filtered to contain just
the most recent version of each. Does it matter then what order the
repositories are visited?
Martin Morgan
From: R-package-devel on behalf of Greg
Hunt
Date: Sunday, March 31, 2024 at 7:35 AM
To: Dirk Eddelbuettel
Cc: List r-package-devel
Subject: Re: [R-pkg-devel] Order
nd an exploratory
https://github.com/Bioconductor/bioc2u; I don't know the status of that project.
At some point the scale tips from installing packages from standard
repositories to using a local clone
https://bioconductor.org/about/mirrors/mirror-how-to/.
Martin Morgan
From: R-package
CRAN knows about Bioconductor packages, so add phyloseq to Depends: , Imports:,
or Suggests: as appropriate.
These CRAN packages seem to Import phyloseq, for instance
> db = available.packages(repos = "https://cloud.R-project.org";)
> rownames(db)[grepl("phyloseq", db[,"Imports"])]
[1] "adaptive
CRAN is fine with Bioconductor Depends: and Imports: dependencies, as
previously mentioned. This is because the CRAN maintainers explicitly configure
their system to know about Bioconductor package repositories.
Users face a different challenge -- many users will not have identified (e.g.,
via
I would not follow the instructions in RTIGER�s README for installing
Bioconductor packages.
BiocManager::install(�RTIGER�) would install both CRAN and Bioconductor
dependencies of RTIGER, and would be my preferred instruction in a README or
INSTALL file. A complete instruction might be to inst
I�m not particularly experienced with this but wrote a �proof-of-concept�
skeleton of a package at https://github.com/mtmorgan/ocl . The basics are
* Import OpenCL in the DESCRIPTION file
* Write OpenCL scripts in inst/ (dnorm implemented in OpenCL)
* Use the helper function in R/ocl
nductor community. Anyway, I've been learning a
lot from this discussion. Thanks all!!
Best,
Tiago
Em sex., 3 de set. de 2021 às 12:58, Martin Morgan
<mailto:mtmorgan.b...@gmail.com> escreveu:
The specific repository you've chosen is not what you want to do. This will
always insta
0-Bioconductor repository. That's a lot to tell your users...
Maybe others in the R community have a better way (the key information is in
tools:::.BioC_version_associated_with_R_version(), but that is not an exported
function so not recommended for CRAN packages...)
Martin Morgan
On 9/1/21
ld still have a value section, I think...
627 stats-defunct.Rd stats-defunct arima0.diag FALSE
I guess it makes sense for defunct functions not to be fully documented,
though maybe it would be helpful for those trying to migrate their code...
Martin Morgan
On 6/23/21,
Bioconductor build system – the lagging package Is
usually promptly updated so the published dependency is satisfied.
From: Henrik Bengtsson
Date: Tuesday, May 18, 2021 at 2:41 PM
To: Martin Morgan
Cc: "Dalgleish, James (NIH/NCI) [F]" ,
"r-package-devel@r-project.org"
Subje
indows-ix86+x86_64 builder mentioned in the post has the wrong
version of rtracklayer for R-devel.
Martin Morgan
On 5/18/21, 11:49 AM, "R-package-devel on behalf of Henrik Bengtsson"
wrote:
It's a problem with Bioconductor and a broken release history of
'rtracklay
igh likelihood that it will be fixed,
so either be patient or ask the rtracklayer maintainer directly to address this
by, e.g., opening an issue at https://github.com/lawremi/rtracklayer
Martin Morgan
On 4/7/21, 6:32 AM, "R-package-devel on behalf of Gordon Brown"
wrote:
Hi,
From the Bioconductor 'devel' (3.13, used with R-devel) 'landing page' for
rtracklayer
https://bioconductor.org/packages/devel/rtracklayer
The 'build' badge is red; clicking on it shows a build system problem with
rtracklayer on Windows. Scrolling on the landing page to the bottom shows
Source
so I don't know what I'm looking for...
