I know I'm a curmudgeon, but it seems to me that if their "company
policy" is causing a problem while trying to use free software, then the
company should pay to fix it.
Kevin
On 8/26/2024 10:42 AM, Therneau, Terry M., Ph.D. via R-devel wrote:
The survival package makes significant use of t
I believe this is documented behavior. The 'read.csv' function is a
front-end to 'read.table' with different default values. IN this
particular case, read.csv sets fill = TRUE, which means that it is
supposed to fill incomplete lines with NA's. It also sets header=TRUE,
which is presumably what
difftime is an S3 class, not an S4 class. To convert it, include the line
setOldClass("difftime")
and the setMethod call should work.
On 7/9/2013 6:03 AM, Dan Murphy wrote:
I am trying to write S4 methods with "difftime" in the signature but
am being "informed" (? not a warning or error) that
Why would the virus checker cause a problem with this package, and not
any of the dozen other packaqes?
On 9/10/2012 1:24 PM, Duncan Murdoch wrote:
On 10/09/2012 2:15 PM, Kevin R. Coombes wrote:
Hi,
I'm trying to get a package to pass through "R CMD check --as-cran" and
Hi,
I'm trying to get a package to pass through "R CMD check --as-cran" and
have run into a problem that gives me no idea where to look to fix it.
I'm running R version 15.1 on a Windows 7 64-bit machine, with the
current set of Rtools. An attempt to check the package dies at the
following s
I can reproduce the "R for Windows terminal front-end has stopped
working" with both R-2.14.1 and R-2.13.0 (i386), and get the "hang but
not crash" with both of the x64 binaries for those versions.
On 4/17/2012 2:01 PM, Henrik Bengtsson wrote:
I really meant crash and left my report short thin
Change the "na.strings" argument to read.table or read.csv when reading
in the file. By default, na.strings="NA". If you do something like
countryCodes <- read.csv("mySourceFile.csv", na.strings="")
then your problem will go away.
On 4/5/2012 7:26 AM, Adrian Dusa wrote:
On Thu, Apr 5, 2012
First, I can confirm this problem exists today, and can now vaguely
recall seeing it in previous version of R.
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)
There is a bigger problem with heatmap.2 in the gplots package. Using
"symm=TRUE" with no other
It may not (yet) be canonical, but it is (a) easy to remember and (b)
likely to be recognized easily by someone looking at the structure.
On 2/7/2012 5:37 PM, Simon Urbanek wrote:
On Feb 7, 2012, at 4:34 PM, Roebuck,Paul L wrote:
We have an R package which needs to include a JAR file.
Is ther
I prefer the code chunks myself.
Function calls have overhead. In a bioinformatics world with large
datasets and an R default that uses call-by-value rather than
call-by-reference, the function calls may have a _lot_ of overhead.
Writing the functions to make sure they use call-by-reference f
On 1/29/2012 4:35 PM, Paul Johnson wrote:
On Sun, Jan 29, 2012 at 6:10 AM, Prof Brian Ripley
wrote:
On 28/01/2012 22:04, John Fox wrote:
Dear Paul and Gabor,
The Rcmdr GUI uses the tcltk package, so I have some experience with
providing an R tcltk-based GUI for various platforms.
As Gabor
You are, of course, missing the obvious solution, which is to do nothing.
The "endorsement" of a non-free project seems to me to reside only in
your imagination. The primary product produced by "The R Project for
Statistical Computing" is the statistical software environment R, which
is relea
You can also see the odd behavior without wrapping round in another
function:
> round(100.1, digits=)
[1] 100
On 11/18/2011 10:19 AM, Joris Meys wrote:
On Fri, Nov 18, 2011 at 5:10 PM, Gavin Simpson wrote:
round is indicated to not evaluate its arguments. I don't follow the C
code well enoug
Hi Ben,
Just a few things to add.
First, the same phenomenon occurs when you use any character string as
the value of cex; there is nothing special about "*".
Second, you cannot get this phenomenon by trying to do something like
par(cex="*")
because the par function actually checks if the
You probably need the directive
importFrom(graphics, "plot")
in your NAMESPACE file. This lets the system know that you are using
the same "plot" function that it already knows about. And your code
should be careful not to trash a previous conversion of plot to an S4
generic function, usua
I have no idea what "aleph" is now or is likely to become.
If I follow your URL for the mailing list and click on the "archives"
link, it tells me that there are no posts and the archive is empty,
which makes it rather difficult to find out what aleph is (or why I
should care).
Perhaps there
There are plenty of good reasons for non-developers to run different
versions of R. For instance, I care a lot about reproducibility. With
every new release of R, lots of things change. With every new release
of the packages I use, lots of things change. All of my analyses are
performed usin
I think it would be even more useful if we could get Sweave to easily
produce PNG figures instead of just PDF/EPS. In the current state of
things, making PNG versions is more cumbersome than making PDF versions,
so I'm not surprised that most people don't go to that trouble most of
the time.
This is probably the same underlying bug, but it is not caused by
semicolons.
If you use keep,soure=TRUE with expand=FALSE and interpolate a code
chunk, the name of the chunkl is sent to the TeX file once for every
line in the chunk. Specifically, the source file:
%%%
\documentclass{
nreuters.com
http://labs.thomsonreuters.com
On 1/27/11 4:12 PM, "Prof Brian Ripley" wrote:
On Thu, 27 Jan 2011, Kevin R. Coombes wrote:
Hi,
I'm putting together an R package. In explaining how it works (in the
Rd
files), I want to refer to another package. The other packa
Hi,
I'm putting together an R package. In explaining how it works (in the
Rd files), I want to refer to another package. The other package is not
used anywhere in the actual code nor in the examples. So, there is no
reason to include the other package in the Depends, Suggests, or Imports
li
Hi,
I have a data frame that includes several names that (if typeset
correctly) require accented characters not available in the ASCII
character set.
