nds a little hacky even for my taste ;).
Cheers,
Simon
On 1/05/2024, at 6:03 AM, Kevin R. Coombes wrote:
Hi,
I am working on a new package that primarily makes use of "igraph" representations of certain mathematical graphs, in
order to apply lots of the comp sci algorithms already implem
Hi,
I am working on a new package that primarily makes use of "igraph"
representations of certain mathematical graphs, in order to apply lots
of the comp sci algorithms already implemented in that package. For
display purposes, my "igraph" objects already include information that
defines
If it is the .git pack that is the problem, you can keep it out of the
tarball by creating a file in the main package directory (where
DESCRIPTION lives) called ",Rbuildignore". Put a line in that file that
reads
\.git/(.*)
That will keep anything in the .git folder from being included.
On
Produce a PDF file yourself, then use the "as.is" feature of the R.rsp
package.
Specifically, include this line in your DESCRIPTION file:
VignetteBuilder: R.rsp
Let's say the pdf file is called "myfile.pdf". Create a file called
"myfile.pdf.asis" that contains the vignette instructions. Put
1. Yes, remove the "lazyData" line from the DESCRIPTION file.
2. Do you have "stats" in the "Imports" line in the DESCRIPTION file? If
not, put it in along with the "importFrom" line in the NAMESPACE file.
On 3/31/2023 4:51 PM, Dennis Boos wrote:
Recently I got a message from CRAN that my
Disk space is unquestionably an issue for places like CRAN or
BioConductor that host all R packages. I would be surprised if it
matters to individual users of a single package in a world where a 4TB
external hard drive costs about $100 US.
On 1/23/2023 7:23 AM, Kern, Lori wrote:
I would also
Did you have to split the packages to get the CI/CD tools to work?
Because,to me, it looks as though I can install multiple different R
packages from the same git project, using something like
library(devtools)
install_gitlab("krcoombes/[PROJECT]", "pkg/[PACKAGE]")
Best,
Kevin
On 1/8/2023
ftover keybinding that uses the
underscore key to insert the left arrow. Apparently, I'm ancient myself.)
Kevin
On 1/8/2023 5:04 AM, Duncan Murdoch wrote:
On 07/01/2023 8:43 p.m., Kevin R. Coombes wrote:
Hi,
I am in the middle of developing a new package, which contains a
markdown-knitr-html vi
:10 -0500
"Kevin R. Coombes" wrote:
(1) How is it possible that the same code works error
free in the RStudio contexts, but fails in the attempt to build the
package?
When knitting the vignette from RStudio, it uses the package you
already have installed. When knitting the vignette
Hi,
I am in the middle of developing a new package, which contains a
markdown-knitr-html vignette. When I try to run
R CMD build [mypackagedirectory]
I get an error message
Quitting from lines 330-336
Error: processing vignette failed with diagnostics:
invalid z limits
If I run the same
Hi,
I am writing a package that Imports several other packages. One of my
imported packages eventually imports (through a chain of dependencies)
"lifecycle", and another eventually imports "rlang". Both "rlang" and
"lifecycle" define and export functions called "last_warnings". As a
result,
get
> flagged as misspelled words when I submit updates. I generally just
> put an explanation for each one in the "optional comment" section of
> the submission form. It's pretty simple and seems to work out well.
>
> On Fri, Jul 16, 2021 at 9:08 AM Kevin R. Coombes
> m
irement.
I would encourage you to pause for a day or two before sending off messages
like this in the future... a lesson I have learned the hard way myself.
On July 16, 2021 9:08:27 AM PDT, "Kevin R. Coombes"
wrote:
Hi,
I have been updating a couple of R packages this morning. One of th
Hi,
I have been updating a couple of R packages this morning. One of them
triggered a manual inspection for "possibly mis-spelled words in
DESCRIPTION" for my last name (Coombes) --- even though none of the
other 20 packages that I maintain has ever triggered that particular
NOTE. A second
# get ready
> ggplot(myData, aes_string(x = "myX", y = "myY")) +
> # add my decorations
> theme_bw()
> }
>
> It is probably already the case for your function but you need to
> include #' @import ggplot2 in
Hi,
I'm trying to help clean up an R package for someone else to submit to
CRAN. He has used ggplot2 to implement a plotting function for the kinds
of things that his packages generates. His plotting routine basically
looks like (after changing names to protect the innocent):
myPlot <-
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
sts if one of them sets a
method that you're using.
