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 <hpa...@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 <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. >> _______________________________________________ >> Bioc-devel@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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