Martin Morgan
On 11/11/20, 4:44 PM, "R-package-devel on behalf of Duncan Murdoch"
wrote:
Here's what I think is happening.
In the movMF:::.onLoad function there's a test whether flexmix is
installed. If found,
nodes produced errors; first error: could not find function "foo"
Do you really need to use `:::`?
Martin Morgan
On 9/13/20, 3:52 PM, "R-package-devel on behalf of David Kepplinger"
wrote:
Dear list members,
I submitted an update for my package and got automatically
Here is the build report for KEGGgraph
http://bioconductor.org/packages/release/bioc/html/KEGGgraph.html
where it builds, and is available, across all platforms. This does not seem to
be a Bioconductor problem, but rather a CRAN configuration issue.
Martin Morgan
Bioconductor
On 9/1/20, 12
it is necessary to obey licensing terms of the prior work, and
important to acknowledge, above and beyond the specific licensing terms, the
contributions individuals make.
Martin Morgan
On 6/2/20, 5:57 AM, "R-package-devel on behalf of Adelchi Azzalini"
wrote:
The point in qu
This is the same as
https://stat.ethz.ch/pipermail/r-package-devel/2020q1/005256.html
and due I believe to stale packages on the CRAN windows builder; the solution
is I believe on the CRAN side.
Martin Morgan
On 4/7/20, 6:14 PM, "R-package-devel on behalf of Ryan Sartor&quo
::valid()
returns TRUE and / or update all packages to the most recent available
BiocManager::install(ask = FALSE)
I'm not sure about CRAN, but am confident that it will eventually clear itself
up... (not much comfort, I know...)
Martin Morgan
On 3/31/20, 11:42 AM, "R-package-devel on
so apparently there is a generics package that defines 'fit'... if you're
playing in the tidyverse then it seems like you should @importFrom generics fit
and @export fit.
Martin Morgan
On 3/11/20, 1:50 PM, "R-package-devel on behalf of Henrik Bengtsson"
wro
dge cases (like long
path names or movement across volumes?) better.
Martin Morgan
On 2/11/20, 9:31 AM, "R-package-devel on behalf of Gábor Csárdi"
wrote:
It is actually rather complicated, because .Rbuildignore can have
regular expressions, that refer to files or directori
builder, and
the reason why you are not able to reproduce it.
Martin Morgan
On 1/31/20, 9:04 AM, "R-package-devel on behalf of Dirk Eddelbuettel"
wrote:
On 31 January 2020 at 09:11, Borini, Stefano wrote:
| Thanks. What is the recommended strategy in this case? Keep
what are the correct paths?
On 1/27/20, 3:32 PM, "R-package-devel on behalf of Uwe Ligges"
wrote:
Thanks, one suspicious part from the log below is
-LC:/extsoft/lib/i386
which is clearly not in any variable we define on CRAN.
Looking close shows that
> Rhtsl
RShowDoc("R-exts") setion 1.5.1 Specifying imports and exports indicates that
imports() has an except= argument, so
import(adegenet, except = plot)
might do the trick. Use it in your package as `adegenet::plot()`.
Martin Morgan
On 11/6/19, 8:31 PM, "R-package-devel on b
aking the
time to offer your help, and am really grateful for your suggestions.
Sincerely,
Divyansh
On 9/23/19, 7:44 AM, "Martin Morgan" wrote:
Probably the easiest 'solution' is to remove the version dependencies,
e.g., 'org.Hs.eg.db, org
e the version of the package BiocVersion (it should be 3.10.1 in
R-devel) is incorrect.
Martin Morgan
Bioconductor
On 9/23/19, 6:06 AM, "R-package-devel on behalf of Agarwal, Divyansh"
wrote:
Dear R developers community,
I’m trying to build and submit an R packag
r two use cases are below, specifically the
unique circumstances of 'in tests only'. I would guess that a relative path
would not work, in general, because the path would be relative to the current
working directory, which of course changes, rather than relative to the path of
the shared
Since ncdf4 (and emld) both use S3 class systems, it is sufficient to simply
declare
setOldClass("ncdf4")
some time prior to using setAs() .
