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
s is only defined in the current release version of S4Vectors, which is the
only version expected to straddle R versions with different signatures.
Martin Morgan
>
> Maybe a red herring...
>
> ~Malcolm
>
> > -Original Message-
> > From: R-devel [
>From the Bioconductor side of things, the general feeling is that this is a
>step in the right direction and worth the broken packages. Martin Morgan
From: R-devel [r-devel-boun...@r-project.org] on behalf of Martin Maechler
[maech...@stat.math.e
e does not allow connections to port 11001. Either way, the
direction toward a solution is to speak with your system administrator. If it
is firewall, then they are unlikely to accommodate you; the strategy is to run
your cluster exclusively on one side of the firewall.
Mar
I see as below, where getGeneric and getMethod imply a different signature; the
signature is mode="any" for both cases in R version 3.2.3 Patched (2016-01-28
r70038)I don't know how to reproduce Jeff's error, though.
> library(Matrix)
> as.vector
function (x, mode = "any")
.Internal(as.vector(x
Within R these are determined by \VignetteIndexEntry{}. I think you are
referring to the order on the CRAN landing page for your package
https://cran.r-project.org/web/packages/bst/index.html, and then the question
is for a CRAN member.
In Rnw
\documentclass{article}
% \VignetteIndexEntry{01-
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
the signature is computed with the request type (HEAD
vs. GET), and so the same URL doesn't work for both. (See
http://stackoverflow.com/a/20580036/412655)
Any help would be appreciated!
I think I introduced this, in
No I don't think there is a way to avoid the HEAD request.
From: Winston Chang
Sent: Wednesday, June 22, 2016 12:01:39 PM
To: Morgan, Martin
Cc: R Devel List
Subject: Re: [Rd] dowload.file(method="libcurl") and GET vs. HEAD requests
Tha
NULL; loadNamespace("tools")
Thanks, it's a bug fixed with
----
r70933 | morgan | 2016-07-18 16:35:39 -0400 (Mon, 18 Jul 2016) | 5 lines
assignNativeRoutines looks only in package namespace
- previously looked for sy
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
ssociated with lines of code
svn annotate doc/manual/R-exts.texi | less
A quick google search (svn diff visual display) lead me to
svn diff --diff-cmd meld -c73909
for my platform, which pops up the diffs in a visual context.
Martin Morgan
And your description seems wrong:
there is now a
(I don't see lapply / vapply referenced as primitive in the original text
changed by the commit).
Martin Morgan
On 7/10/20, 3:52 AM, "R-devel on behalf of Martin Maechler"
wrote:
>>>>> Cole Miller
>>>>> on Thu, 9 Jul 2020 20:38:10
2, 1));
allocates a vector of length 2 at
SEXP out = PROTECT(Rf_allocVector(INTSXP, nc));
but writes three elements (the 0th, 1st, and 2nd) at
for (int i = 0; i != nr; ++i) {
out_int[i] = int_mat_int[n - 1 + i * nr];
}
Martin Morgan
On 9/11/20, 9:30 PM, &q
te
'not yet initialized' and distinct from character(0) or NA_character_, but want
to mention those often appropriate alternatives.
With
setClassUnion("maybeNumber", c("numeric", "logical"))
every instance of numeric _is_ a maybeNumber, e.g.,
>
haracter", "numeric"))
Error in setOldClass(c("character", "numeric")) :
inconsistent old-style class information for "character"; the class is
defined but does not extend "numeric" and is not valid as the data part
In addition: Warning message:
In
(csym, psym);
+ UNPROTECT(1);
}
return class;
}
seems to remove the warning; I'm guessing that the other SEXP already exist so
don't need protecting?
Martin Morgan
On 10/29/20, 12:47 PM, "R-devel on behalf of luke-tier...@uiowa.edu"
wrote:
I have options(useFancyQuotes = FALSE) in my ~/.Rprofile.
