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 <hpa...@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.
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--
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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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