On Wed, Mar 27, 2019 at 9:05 AM Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:
> On Wed, Mar 27, 2019 at 1:06 AM Aaron Lun <
> infinite.monkeys.with.keyboa...@gmail.com> wrote:
>
> > > well, we can't fix this in old branches of Bioc.
> >
> > Sure, but one could say that about
On Wed, Mar 27, 2019 at 1:06 AM Aaron Lun <
infinite.monkeys.with.keyboa...@gmail.com> wrote:
> > well, we can't fix this in old branches of Bioc.
>
> Sure, but one could say that about breaking changes to any CRAN package.
> Nothing particularly special about BH on that point.
>
Indeed, and
well, we can't fix this in old branches of Bioc.
Sure, but one could say that about breaking changes to any CRAN package.
Nothing particularly special about BH on that point.
My POV is that we need to consider - in some sense - lock down CRAN with
a Bioc release.
That's probably worth
My 2 cents - API-breaking changes to BH are no more of an issue than
breaking changes to any other CRAN package. We just hope that it doesn't
happen too often and we deal with it when the time comes; that's the
whole point of getting frequent release builds to check for these cases.
If we
I am out of date on this, but when I looked into it last time (years ago)
BH only included headers and it used to be that the graph part of boost
went beyond headers only. If it's headers-only perhaps the danger is
reduced.
On Mon, Mar 25, 2019 at 11:39 AM Vincent Carey
wrote:
>
>
> On Mon, Mar
On Mon, Mar 25, 2019 at 10:57 AM Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:
> There are no issues with depending on CRAN packages.
>
> But I would advise caution. On one hand it is great that boost gets
> updated regularly. On the other hand, it could lead to incompatibilities
>
There are no issues with depending on CRAN packages.
But I would advise caution. On one hand it is great that boost gets updated
regularly. On the other hand, it could lead to incompatibilities with RBGL
and then you have to update that package rapidly. Also - and this is
something we could
...also Bioconductor knows all about CRAN -- see the repositories returned by
> BiocManager::repositories()
BioCsoft
"https://bioconductor.org/packages/3.9/bioc;
BioCann
Could be an issue with the configure script. Will check.
- Sam
On 3/25/19 7:32 AM, Vincent Carey wrote:
>
> External Email - Use Caution
>
> The error on linux for 3.9:
>
> ##
>
I think the usual incantation in configure files is ${R_HOME}/bin/R ... R_HOME
is the path to R set by the command that starts to build or install the
package, whereas Rscript is found on the search path.
Martin
On 3/25/19, 7:33 AM, "Bioc-devel on behalf of Vincent Carey"
wrote:
The
The error on linux for 3.9:
##
##
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RBGL
###
Dear Bioconductor,
The devel version of package RBGL is flunking build.
This package has been modified to include header files in the CRAN
package 'BH' instead of using a local tarball of the header files. We
consider this an improvement because the 'BH' maintainers update their
package
12 matches
Mail list logo