Martin Morgan
On 7/13/21, 11:37 AM, "R-devel on behalf of Frederick Eaton"
wrote:
Dear R Team,
I am running R from the terminal command line (not RStudio). I've noticed
that R has been using Unicod
libRlapack.dylib
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
loaded via a namespace (and not attached):
[1] compiler_4.2.0
(I have built my own R on macOS; similar behavior is observed on a Linux
machine)
Any hints welcome,
Martin Morgan
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
the UTF-8
mode for regular expressions is used, ?regex has more)
However, I think it is better to formulate regular expressions to cover
all of Unicode, so do something like e.g. "only keep ASCII digits, ASCII
space, ASCII underscore, but remove all other characters"
I build my own R from source on an M1 mac. I have a clean svn checkout in one
directory ~/src/R-devel. I switch to ~/bin/R-devel and the first time run
cd ~/bin/R-devel
~/src/R-devel/configure --enable-R-shlib 'CFLAGS=-g -O0'
CPPFLAGS=-I/opt/R/arm64/include 'CXXFLAGS=-g -O0'
make -j
At some poi
Date: Tuesday, May 30, 2023 at 4:54 PM
To: Martin Morgan , R-devel
Subject: Re: [Rd] Building R from source always fails on
tools:::sysdata2LazyLoadDB
On 5/30/23 22:09, Martin Morgan wrote:
> I build my own R from source on an M1 mac. I have a clean svn checkout in one
> directory ~/s
t I realized that the R-SIG-mac mailing list might have been more
appropriate, but I did not see the issue discussed there.
Martin
From: Prof Brian Ripley
Date: Wednesday, May 31, 2023 at 3:46 AM
To: Martin Morgan
Cc: Tomas Kalibera , R-devel
Subject: Re: [Rd] Building R from source always fails
this with data.frame df |> print(n = 2), which is an error (`n`
partially matches `na.print`, and 2 is not a valid value); both methods
silently ignore the typo print(m = 2).
Martin Morgan
From: R-devel on behalf of Henrik Bengtsson
Date: Tuesday, February 6, 2024 at 4:34 PM
To: Iz
ended; see section 1.5.1 of
Writing R Extensions (though as a lazy programmer I kind of like the pattern
"^[^\\.]").
Martin Morgan
-pd
On Jun 5, 2013, at 18:48 , Jombart, Thibaut wrote:
Dear all,
It is my understanding that using 'importFrom' in the NAMESPACE o
On 08/20/2013 11:41 AM, ivo welch wrote:
A second enhancement would be a "smart string", which knows that
everything inside {{...}} should be evaluated.
stopifnot( is.matrix(m), "m is not a matrix, but a {{class(m)}}" )
a variant with more traditional syntax might be
if (!is.matrix(m))
Section 1.3.3 of Writing R Extensions says
"The recommended method of building binary packages is to use
R CMD INSTALL --build pkg where pkg is either the name of a source tarball (in
the usual .tar.gz format) or the location of the directory of the package source
to be built. "
(a) vignette
On 09/23/2013 02:53 PM, Prof Brian Ripley wrote:
The issue is not the ownership (uname) but the uid. A tarball can only store
uids up to 'nobody' (usually 32767), and certainly larger ones cannot be
unpacked portably.
The many identical warnings can obscure useful messages, e.g., about invalid
On 12/05/2013 07:00 PM, Dario Strbenac wrote:
Hello,
With R version 3.0.2 Patched (2013-10-30 r64123) I don't see warnings that I
get in R Under development (unstable) (2013-11-03 r64145)
The warnings are like :
Undocumented S4 methods:
generic '[' and siglist 'BayMethList,ANY,ANY'
The fu
On 12/16/2013 09:18 AM, Krzysztof Mlynarczyk wrote:
Yes, it turned out that using R_PreserveObject and R_ReleaseObject
solved that problem.
Instead I think you want to use the third argument to R_MakeExternalPtr to
protect the SEXP's you'd like to persist for the duration of the object, maybe
On 01/09/2014 07:53 PM, Norm Matloff wrote:
Thanks, Hadley and Simon.