Duncan Murdoch
On 11/11/2020 3:31 p.m., Kevin R. Coombes wrote:
> Oh, I forgot to mention explicitly that checking (with --as-cran) on the
> development version of R on Windows also produces no errors or warnings.
u're using.
Duncan Murdoch
On 11/11/2020 3:31 p.m., Kevin R. Coombes wrote:
Oh, I forgot to mention explicitly that checking (with --as-cran) on the
development version of R on Windows also produces no errors or warnings.
On 11/11/2020 1:39 PM, Kevin R. Coombes wrote:
Hi Duncan,
I just sen
Oh, I forgot to mention explicitly that checking (with --as-cran) on the
development version of R on Windows also produces no errors or warnings.
On 11/11/2020 1:39 PM, Kevin R. Coombes wrote:
Hi Duncan,
I just sent a longer version of this message, but it looks to me like
the underlying
ain
later today if nobody else figures it out.
Duncan Murdoch
On 11/11/2020 12:03 p.m., Kevin R. Coombes wrote:
Hi Duncan,
Oops; I didn't realize I had forgotten to push updates to the OOMPA web
site.
The code for Mercator is contained as part of the Thresher project in
the subversion
? I can take a closer
look.
Best,
Uwe Ligges
On 11.11.2020 17:30, Duncan Murdoch wrote:
Uwe suggested you suggest flexmix, but I see below you already tried
that.
I'd like to take a look, but I can't find your package. The existing
version on CRAN gives the URL as http://oompa.r-for
it mentioned there.
Duncan Murdoch
On 11/11/2020 8:44 a.m., Kevin R. Coombes wrote:
Hi,
I am trying to figure out how to fix warnings from two of the CRAN
machines on the submission of an update to a package. The only change to
my package was to add a "show" method to one of the S4 clas
uation in the future.
Best,
Kevin
On 11/11/2020 11:14 AM, Uwe Ligges wrote:
You have to suggest flexmix.
Best,
Uwe Ligges
On 11.11.2020 14:44, Kevin R. Coombes wrote:
Hi,
I am trying to figure out how to fix warnings from two of the CRAN
machines on the submission of an update to a package. T
Hi,
I am trying to figure out how to fix warnings from two of the CRAN
machines on the submission of an update to a package. The only change to
my package was to add a "show" method to one of the S4 classes, which
was requested by a reviewer of the paper we submitted. The inability to
get
Hi,
I am developing a package and getting a NOTE from R CMD check about
licenses and ultimate dependencies on a restrictive license, which I
can't figure out how to fix.
My package imports flowCore, which has an Artistic-2.0 license.
But flowCore imports cytolib, which has a license from the
Hi,
I am in the process of submitting a "workflow" article about an R
package (which is onCRAN) to F1000Research. The associate editor that I
am dealing with wants a "DOI" for the source code of the package being
described in the manuscript. I have already explained that CRAN
archives all
Wait; I have options on how to configure conflict resolution? Can you
tell me where to read more about this feature?
Thanks,
Kevin
On 6/22/2020 10:51 PM, luke-tier...@uiowa.edu wrote:
On Tue, 23 Jun 2020, Bert Gunter wrote:
"Users don't get warned about overriding names in packages
For academics, aren't those citations the currency in which they are
supposed to be paid (at least for R packages)?
Kevin
On 6/2/2020 3:24 PM, Avraham Adler wrote:
On Tue, Jun 2, 2020 at 5:04 PM Spencer Graves <
spencer.gra...@effectivedefense.org> wrote:
QUESTION: How much money have
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
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
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
have run into a problem
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
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
On 1/29/2012 4:35 PM, Paul Johnson wrote:
On Sun, Jan 29, 2012 at 6:10 AM, Prof Brian Ripley
rip...@stats.ox.ac.uk 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
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 Simpsongavin.simp...@ucl.ac.uk wrote:
round is indicated to not evaluate its arguments. I don't
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 released
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, usually
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 is
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
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:
%%%
, Prof Brian Ripleyrip...@stats.ox.ac.uk 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 package is not
used
anywhere in the actual code nor in the examples
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
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
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
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),
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
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 the
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
running Windows XP Professional, Service Pack 3.
With the update, I decided to update a set of packages that I
maintain by compiling them
an
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
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
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
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
, 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 or testing the packages
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 there any way to convince the selection box (or its developers) to
include the version information that is already available?
The selection box is adamant
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, describe
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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