I'd like to include this data frame as example data in an R package.
I'd also like the R CMD check warning about the use of non-ASCII
charac
Hi,
On my 64-bit machine, there are two subdirectories:
i386
x64
I usually want to use the 64-bit executable. However, some packages
have not yet been compiled for a 64-bit machine, so for those I need to
use the 32-bit i386 subdirectory.
Kevin
On 12/8/2010 10:32 AM, Gabor Groth
Hi Terry,
This may not really be a complete answer, but there seems to be a
difference in eval'ing an expression compared to eval'ing a call (even
though both are documented in the help page for eval as working just fine).
If you insert the line
print(eval(expression(zed), parent.frame())
The phrase that caught my attention in your post is the one about
"running package.skeleton() over and over". When I'm developing
packages, I never run it more than once. And I usually delete a lot of
the files it produces (since I like to organize my functions in logical
batches and not in
It seems to me that preserving information about the kind of number
(or not) present would be useful. I rather like the fact that
as.numeric(as.character(NaN))
and
as.numeric(as.character(Inf))
both work as the identity operator on numeric-like objects. (In this
context, note that both i
Hi,
I got the following comment from the reviewer of a paper (describing an
algorithm implemented in R) that I submitted to BMC Bioinformatics:
"Finally, which useful for exploratory work and some prototyping,
neither R nor S-Plus are appropriate environments for deploying user
applications
[1] I agree that sessionInfo() can be taken further.
[2] I even more strongly agree that it would be a bad idea to allow
packages to add features that cause the base sessionInfo() function to fail.
Why not add an extra function called something like
"packageSessionInfo()" that would provide th
fo() and file.exists() to
infer the rights. It is still not 100% but (hopefully) closer than
file.access().
/H
On Tue, Jul 21, 2009 at 1:55 PM, Kevin R.
Coombes wrote:
Hi,
The problem almost certainly has something to do with Samba. We also have a
NetApp file system, and copying the pack
incorrect indication? If that gives the correct answer, then, look
for changes in the file.access code.
-- Tony Plate
Kevin R. Coombes wrote:
Hi,
The problem almost certainly has something to do with Samba. We also
have a NetApp file system, and copying the package source to that
drive and
m is by trying
these calls on the directory in question from an interactive R session.
(They seem to work as intended on my Windows system with a NetApp file
system mounted on a letter drive.)
-- Tony Plate
Kevin R. Coombes wrote:
Hi,
I have just updated R from version 2.8.1 to version 2.9.1. I am
Hi,
I have just updated R from version 2.8.1 to version 2.9.1. I am running
Windows XP Professional, Service Pack 3.
With the update, I decided to update a set of packages that I maintain
by compiling them for the new version. Everything worked fine except
for one package. This package is
Also attributed (incorrectly) to both Yogi Berra and Mark Twain. The
Twain attribution leads (because he published numerous essays and short
stories in The Galaxy magazine) to one possible (and documentable) source:
"[I]f we found a character in a novel represented as habitually
uttering
Hi,
The following idea only partially answers your question
I have successfully written a GUI using the tcl/tk package that ships
with standard R. It is then possible (in Windows) to create a shortcut
icon that runs the following command:
C:\R\R-2.8.1\bin\R.exe --vanilla -e library(Sup
Prof Brian Ripley wrote:
On Wed, 4 Mar 2009, Terry Therneau wrote:
[SNIP]
2. In the pdf for the survival package, or at least the one generated
by R CMD check, the entries are in a random order. Can I fix this?
It makes reading the document to look for errors rather challenging.
(That is,
Hi Nicholas,
You raise a very good point. As an R user (who develops a couple of
packages for our own local use), I sometimes find myself cringing in
anticipation of a new R (or BioConductor) release. In my perception
(which is almost certainly exaggerated, but that's why I emphasize that
it
oaded. That would still only let you pick one but at
least you would know which one.
On Mon, Dec 15, 2008 at 11:43 AM, Duncan Murdoch wrote:
On 12/15/2008 10:58 AM, Kevin R. Coombes wrote:
I knew that (but forgot to include it in my statement of the question).
Thanks for pointing it out.
Is th
, Kevin R. Coombes wrote:
Hi,
Terry Therneau's question about package development reminded me of a
different issue. I maintain several packages along with a repository
for them at "http://bioinformatics.mdanderson.org/OOMPA/";. Several
people are working on adding features
Hi,
Terry Therneau's question about package development reminded me of a
different issue. I maintain several packages along with a repository for
them at "http://bioinformatics.mdanderson.org/OOMPA/";. Several people
are working on adding features or testing the packages. So, I often want
to
Hi Terry,
You can do this with Sweave (and something smart like emacs with ESS
installed as your editor), but you have to work at it a little. The key
is the fact that a couple of releases ago they added options for
"keep.source" and "expand". For example, you do the following:
First, descri
Hi,
I recently provoked some discussion over on the BioConductor developer
list about testing and R CMD check. In brief, the salient points that
arose from the discussion are:
[1] Because of the need for a nightly build of BioConductor, the tests
(in the ./tests directory) of a package that
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