The reason I asked today was that when reference classes first came out,
it had appeared to me that there is no peformance advantage to using
reference classes, that it was mainly a style issue (encapsulation,
etc.). Unless
eapply duplicates the elements of the environment it is being applied to
> env = new.env(); x = 1; tracemem(x)
[1] "<0x1758cd18>"
> env[["x"]] = x
> xx <- eapply(env, length)
tracemem[0x1758cd18 -> 0x1758cbc8]: eapply
but duplication seems unnecessary. I think this is because of 'duplicate' in
On 02/11/2014 09:06 AM, Winston Chang wrote:
To state the issue that Kirill raised in a different way... A package
with S4 or reference classes and Depends:methods can throw an error
when you do something as simple as this:
Rscript -e "mypackage::foo()"
But this will work:
Rscript -e "libr
With this file
/tmp$ cat tmp.Rnw
\documentclass{article}
\begin{document}
<>=
v = seq(0, 60i, length=1000)
plot(abs(v)*exp(v), type="l", col="Royalblue")
@
\includegraphics{tmp-figureexample}
\end{document}
This command
/tmp$ R --vanilla CMD Sweave tmp.Rnw
Output file: tmp.tex
does not produc
tle: Documenting reference classes
Version: 0.0.1
Date: 2012-08-05
Author: Martin Morgan
Maintainer: Martin Morgan
Description: This package implements a simple 'reference' class
Depends: methods
Imports: methods
License: Apache License 2.0
Collate: b
Trying to Stangle / Sweave a file
$ cat vignette.Rnw
%\VignetteEngine{knitr}
\documentclass{article}
\begin{document}
\end{document}
results in a misleading error message:
~/tmp$ R CMD Stangle vignette.Rnw
Error: Vignette engine package not specified
Execution halted
when what is missing is th
In C++ code for use in a R-3.1.0 package, my specific problem is that I would
like to use if it is available, or if not,
or if all else fails.
I (think I) can accomplish this with configure.ac as
AC_INIT("DESCRIPTION")
CXX=`"${R_HOME}/bin/R" CMD config CXX`
CXXFLAGS=`"${R_HOME}/bin/R" CMD
attendant trade-offs -- as a guiding
principle and as a pragmatic solution avoid my complicated unordered_map
configure dance for now.
Thanks all for the various inputs.
Martin Morgan
The map and unordered_map classes are a corner case, as they offer the same
functionality but latter has mu
In a package 'vig' R CMD build vig (or tools::buildVignettes(dir="vig") with
$ cat vig/vignettes/vig1.Rnw
\documentclass{article}
\begin{document}
<<>>=
x <- 1
@
\end{document}
$ cat vig/vignettes/vig2.Rnw
\documentclass{article}
\begin{document}
<<>>=
x
@
\end{document}
produces vig2.pdf where
to bibentry points to *Entry Fields*, but the 'url' tag is
not mentioned there, even though url appears in the examples; if the list of
supported tags is not easy to enumerate, perhaps some insight can be provided at
this point as to how the supported tags are determined?
Thanks
Marti
On 05/23/2014 05:35 AM, Achim Zeileis wrote:
On Thu, 22 May 2014, Martin Morgan wrote:
The following citEntry includes a url with %3A and other encodings
citEntry(entry="article",
title = "Software for Computing and Annotating Genomic Ranges",
author = p
gines that ignore tangle.
It is very valuable to all parties to write a vignette with code that is fully
evaluated; otherwise, it is too easy for bit rot to seep in, or to 'fake' it in
a way that seems innocent but is misleading.
Martin Morgan
is comfortable with vignettes that do
using
the BiocStyle package for their vignette, and the BiocStyle package suggests the
appropriate builder.
Martin Morgan
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206
On 08/27/2014 08:33 PM, Gavin Simpson wrote:
On Aug 27, 2014 5:24 PM, "Hadley Wickham"
I'd say: Depends is a historical artefact from ye old days before
package namespaces. Apart from depending on a specific version of R,
you should basically never use depends. (The one exception is, as
mentio
the class PkgC use PkgB's
special functionality without ever manipulating the object of PkgA.
