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

Rainer Johannes Johannes.Rainer at eurac.edu
Wed Dec 20 07:56:02 CET 2017

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 <hpages at fredhutch.org> wrote:
> 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: 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
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> Fax:    (206) 667-1319
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