All versions of Bioconductor are closely associated to a version of R to
ensure proper testing. We do not currently test packages outside the
current release and devel versions of Bioconductor. The current
Bioconductor release will always run on the current version of R. The
current Bioconductor
So the version of R depended on determines the version of Bioconductor that
the BBS will use when testing the package?
On Tue, 23 Apr 2024 at 04:41, Anatoly Sorokin wrote:
> Hi,
> You can even set 3.5 if your code working with that version of R, but
> BiocManager won't load the latest Biocondu
Hi,
You can even set 3.5 if your code working with that version of R, but
BiocManager won't load the latest Bioconductor version (3.19) unless you
have R 4.4.
Cheers,
Anatoly
On Tue, Apr 23, 2024 at 2:57 AM Richard Heery
wrote:
> Hi all,
>
> I'm wondering what we should now list as the R versio
If you're submitting a new package, you might be asked to set this to R
(>= 4.4). At least it used to be that way but I'm not sure this is still
enforced.
Otherwise you don't need to do anything.
Best,
H.
On 4/22/24 10:56, Richard Heery wrote:
> Hi all,
>
> I'm wondering what we should now li
Hi all,
I'm wondering what we should now list as the R version in the Depends
section of the description file: the current version 4.3.3 or the
development version 4.4?
Cheers,
Richard
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___
Bioc-devel@r-pro
& Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel on behalf of Alexey
Sergushichev
Sent: Tuesday, February 20, 2018 4:26:35 AM
To: Vincent Carey
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] R version check in BiocChech
&
> It _is_ the developer's choice. But a developer of packages for the
Bioconductor
> project commits to using R-devel during certain pre-release phases,
depending
> on proximity in time to a point release of R. (See
http://bioconductor.org/developers/how-to/useDevel/)
> for full details.) BiocCh
On Mon, Feb 19, 2018 at 11:27 AM, Alexey Sergushichev
wrote:
> Kevin,
>
> > It does not request users to make R-devel a _requirement_ of their
> package.
>
> Sadly it does for new packages. New packages submitted to Bioconductor 3.7
> are _required_ to have R >= 3.5 dependency, otherwist BiocChec
> > Personally, I haven't found it to be particularly difficult to update R,
> > or to run R-devel in parallel with R 3.4, even without root privileges.
>
> I find it much harder for a normal user to install R-devel (and update
> it properly, because it's a development version) and running
> '
Kevin,
> It does not request users to make R-devel a _requirement_ of their
package.
Sadly it does for new packages. New packages submitted to Bioconductor 3.7
are _required_ to have R >= 3.5 dependency, otherwist BiocCheck will result
in a warning (
https://github.com/Bioconductor/BiocCheck/blob
I'll just throw in my two cents here.
I think many people underappreciate the benefits of moving to the latest
version of R. If you inspect the R-devel NEWS file, there's a couple of
nice fixes/features that a developer might want to take advantage of:
- sum() doesn't give NAs upon integer over
Hi Alexey,
I do agree with you that there is no harm in testing against other version
of R. In a way, that is even good practice, considering that many HPC users
do not always have access to the latest version of R, and that Travis is
making this fairly easy.
Now, with regard to your latest reply
Hello Kevin,
Well, bioc-devel packages are tested against bioc-devel (and R-3.5) in any
case. What I'm saying is that aside from testing the package against
bioc-devel, I can as well test against bioc-release too on my own. If the
package doesn't work with bioc-devel it shouldn't pass bioc-devel c
Dear Alexey,
The reason is somewhat implicitly given at
https://www.bioconductor.org/developers/how-to/useDevel/ :
"Package authors should develop against the version of *R* that will be
available to users when the *Bioconductor* devel branch becomes the
*Bioconductor* release branch."
In other w
Dear Bioconducotr community,
I wonder, what is the reason behind requirement for dependency R >= 3.5
(currently) for new packages?
As a developer I really want an installation of my package to be as easy as
possible and want my package to be easily installed from github. So
currently, when I deve
Hello,
may I ask a question about the R version dependence?
