[Bioc-devel] fixing 'path' not being exported by 'Rsamtools'
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 Herv?, 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, Herv? Pag?s 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: Herv? Pag?s <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.
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Herv? Pag?s 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 Fax: (206) 667-1319