[Bioc-devel] fixing 'path' not being exported by 'Rsamtools'

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 for the inconvenience,

H.


On 12/19/2017 12:31 AM, Robert Castelo wrote:

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:

https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioconductor.org_checkResults_3.7_bioc-2DLATEST_VariantFiltering_malbec2-2Dbuildsrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=CGWaZ89uHETvNkQs0YnvQvKoYsuiD20EQ4nrbi0q3WU&s=4YrMshnMnZYQexNOs5qmPLZ-7avBU6Ak3aFJxWxV-fI&e= 


it seems this is related to the following recent change in Rsamtools:


commit 4c9af13619f8b16955682072da316a0a961a5623
Author: Herv? Pag?s <hpages at fredhutch.org>
Date:   Fri Dec 15 10:07:38 2017 -0800

     use new path() generic defined in BiocGenerics instead of own


by which, if i understand this correctly, Rsamtools does not export 
the 'path()' method anymore and from now on it should be imported from 
BiocGenerics.

i've made the change in VariantFiltering of removing the import of the 
'path()' method and i'm importing the whole 'BiocGenerics' but i still 
get the error:

Error : object ?path? is not exported by 'namespace:Rsamtools'

when i try to build the package with the vignettes or if i build it 
without them but i try to install it. i thought that maybe because 
'Gviz' has the same problem and VariantFiltering imports 'Gviz', the 
problem could be now with 'Gviz' but i do not see anywhere that 'Gviz' 
imports 'path()' from Rsamtools.

i'm a bit lost, can i fix this somehow or does this depend on fixing 
something more upstream?

thanks!

robert.