going to have a significantly longer stable lifetime than the NCBI URL.
So, for now at least, I think I will leave them both.
Best,
Kevin
On 4/7/2025 11:35 AM, Ivan Krylov wrote:
В Mon, 7 Apr 2025 11:10:21 -0400
"Kevin R. Coombes" пишет:
But version R 4.5.0 RC comes back with;
Hi,
I am systematically going through the packages that I maintain on CRAN
to clean up some administrative details. Specifically, I am (1) changing
all DESCRIPTION files to use Authirs@R, (2) updating the links in man
files to include package anchors, and (3) making sure that the output of
ca
If it is *only *in sysdata.Rda, then it is accessible to your package
code but is not available to users. (They can't, for example, use the
"data" function to load it themselves.) So, there is no reason to
document it. Just like there is no reason to document functions in your
R scripts that we
Thanks for the quick (detailed) response.
On 1/31/2025 12:23 PM, Martin Maechler wrote:
Kevin R Coombes
on Fri, 31 Jan 2025 11:48:33 -0500 writes:
> Hi,
> I have a package that has been in CRAN for years and is now failing
> checks because some of the output
Hi,h
I have a package that has been in CRAN for years and is now failing
checks because some of the output of a test script is differing on some
machines in the fifth or sixth decimal place. I have managed to fix most
of these issues (by using the "digits" argument in calls to "summary" to
hid
Hi,
I currently have a package on CRAN called "plasma" (which is an acronym
for an algorithm). Reviewers of the paper submitted to describe this
package/algorithm have requested that the name be changed to PLASMA to
make sure that users don't somehow think we are talking about the
similarly n
Hi,
This is a follow-up to an earlier question where I asked about R CMD
check on Windows to be able to check R packages in a manner closer to
the checks on CRAN machines before i submit (new or updated) packages.
From the answers to the previous question, I learned the (magic)
environment v
Thank you!
On 8/17/2024 9:24 AM, Ivan Krylov wrote:
В Sat, 17 Aug 2024 09:17:40 -0400
Ben Bolker пишет:
does there exist/has someone compiled a list of
the environment variables that determine R CMD check's behaviour?
https://cran.r-project.org/doc/manuals/R-ints.html#Tools
But the _R_CHECK
Hi,
I maintain a bunch of packages on CRAN. When updating packages, I often
find two sort of NOTES on some of the platforms that CRAN checks that
don't show up on my stupid Windows (I know that's redundant; you don't
have to tell me) machine at home. The two most common issues are
* spelling
Hi,
I seem to have gotten myself confused about inheritance of S4 classes
and the dispatch of inherited methods.
The core situation is that
* The graphics package already defines the function "hist"
* My package A creates an S4 generic "hist", using the existing
function as the default
Hi,
I have been maintaining packages in R-Forge for many tears. Last week I
sent an email to r-fo...@r-project.org to report problems with the build
process. It appears that any changes I have pushed to R-Forge over
approximately the last two months have resulted in the package remaining
in t
by calling the generic from
Rgraphviz, but that sounds 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
o
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 node
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 i
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 pac
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 1
a leftover 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-kni
20:43:10 -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 vign
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 ma
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,
that commonly 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 Kevi
e past lead to this requirement.
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 pa
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 pack
myPlot <- function(myData, ...) {
> # 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 ne
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 <- fucnt
s that you don't even use, so you
shouldn't have to change your dependency lists 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
ts 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.
On 11/11/2020 1:39 PM, Ke
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
ugging that. I'll try again
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 Thr
mix, so likely something S4 related? 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 o
but I can't see 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" met
ind of situation 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
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 this
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 ver
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 they've
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 peo
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