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
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
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
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
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"
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
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
(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:
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
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.,
>
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
(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
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
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
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
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():
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
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
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
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
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
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
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
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.
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
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
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
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,
.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
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
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 (
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
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
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
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
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 08/25/2015 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
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
ts
"plot.prcomp" "plot.princomp" "plot.profile.nls"
graphicsstatsstats
"plot.raster" "plot.spec" "plot.stepfun"
stats graphics
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
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 $(R_HOME)/bin/R --vanilla pkge-Ex.R
followed by the usual strategy of
On 05/14/2015 04:33 PM, Henrik Bengtsson wrote:
On May 14, 2015 15:04, "January Weiner" wrote:
Dear all,
I am writing a vignette that requires a file which I am not allowed to
distribute, but which the user can easily download manually. Moreover, it
is not possible to download this file autom
On 05/12/2015 05:31 AM, Martin Maechler wrote:
Martin Morgan
on Mon, 11 May 2015 10:18:07 -0700 writes:
> On 05/10/2015 08:19 AM, Martin Morgan wrote:
>> Loading an S4 object from a file without first loading the library
sometimes (?,
>> the example b
On 05/10/2015 08:19 AM, Martin Morgan wrote:
Loading an S4 object from a file without first loading the library sometimes (?,
the example below and actual example involves a virtual base class and the show
generic) leads to incorrect dispatch (to the base class method).
The attached package
ad(file='b.Rda'); b"
B
but loading the object without first loading PkgA leads to dispatch to
show,A-method.
~/tmp$ R --vanilla --slave -e "load(file='b.Rda'); b"
Loading required package: PkgA
A
Martin Morgan
--
Computationa
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
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
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
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
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
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
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
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
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 10/03/2014 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
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
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
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
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
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
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
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
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
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 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
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
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
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
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
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 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
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 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 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
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 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))
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 05/08/2013 10:25 AM, Simon Urbanek wrote:
On May 7, 2013, at 11:35 PM, Peter Meilstrup wrote:
Encountered an error in scripting, which can be reproduced using Rscript as
follows:
$ Rscript -e "library(httr); handle('http://cran.r-project.org')"
Error in getCurlHandle(cookiefile = cookie_p
On 05/02/2013 01:35 PM, Duncan Murdoch wrote:
On 13-05-02 3:05 PM, Terry Therneau wrote:
I have a debugging environment for the survival package, perhaps unique to me,
but I find
it works very well.
To wit, a separate directory with copies of the source code but none of the
package
accuements of
On 04/26/2013 07:50 AM, Adam Seering wrote:
Hi,
I've been playing around with the R source code a little; mostly just
trying to familiarize myself. I have access to some computers on a reservation
system; so I've been reserving a computer, downloading and compiling R, and
going from there.
On 04/19/2013 01:16 AM, Prof Brian Ripley wrote:
On 17/04/2013 21:25, Michael Lawrence wrote:
It's tough to reliably reproduce, but I often get stack imbalance warnings
when calling max.col() on non-real/double matrix. The code is conditionally
PROTECTing but not incrementing its nprot counter f
muffleWarning")
} )
...which are then caught as
withCallingHandlers({
warning(w) # 'curves'; caught
warning("another warning")
}, curves=function(w) invokeRestart("muffleWarning"))
The tricky part is to come
On 04/14/2013 07:11 PM, luke-tier...@uiowa.edu wrote:
There were a couple of bug fixes to somewhat obscure compound
assignment related bugs that required bumping up internal reference
counts. It's possible that one or more of these are responsible. If so
it is unavoidable for now, but it's worth
For what it's worth, the package loads many DLLs in its NAMESPACE via repeated
calls to useDynLib. antsImageRead is not in the first DLL loaded, and from
NEWS.Rd, the problem comes from
o A foreign function call (.C() etc) in a package without a PACKAGE
argument will only look in
On 04/01/2013 05:37 PM, Henrik Bengtsson wrote:
Hi,
things have indeed changed on how non-Sweave vignettes are built (this
happened around R devel 2013-03-05 r62130). However, it's not clear
to me what changes would be behind your problems, if any.