Martin
On 5/24/19, 6:41 PM, "R-package-devel on behalf of Emmanuel Blondel (GMAIL)"
wrote:
Dear all, I write here as i'm in process to submit
message() / warning() / stop() write to stderr whereas print() / cat() write
(by default) to stdout. Even without being able to suppress messages, it is
well-established practice (the story is that this is the reason why 'stderr'
was introduced into unix,
https://www.jstorimer.com/blogs/working
R-3.5.* -- CRAN apparently uses 3.5.* package binaries (for both CRAN
& Bioconductor) in R-devel.
Martin Morgan
On 3/6/19, 10:00 AM, "R-package-devel on behalf of Yonghui Dong"
wrote:
Dear all,
I remember somebody has asked a similar question days ago, but the probl
Bioconductor 3.8 is the current release version of Bioconductor, and should be
used by CRAN for current release versions of R. This seems perhaps like a stale
installation on the Windows machine.
A link to the actual check report would be helpful.
Martin
On 2/27/19, 9:25 AM, "R-package-devel
load BiocInstaller should simply fail.
Martin Morgan
On 2/20/19, 2:06 AM, "R-package-devel on behalf of dhamma pal"
wrote:
Hi.
Following is the check results from CRAN server, though I didn't get any
warning on my PC.
package maGUI_2.3.tar.gz does not pa
e translated into other languages so pattern matching is not
robust. In one's own code one could signal and handle specific classes of
objects
withCallingHandlers({
cond <- simpleWarning("foo")
class(cond) <- c("my_warning", class(cond))
warning(cond)
which is actually a fun test of one's understanding of R's assignment and
symbol look-up rules.
Martin Morgan
On 1/29/19, 4:50 PM, "R-package-devel on behalf of Gábor Csárdi"
wrote:
You don't need .onLoad for this, just put the environment into
Did you mention where your package source can be downloaded from, e.g., github?
Because obviously it is then much easier for people to help.
Martin Morgan
On 1/20/19, 12:55 PM, "R-package-devel on behalf of Troels Ring"
wrote:
Thank you so much - I used the search in files f
Add a tag to the DESCRIPTION file or configure.ac-like indicating the git
(presumably) revision, perhaps like https://stackoverflow.com/a/11535358/547331
?
On 1/4/19, 1:42 PM, "R-package-devel on behalf of Dirk Eddelbuettel"
wrote:
On 4 January 2019 at 19:24, Iñaki Ucar wrote:
|
I cannot tell whether this will be helpful or not. It looks to me like the
warning occurs when one of your dependencies uses BiocInstaller. You could
create a database of all available packages
chooseCRANmirror()
chooseBioCmirror()
db = available.packages()
find the installation dependenc
assign("dS",dS,envir=environment(cev))
so that assignment is to the unlocked new.env(). Presumably the new code
assigns to bar's original environment, which is the (locked, once the
package is loaded) package name space.
Martin Morgan
Or maybe not.
Duncan Murdoch
Can anyon
kage(s) not present in Imports: or Depends: of DESCRIPTION :
'methods'
... ?
Martin Morgan
Duncan Murdoch
but without the importFrom, you see a number of NOTE's
no visible global function definition for 'hasArg'
I don'
On 04/16/2018 12:31 PM, Duncan Murdoch wrote:
On 16/04/2018 12:06 PM, Martin Maechler wrote:
Duncan Murdoch
on Mon, 16 Apr 2018 11:52:10 -0400 writes:
> On 16/04/2018 11:35 AM, Ramon Diaz-Uriarte wrote:
>> Dear All,
>>
>> Two recent threads in the bioconductor devel
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