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

Robert Castelo robert.castelo at upf.edu
Tue Dec 19 09:31:13 CET 2017


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:


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

commit 4c9af13619f8b16955682072da316a0a961a5623
Author: Hervé Pagès <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 

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?



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