Martin Morgan
Hadley
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnol
In the context of installing a Bioconductor package using our biocLite()
function, install.packages() warns
> install.packages("RUVSeq", repos="http://bioconductor.org/packages/2.14/bioc";)
Installing package into
'/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1-2.14'
(as 'lib' is unspeci
On 10/03/2014 04:17 PM, Daniel Fuka wrote:
Dear mac folks,
I have started porting a large legacy toolset maintained in windows
and heavily mpi laden so it can be used across platforms in R... so I
am building a package out of it. On this note, I am noticing that
almost all of the mpi dependent p
On 10/03/2014 04:58 PM, Martin Morgan wrote:
On 10/03/2014 04:17 PM, Daniel Fuka wrote:
Dear mac folks,
I have started porting a large legacy toolset maintained in windows
and heavily mpi laden so it can be used across platforms in R... so I
am building a package out of it. On this note, I am
On 10/31/2014 05:55 PM, Gábor Csárdi wrote:
On Fri, Oct 31, 2014 at 8:16 PM, William Dunlap wrote:
You can put the following 3 objects, an environment and 2 functions
that access it, in any package that need some package-specific
storage (say your pkgB1 and pkgB2).
.pkgLocalStorage <- new.e
If I understand correctly, all vignettes in a package are built in the same R
process. Global options, loaded packages, etc., in an earlier vignette persist
in later vignettes. This can introduce user confusion (e.g., when a later
vignette builds successfully because a package is require()'ed in
ter a finalizer that runs when there are no longer references to the R
object, see ?reg.finalizer or the interface to R and C finalizers in
Rinternals.h. If you return more than one reference to a key, then of course
you'll have to manage these in your own C++ code.
Martin Morgan
27;s underlying code; see
?browseVignettes and ?vignette for installed packages, and ?Stangle in R and R
CMD Stangle for extracting the R code from stand-alone vignettes to .R files.
Martin Morgan
Kind regards,
j.
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fai
not overly optimistic
about setting the locale within a session.
Martin Morgan
On 11/23/2014 03:44 AM, Prof Brian Ripley wrote:
On 23/11/2014 09:39, peter dalgaard wrote:
On 23 Nov 2014, at 01:05 , Henrik Bengtsson wrote:
On Sat, Nov 22, 2014 at 12:42 PM, Duncan Murdoch
wrote:
On 22/11/201
ion of the function... The
implementation detail is in the comment -- FUN(X[i], ...) is evaluated in the
frame of lapply.
Martin Morgan
So, essentially, my question is whether the vapply code "should" be changed or
whether a .Internal implementation should always a
ot;IntegerVector doubleThis(const IntegerVector x) { return x
* 2; }")
Rcpp::cppFunction("std::vector incrThis(std::vector x) { x[0] += 1;
return x; }")
or that Rcpp should become more careful (i.e., should not allow!) modifying
arguments with NAMED != 0.
Martin (Mor
istinguish between stats::density() and
igraph::density(). Maybe the example is not meant literally.
Being able to easily flag non-imported, non-base symbols would definitely
improve the robustness of package code, even if not helping the end user
disambiguate duplicate symbols.
Martin Morgan
ad(file='b.Rda'); b"
B
but loading the object without first loading PkgA leads to dispatch to
show,A-method.
~/tmp$ R --vanilla --slave -e "load(file='b.Rda'); b"
Loading required package: PkgA
A
Martin Morgan
--
Computationa
On 05/10/2015 08:19 AM, Martin Morgan wrote:
Loading an S4 object from a file without first loading the library sometimes (?,
the example below and actual example involves a virtual base class and the show
generic) leads to incorrect dispatch (to the base class method).