Build your vignette with the following buildV
When R is configured with CFLAGS=-O2, clock_gettime is included
$ nm src/main/libR.a | grep clock_gettime
U clock_gettime
whereas when configured with -O0 it is not
$ nm src/main/libR.a | grep clock_gettime
$
Similarly when built as a shared library the linker flags include or
On 03/15/2013 04:42 AM, Martin Maechler wrote:
Martin Morgan
on Wed, 13 Mar 2013 12:43:59 -0700 writes:
> In this post
> https://stat.ethz.ch/pipermail/bioc-devel/2013-March/004152.html
> a package author reports that S4 dispatch fails. I can reproduce thi
In this post
https://stat.ethz.ch/pipermail/bioc-devel/2013-March/004152.html
a package author reports that S4 dispatch fails. I can reproduce this with a
PkgA (attached; 'intervals' is a relatively light-weight CRAN package) that has
DESCRIPTION with
Depends: intervals
Imports: graphics
- dstruct.c (revision 62113)
+++ dstruct.c (working copy)
@@ -59,6 +59,7 @@
if (result == R_NilValue) {
result = allocSExp(type);
SET_PRIMOFFSET(result, offset);
+ SET_VECTOR_ELT(PrimCache, offset, result);
}
else if (TYPEOF(result) != type)
error("reque
On 02/25/2013 01:28 PM, Hadley Wickham wrote:
To summarize, it appears that the only way to call functions from a
suggested package is by using either 'require' (which will dynamically
attach it) or the double colon method. Is this something that should be
mentioned in R-exts?
Except the double
I be doing
if (tools:::.OStype() == "unix") {
importFrom(parallel, mccollect, mcparallel)
}
in my NAMESPACE? I have a recollection that this has come up before, perhaps
even in the parallel package, but I'm not able to find anything.
Thanks,
Martin Morgan
--
Computational Bi
On 02/03/2013 09:36 AM, Martin Morgan wrote:
On 02/02/2013 02:34 PM, Tim Bergsma wrote:
r-devel,
In a development version of the CRAN package metrumrg, I write ...
require(reshape)
setGeneric('cast')
setOldClass(c('keyed','data.frame'))
setMethod('cast
ction."
You haven't mentioned your DESCRIPTION or NAMEPSACE file, but the right thing to
do is
DESCRIPTION:
Depends: reshape
NAMESPACE:
importFrom(reshape, cast)
R/somefile.R:
setGeneric("cast")
Perhaps your current setGeneric is being performed inside the namespace w
With
> R.version.string
[1] "R Under development (unstable) (2013-01-26 r61752)"
'split.default' recycles a short factor for unclassed 'x', but not for an
instance of x that is a class
> split(1:5, 1:2)
$`1`
[1] 1 3 5
$`2`
[1] 2 4
Warning message:
In split.default(1:5, 1:2) :
data length
While trying to install a package, I received this error
** preparing package for lazy loading
Error in matchSignature(signature, fdef, where) :
more elements in the method signature (2) than in the generic signature (1)
A more helpful variant is
Error in matchSignature(signature, fdef, wher
On 12/17/2012 12:57 AM, Ulrich Bodenhofer wrote:
On 12/15/2012 06:26 AM, Martin Morgan wrote:
In ?setMethod there is this paragraph
It is possible to have some differences between the formal
arguments to a method supplied to 'setMethod' and those of the
generic. Rough
On 12/14/2012 09:46 AM, Ulrich Bodenhofer wrote:
Hi,
I just figured out that I accidentally posted my message in HTML, so I am
retrying in plain text only. Sorry.
I am currently extending one of our CRAN packages and ran into an unexpected
problem when checking the source package. I got some wa
real example. Martin
Thanks for the catch.
John
On 12/8/12 3:05 PM, Martin Morgan wrote:
PkgA wishes to write a method for 'unique' on S4 class 'A'. ?Methods
indicates that one should
setGeneric("unique")
setClass("A")
unique.A <- function(x,
S3 and S4 symbols defined, but this seems to be required? A
workaround might extend the check to include getGeneric(genname)@default.
This scenario is reproducible in the attached tarball
tar xzf PkgAB.tar.gz
R CMD INSTALL PkgA
R CMD check PkgB
Martin Morgan
--
Computational Biology / Fre
The attached diff address the following issues in mclapply
mclapply coerces non-lists or objects (S3 or S4) to lists, but a list may not be
an efficient representation and is not required if the object implements length,
[, and [[ methods (lapply must also work on the object, either through coe
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