Currently I am trying to submit a package to Bioconductor repository. When
my package was built at bioconductor.org, I got a warning message
"* WARNING: Update R version dependency from 2.3.0 to 3.4."
So I changed the R dependency to 3
Hi Martin,
Great, many thanks for your support and advice. The bug is now fixed for
all the reporters. The solution was simple - I removed both:
#include
using namespace Rcpp;
from the cpp file and then used Rcpp:: everywhere I needed an Rcpp
function. So that the header at the end looked like
On 01/05/2017 11:10 AM, Vladimir Kiselev wrote:
Dear Martin,
Many thanks for your reply, it was really helpful. My collaborator ran
the commands you suggested and got the following output:
*
$ Rscript norm_laplacian.R
/home/jake/miniconda3/lib/R/bin/R CMD SHLIB -o 'sourceCpp_2.so'
'norm_la
Dear Martin,
Many thanks for your reply, it was really helpful. My collaborator ran the
commands you suggested and got the following output:
*
$ Rscript norm_laplacian.R
/home/jake/miniconda3/lib/R/bin/R CMD SHLIB -o 'sourceCpp_2.so'
'norm_laplacian.cpp'
g++ -I/home/jake/miniconda3/lib/R/inc
On 01/05/2017 06:41 AM, Vladimir Kiselev wrote:
My package (SC3 - http://bioconductor.org/packages/3.4/bioc/html/SC3.html)
has a function that causes R version/platform-dependent seqfault. Here is
the function (it's in C++ using RccpArmadillo):
arma::mat norm_laplacian(arma::mat A) {
A = exp
My package (SC3 - http://bioconductor.org/packages/3.4/bioc/html/SC3.html)
has a function that causes R version/platform-dependent seqfault. Here is
the function (it's in C++ using RccpArmadillo):
arma::mat norm_laplacian(arma::mat A) {
A = exp(-A/A.max());
arma::rowvec D_row = pow(sum(A),
On 09/15/2013 07:12 AM, Wolfgang Huber wrote:
Dear Julian
thanks.
Since this has come up here and elsewhere, and since the next Bioc release is coming up,
let's remind ourselves that we should make development against 3.0.1 Patched (2013-09-03
r63824) -- "Good Sport".
Martin - should this be
Dear Julian
thanks.
Since this has come up here and elsewhere, and since the next Bioc release is
coming up, let's remind ourselves that we should make development against 3.0.1
Patched (2013-09-03 r63824) -- "Good Sport".
Martin - should this be noted on
http://www.bioconductor.org/developers
On Tue, May 21, 2013 at 1:01 PM, Dan Tenenbaum wrote:
> Hi Steffen,
>
>
>
> On Tue, May 21, 2013 at 12:40 PM, Steffen Neumann
> wrote:
>> Hi,
>>
>> On Tue, 2013-05-21 at 11:47 -0400, James W. MacDonald wrote:
>>> Not that I can recall. But I do agree that it is at minimum redundant
>>> and proba
Hi Steffen,
On Tue, May 21, 2013 at 12:40 PM, Steffen Neumann wrote:
> Hi,
>
> On Tue, 2013-05-21 at 11:47 -0400, James W. MacDonald wrote:
>> Not that I can recall. But I do agree that it is at minimum redundant
>> and probably just wrong to have R-version requirements for BioC packages.
>
> I
Hi,
On Tue, 2013-05-21 at 11:47 -0400, James W. MacDonald wrote:
> Not that I can recall. But I do agree that it is at minimum redundant
> and probably just wrong to have R-version requirements for BioC packages.
I'd like to disagree. BioC *promises* that stuff works together
at a certain point
Not that I can recall. But I do agree that it is at minimum redundant
and probably just wrong to have R-version requirements for BioC packages.
And seriously? 500 packages? I find that surprising.
Best,
Jim
On 5/21/2013 11:38 AM, Martin Morgan wrote:
Pulling this over to Bioc-devel. It's temp
Pulling this over to Bioc-devel. It's tempting to strip this from the
DESCRIPTION files of the ~500 packages that include it. It's not useful in the
context of the Bioconductor release schedule, and makes a forward promise that
cannot be guaranteed.
Is this something that has come up before?
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