Yes, please follow Hervé's instructions. On Fri, Nov 2, 2018 at 3:41 PM Håkon Tjeldnes <hauken_hey...@hotmail.com> wrote:
> Just a quick question, in 3.8 we used biogenerics::lengths for ORFik, > since it was much faster than base, for our dataset 1 second vs 30 minutes. > We should change to S4 version of lengths now ? > > Get Outlook for Android<https://aka.ms/ghei36> > > ________________________________ > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Pages, > Herve <hpa...@fredhutch.org> > Sent: Friday, November 2, 2018 6:08:13 PM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Error : object 'lengths' is not exported by > 'namespace:BiocGenerics' > > Hi developers, > > Starting with R 3.6, base::lengths() can now be treated as an S4 generic > function (like base::length() or base::names()) so there is no need for > us to define our own lengths() generic function in BiocGenerics. > Therefore we've removed the lengths() generic from BiocGenerics (in > version 0.29.1). Note that you can see the S4 generic associated with > base::lengths() by calling getGeneric("lengths") in a fresh R session: > > > getGeneric("lengths") > standardGeneric for "lengths" defined from package "base" > > function (x, use.names = TRUE) > standardGeneric("lengths") > <bytecode: 0x3548c90> > <environment: 0x3540928> > Methods may be defined for arguments: x > Use showMethods("lengths") for currently available ones. > > This used to return NULL in R < 3.6. > > Because of these changes, packages that currently explicitly import > lengths or a lengths method in their NAMESPACE are failing to install > with an error that looks like this: > > ** byte-compile and prepare package for lazy loading > Error : object 'lengths' is not exported by 'namespace:BiocGenerics' > ERROR: lazy loading failed for package 'BubbleTree' > > The packages currently affected by this are: BubbleTree, csaw, > GA4GHclient, matter, NADfinder, and SomaticSignatures. The fix is to > simply remove any explicit import of lengths from the NAMESPACE. > > Note that many other software packages currently fail to install in BioC > 3.9 because they depend on one of the above packages. > > Please let us know if you have questions or need assistance with this. > > H. > > -- > 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://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=02%7C01%7C%7C7c4bb0f70b934115a93708d6410fbb9d%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636767933158117589&sdata=0UfC1T6Q52n1V%2FcKb6vR4RT0h5m0DXuWv4C6EwJ2YCA%3D&reserved=0 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel