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
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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
On Wed, 2 Jun 2021, 22:31 Duncan Murdoch, wrote:
> On 02/06/2021 4:33 p.m., xiaoyan yu wrote:
> > I have a R Script Predict.R:
> > set.seed(42)
> > C <- seq(1:1000)
> > A <- rep(seq(1:200),5)
> > E <- (seq(1:1000) * (0.8 + (0.4*runif(50, 0, 1
> > L <- ifelse(runif(100
REprintf and R_FlushConsole.
Best regards,
Morgan
On Sat, Apr 17, 2021 at 12:36 AM Simon Urbanek
wrote:
> Sorry, unable to reproduce on macOS, in R console:
>
> > dyn.load("test.so")
> > .Call("printtest",1e4L)
>
>Processing data chunk 1
] 100%NULL] 0%
I am using R 4.0.4 (Mac) / 4.0.5 (Windows)
Is that a bug or am I doing something wrong?
Thank you
Best regards,
Morgan
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My apologies to Professor Neal.
Thank you for correcting me.
Best regards
Morgan
On Mon, 22 Mar 2021, 05:05 , wrote:
> I think it is "Professor Neal" :)
>
> I also appreciate the pqR comparisons.
>
> On Wed, Mar 17, 2021 at 09:23:15AM +, Morgan Morgan wrote:
&
ther improved as I did
not really try hard.
If there is interest in both the implementation and cross community
sharing, please let know
Best regards,
Morgan
On Wed, 17 Mar 2021, 00:37 Radford Neal, wrote:
> Those interested in faster sorting may want to look at the merge sort
>
different than positive double...
Please read the pdf link I sent, everything is explained in it.
Thank you
Morgan
On Mon, 15 Mar 2021, 16:52 Avraham Adler, wrote:
> Isn’t the default method now “radix” which is the data.table sort, and
> isn’t that already parallel using openmp where ava
(free of charge of course!).
Thank you
Best regards
Morgan
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(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
Sorry Dirk, I don't remember discussing this topic or alternatives with you
at all.
Have a nice day.
On Tue, 30 Jun 2020, 14:42 Morgan Morgan, wrote:
> Thanks Jan and Tomas for the feedback.
> Answer from Jan is what I am looking for.
> Maybe I am not looking in the right place
Thanks Jan and Tomas for the feedback.
Answer from Jan is what I am looking for.
Maybe I am not looking in the right place buy it is not easy to understand
how these LCONS, CONS, SETCDR...etc works.
Thank you
Best regards
Morgan
On Tue, 30 Jun 2020, 12:36 Tomas Kalibera, wrote:
> On 6/30
Hi All,
I was reading the R extension manual section 5.11 ( Evaluating R expression
from C) and I tried to build a simple call to the sum function. Please see
below.
call_to_sum <- inline::cfunction(
language = "C",
sig = c(x = "SEXP"), body = "
SEXP e = PROTECT(lang2(install(\"sum\"), x));
version of the unique and duplicated function. The function
unique is particularly slow for data.frame. So far I got a 100x speedup.
Best regards
Morgan
On Tue, 23 Jun 2020, 21:11 Jim Hester, wrote:
> It looks to me like internally .subset2 uses `get1index()`, but this
> function is decla
m the name of the column without having to loop over columns names to
find the index?
Thank you
Best regards
Morgan
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Sorry, posting back to the list.
Thank you all.
Morgan
On Thu, 21 May 2020, 16:33 Henrik Bengtsson,
wrote:
> Hi.
>
> Good point and a good example. Feel free to post to the list. The purpose
> of my reply wasn't to take away Peter's point but to emphasize that
> bas
For idx= 1, 2, 3, 4 the last line is equal to TRUE. For 5, 6 and many
others the difference is small but still.
Is that expected or is it a bug?
Thank you
Best Regards
Morgan Jacob
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"kit" package (I am
the author) on CRAN.
I will continue working on the package in my spare time if I see that users
are missing basic functionalities not implemented in base R.
Have a great weekend.
Kind regards
Morgan Jacob
[[alternative HTML versi
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
Thank you for your time.
Best regards
Morgan
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Morgan
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aggregate(`Petal.Width` ~ addNA(Species), df, sum) # include NA
data.table and dplyr include NA by default.
Python pandas has an aggreagate function inspired by base R aggregate. An
option has been added to include NA.
Thank you
Best regards
Morgan
[[alternative HTML version deleted
Thank you for your reply Jiefei.
I think in theory your solution should work. I'll have to give them a try.
On Mon, 4 Nov 2019 23:41 Wang Jiefei, wrote:
> Hi Morgan,
>
> My solutions might not be the best one(I believe it's not), but it should
> work for your que
ments before going to the C call? Do I have to
do it at the R level or can it be done at the C level?
Thank you very much in advance.
Best regards
Morgan
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-matrix
Best
Morgan
On Fri, 11 Oct 2019 23:36 Gabor Grothendieck,
wrote:
> The link you posted used the same inputs as in my example. If that is
> not what you meant maybe
> a different example is needed.
> Regards.
>
> On Fri, Oct 11, 2019 at 2:39 PM Pages, Herve wrote:
&
Your answer makes much more sense to me.
I will probably end up adding the function to a package.
Some processes and decisions on how R is developed seems to be obscure to
me.
Thank you
Morgan
On Fri, 11 Oct 2019 15:30 Avraham Adler, wrote:
> It’s rather difficult. For example, the bas
I think you are confusing package and function here. Plus some of the R
Core packages, that you mention, contain functions that should probably be
replaced by functions with better implementation from packages on CRAN.
Best regards
Morgan
On Fri, 11 Oct 2019 15:22 Joris Meys, wrote:
>
>
How do you prove usefulness of a feature?
Do you have an example of a feature that has been added after proving to be
useful in the package space first?
Thank you,
Morgan
On Fri, 11 Oct 2019 13:53 Michael Lawrence,
wrote:
> Thanks for this interesting suggestion, Morgan. While there is
On Fri, 11 Oct 2019 10:45 Duncan Murdoch, wrote:
> On 11/10/2019 6:44 a.m., Morgan Morgan wrote:
> > Hi All,
> >
> > I was looking for a function to find a small matrix inside a larger
> matrix
> > in R similar to the one described in the following link:
>
from the R core team (if you wish) and
suggest an implementation in C.
Thank you
Best regards,
Morgan
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nk you
Best regards
Morgan
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lease let me if you need more informations.
Thank you
Best regards
Morgan
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Hi,
Is there a way to resize a matrix defined as follows:
SEXP a = PROTECT(allocMatrix(INTSXP, 10, 2));
int *pa = INTEGER(a)
To row = 5 and col = 1 or do I have to allocate a second matrix "b" with
pointer *pb and do a "for" loop to transfer the value of a to b?
Thank you
the main tool to extend R?
What is our view on the (not so well known) dotCall64 package which is an
interesting alternative for extending R?
Thank you
Best regards,
Morgan
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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;
}
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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
Thank you all for these explanations.
Kind regards,
Morgan
On 11 Jun 2017 02:47, "Duncan Murdoch" wrote:
> On 10/06/2017 6:09 PM, Duncan Murdoch wrote:
>
>> On 10/06/2017 2:38 PM, Morgan wrote:
>>
>>> Hi,
>>>
>>> I had a question that mi
don't want to team up? Is it because you don't want? Any
particular reasons? Different philosophies?
Thank you
Kind regards
Morgan
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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
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
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
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
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
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-
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
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
>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
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 [
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
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