Dear Klaus
Good points. I am not trying to “poach” anything here, and guess you have
discussed this, but with this number of reverse dependencies, it sounds like
the maintainers, contributors and users of ape and phangorn could benefit from
putting the packages on Bioconductor?
>From a quick
Hi all,
no real contribution to this discussion, just some appreciation to all your
hard work.
I just wish CRAN had something like a proper release cycle for packages. I
contribute to two packages phangorn and ape, which have a decent number of
reverse dependencies. So you can't introduce any
> Il giorno 12.05.2023, alle ore 04:43, Kasper Daniel Hansen
> ha scritto:
>
> It seems totally sensible to be able to use BiocManager to install either
> bioc-release or bioc-devel at any time, provided you're running R-devel.
> First, by definition, R-devel is always >= the R used for
e second issue
> >>>> and on the web page you mention, a Bioconductor package
> >>>> developer wishing to use 'Bioc-devel' should, during the
> >>>> mid-April to mid-October release cycle, be using the
> >>>> **release** version of R. This comb
cycle, be using the
>>>> **release** version of R. This combination of R and
>>>> Bioconductor is supported by BiocManager. Similarly, in
>>>> the mid-October to mid-April release cycle, the
>>>> Bioconductor developer should be R-devel, and BoicManager
&
scenarios where a
> >> developer might wish to combine R-devel and Bioc-devel in
> >> the mid-May, to mid-October time frame, e.g., when
> >> developing a CRAN package with Bioconductor dependencies,
> >> or when conscientiously testing
>> on Bioconductor packages. One may also just want to be on
>> the bleeding edge, so using R-devel and living with any
>> consequence that arise from R / Bioconductor version
>> mismatches. Are these less-common scenarios the one that
>> you
/ Bioconductor version mismatches. Are these less-common
> scenarios the one that you are engaged in?
> Martin
> From: Bioc-devel on behalf of Wolfgang
> Huber
> Date: Saturday, May 6, 2023 at 9:43 AM
> To: Vincent Carey
> Cc: bioc-devel@r-project.org
> Subject: R
Huber
Date: Saturday, May 6, 2023 at 9:43 AM
To: Vincent Carey
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocManager::install
Dear Martin and Vince
thank you, very insightful points. Indeed I think it’s primarily a matter of
documentation and priming, and, e.g., adding Martin's
Dear Martin and Vince
thank you, very insightful points. Indeed I think it’s primarily a matter of
documentation and priming, and, e.g., adding Martin's lines prominently enough
e.g. to https://contributions.bioconductor.org/use-devel.html and a reference
to it into the manpage of
Thanks for these observations Wolfgang, I am glad I read to the end,
because as you say,
https://solutions.posit.co/envs-pkgs/bioconductor/
has lots of interesting information. As I personally have no
experience with renv or Connect
much of the motivating detail is opaque to me.
I would
in
From: Bioc-devel on behalf of Wolfgang Huber
Date: Saturday, May 6, 2023 at 4:40 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] BiocManager::install
Hi,
I am wondering whether:
1. it could be easier to install Bioconductor packages (devel or release) on
R-devel (or other non-stan
Hi,
I am wondering whether:
1. it could be easier to install Bioconductor packages (devel or release) on
R-devel (or other non-standard R versions) using BiocManager::install (I may be
stirring a hornet’s nest with that:)
2. whether its documentation needs to be updated and/or its
Hi Matej,
Usually when I find this kind of message it indicates that the package
is installed in different libraries and you are updating in just one
library.
Have you checked that it is installed in multiple libraries? I usually
use something similar to this to identify those packages:
ip1 <-
Dear all,
I encountered strange behavior of BiocManager::install(). When I ask it
to install a package that is flagged as one with available updates, it
gives me the option to upgrade immediately after I install the latest
version. Not a big deal but thought it should not offer that
If it were me I might update version
BiocManager::install(version="3.10")
...
Update xxx packages [y/n]: n
Confirm I've got the right version
BiocManager::version()
and then recover the URLs
BiocManager::repositories()
as arguments to install.packages(). It doesn't make sense to ask for
On Thu, Oct 31, 2019 at 11:52 AM James W. MacDonald wrote:
>
> The main goal for BiocManager is to help end users ensure that their R/BioC
> installation is consistent for the version of R that they are using. So by
> definition, any packages that are outside the versions for a given R/BioC
>
The main goal for BiocManager is to help end users ensure that their R/BioC
installation is consistent for the version of R that they are using. So by
definition, any packages that are outside the versions for a given R/BioC
installation should be up or down-graded to make the installation valid.
(posting this here since I think it's not a support question per se)
Hi, I just started an upgrade from Bioc 3.9 to 3.10 on my local R 3.6.1 setup:
> BiocManager::install(version = "3.10")
Upgrade 73 packages to Bioconductor version '3.10'? [y/n]: y
Bioconductor version 3.10 (BiocManager
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