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 l
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 break
> 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 rele
ssues/108
> >>>> Just to be clear, as noted at the end of the 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
should, during the
>>>> mid-April to mid-October release 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
&
vel, and BoicManager
> >> supports this, too. There are 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 B
gt;> or when conscientiously testing CRAN packages that depend
>> 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
>> mismatche
ise from R / 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
>
f Wolfgang 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., addin
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 BiocMananger:
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 questio
For off-piste use I would have consulted `setRepositories(graphics = FALSE)`
and then
```
## use Sys.setenv() before setRepositories
Sys.setenv(R_BIOC_VERSION="3.18")
setRepositories(ind = 1:4) # CRAN plus Bioc soft, anno, and expt repos
getOption("repos")# check
install.packages("BiocGeneric
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 <- i
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
> i
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.
T
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