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 Jianhong,
I didn't touch the "path" method defined in Rsamtools, only moved
the path() generic from Rsamtools to BiocGenerics. This broke a few
NAMESPACE in other packages that Marcel and I are in the process of
fixing. The build report should already look much better tomorrow
(Wed 20) and mos
Hi,
Could you inform me which modification you did in biomaRt ? or in ENSEMBL ?
Indeed, I have my R package (coMET) use biomaRt to access to data. From the
last update in BiomaRt (12/14/2017), I have a new error message.
Do you change the name of database associated with ENSEMBL ?
This is m
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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
