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

[Robert Castelo]

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 fixed its 
NAMESPACE?

robert.

On 12/20/2017 04:08 AM, Hervé Pagès 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= 
>>
> 

-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550