The attached package
On 05/12/2015 05:31 AM, Martin Maechler wrote:
Martin Morgan
on Mon, 11 May 2015 10:18:07 -0700 writes:
> On 05/10/2015 08:19 AM, Martin Morgan wrote:
>> Loading an S4 object from a file without first loading the library
sometimes (?,
>> the example b
On 05/14/2015 04:33 PM, Henrik Bengtsson wrote:
On May 14, 2015 15:04, "January Weiner" wrote:
Dear all,
I am writing a vignette that requires a file which I am not allowed to
distribute, but which the user can easily download manually. Moreover, it
is not possible to download this file autom
On 05/15/2015 05:05 AM, Charles Determan wrote:
Does anyone else have any thoughts about troubleshooting the R CMD check
environment?
In the pkg.Rcheck directory there is a file pkg-Ex.R.
LANGUAGE=en _R_CHECK_INTERNALS2_=1 $(R_HOME)/bin/R --vanilla pkge-Ex.R
followed by the usual strategy of
On 10/07/2011 06:03 PM, John Fox wrote:
Dear Tim,
-Original Message-
From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org]
On
Behalf Of Tim Triche, Jr.
Sent: October-07-11 3:05 PM
To: Prof Brian Ripley
Cc: r-devel
Subject: Re: [Rd] parallel::mclapply() dummy funct
- Original Message -
> The thing that happens during the check is that the methods package is
> not among the automatically loaded and attached packages.
>
> When the pkgB packages is attached, the Namespaces of pkgA and methods
> are loaded but not attached.
>
> Note that one of the ch
On 10/24/2011 06:04 AM, Evarist Planet wrote:
Dear mailing list,
I have a C function that gives me a wrong result when I run it under Windows
Hi Evarist --
It seems like this can be written reasonably efficiently in R?
getEs <-function(fchr, sign) {
nfchr <- length(fchr)
nsign <- len
With
C:\Users\User>R --version
R version 2.14.0 RC (2011-10-23 r57410)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-mingw32/x64 (64-bit)
running
download.file('http://www.ebi.ac.uk/microarray-as/ae/files/E-TABM-25/E-TABM-25.raw.1.zip',
te
On 10/25/2011 11:57 AM, Martin Morgan wrote:
With
C:\Users\User>R --version
R version 2.14.0 RC (2011-10-23 r57410)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-mingw32/x64 (64-bit)
running
download.file('http://www.ebi.ac.uk/mi
On 10/31/2011 08:53 AM, Aleix Ruiz de Villa wrote:
Dears,
I have a question about copying reference objects using the initialize method.
1) If the latter has no arguments, there is no problem to copy an object.
myClass = setRefClass("myClass", fields = list(value = "numeric") )
myClass$method
On 11/02/2011 11:57 AM, Max Gasner wrote:
Hi there,
I'm working with an object whose internal data representation is very
different from a data.frame (data is stored as a list of big.matrix objects
from the bigmemory package) but to which I'd like to give users
data.frame-like access. I've imple
friendly style?
Hi -- I'm not really understanding your question.
Martin
Thanks again!
2011/11/1 Martin Morgan:
On 10/31/2011 08:53 AM, Aleix Ruiz de Villa wrote:
Dears,
I have a question about copying reference objects using the initialize
method.
1) If the latter has no ar
On 11/14/2011 11:47 AM, dhi...@sonic.net wrote:
dhi...@sonic.net wrote:
Martin Morgan wrote:
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'
On 11/14/2011 01:12 PM, dhi...@sonic.net wrote:
Martin Morgan wrote:
> On 11/14/2011 11:47 AM,dhi...@sonic.net wrote:
> > dhi...@sonic.net wrote:
> >> Martin Morgan wrote:
> >
> > I had done some google searches on this issue, since it seemed l
On 11/18/2011 07:08 AM, Karl Forner wrote:
Hi,
A probably very naive remark, but I believe that the probability of sum(
runif(1) )>= 5 is exactly 0.5. So why not just test that, and
generate the uniform values only if needed ?
My thought as well, but actually the deviates need to have
This bug appears intermittently in R CMD check when reference classes
have finalize methods. The problem is that garbage collection can be run
after the methods package is no longer available. It affects
(periodically) the Bioconductor AnnotationDbi package as well as
packages that contain Rcpp
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