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

[Hervé Pagès]

Hi Robert,

I don't really have a simple automatic way to find what package
upstream needs to have fixed its NAMESPACE.

In this kind of situation I generally start by extracting the
list of software packages that don't install because of a particular
NAMESPACE problem. I do this by combining some grep'ing of the
NAMESPACE file of all software packages (I have a local copy of
all software packages that I keep in sync with git.bioconductor.org)
and some grep'ing of the build report. Then I start to fix these
packages. I often have to proceed in several passes, one per day,
until the problem disappears from the build report. It typically
takes 2 or 3 passes. It's been working OK so far...

H.


On 12/19/2017 11:50 PM, Robert Castelo wrote:
> 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= 
>>>
>>
> 

-- 
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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