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

Hervé Pagès hpages at fredhutch.org
Wed Dec 20 04:08:22 CET 2017

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,


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: 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 
> 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.
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=CGWaZ89uHETvNkQs0YnvQvKoYsuiD20EQ4nrbi0q3WU&s=Y3pZx8EBYDKKcn25cGQf0HdhPOix04Jf0AbF_8L-_qg&e=

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
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