codes are not reported correctly
- download.file creates destfile before discovering that http fails, leaving an
empty file on disk
and am happy to hear of more.
Martin
On 08/27/2015 08:46
ost (but the cost here is in small fractions of a
second...) in terms of symbol look-up (and collision?), but would have
no consequence for those of us with more sane use cases.
Martin Morgan
Patches to the R sources (development trunk in subversion at
https://svn.r-project.org/R/trunk/ ) are ve
ded before trying to
download it; previously R would download the error page as though it
were the content.
I'll give this some thought.
Martin Morgan
-Winston
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-deve
On 07/18/2016 03:45 PM, Andrew Piskorski wrote:
I saw a warning from R that I don't fully understand. Here's one way
to reproduce it:
$ /usr/local/pkg/R-3.2-branch-20160718/bin/R --version | head -n 3
R version 3.2.5 Patched (2016-05-05 r70929) -- "Very, Very Secure Dishes"
Copyright (
On 10/03/2016 01:51 PM, Kynn Jones wrote:
Thank you all for your comments and suggestions.
@Frederik, my reason for mucking with environments is that I want to
minimize the number of names that import adds to my current
environment. For instance, if module foo defines a function bar, I
want my
.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
mzR is a Bioconductor package, so better to ask on the Bioconductor
support forum
https://support.bioconductor.org
Oh, I see you did, and then the advice is to avoid cross-posting!
The missing .o files would have been produced in an earlier compilation
step; they likely failed in some way,
compiler output into an email message, avoding
attachments.
Martin
On 21/12/16 17:06, Martin Morgan wrote:
mzR is a Bioconductor package, so better to ask on the Bioconductor
support forum
https://support.bioconductor.org
Oh, I see you did, and then the advice is to avoid cross-postin
solution would offer itself; I'd guess that the bundle location is
inferred when R is built from source, and somehow there has been a
disconnect between your R installation and certificate location, e.g.,
moving the certificate location after R installation.
Martin Morgan
John R
e "pl = pairlist(1, 2); length(pl) = 1; pl"
> pl = pairlist(1, 2); length(pl) = 1; pl
Error in length(pl) = 1 :
SET_VECTOR_ELT() can only be applied to a 'list', not a 'pairlist'
Execution halted
fixed in r72936 (R-devel) / 72937 (R-3-4-branch).
Mart
since exit() reports NA & 0377
(i.e., 0) and the incorrect assignment to runLast is immediately
over-written by the correct value.
Martin Morgan
Index: src/main/main.c
===
--- src/main/main.c (revision 72935)
+++ src/main/main.
format, ap);
is successful and res >= 0. usedVasprintf is then set to TRUE, and
free(b) called.
It seems like the code is correct as written?
Martin Morgan (the real other Martin M*)
return res;
}
__
R-devel@r-project.org mailing list
On 11/21/2017 04:12 PM, Winston Chang wrote:
Thanks - I'll find another way to send messages to the main thread for printing.
The CRAN synchronicity and Bioconductor BiocParallel packages provide
inter-process locks that you could use to surround writes (instead of
sending message to the main
1 - 100 of 408 matches
Mail list logo
