Hi Robert,
I don't really have a simple automatic way to find what package
upstream needs to have fixed its NAMESPACE.
In this kind of situation I generally start by extracting the
list of software packages that don't install because of a particular
NAMESPACE problem. I do this by combining some
hi Hervé, thanks for figuring out where the change was missing and
fixing VariantFiltering.
out of curiosity, did you find out that the change was required on
ensembldb by examining one by one the upstream dependencies or is there
some automatic way to know what package upstream needs to have
Thanks Herve
I did also fix it in ensembldb but didn't push to Bioc yet - well, have to pull
your changes now instead :)
cheers, jo
> On 20 Dec 2017, at 04:08, Hervé Pagès wrote:
>
> Hi Robert,
>
> Gviz depends on ensembldb which needed to have its NAMESPACE adjusted
> (i.e. import the path(
Hi Robert,
Gviz depends on ensembldb which needed to have its NAMESPACE adjusted
(i.e. import the path() generic from BiocGenerics instead of
Rsamtools). I fixed ensembldb today. I also adjusted VariantFiltering
NAMESPACE (in version 1.15.18) so now you should be able to install
it again.
Sorry
hi,
multiple packages, among them, Gviz or VariantFiltering, currently break
in the build machines with the following error:
Error : object ‘path’ is not exported by 'namespace:Rsamtools'
see, for instance:
http://www.bioconductor.org/checkResults/3.7/bioc-LATEST/VariantFiltering/malbec2-bui
