[Bioc-devel] Error : object 'lengths' is not exported by 'namespace:BiocGenerics'

[Michael Lawrence]

Yes, please follow Hervé's instructions.

On Fri, Nov 2, 2018 at 3:41 PM Håkon Tjeldnes <hauken_heyken using 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-bounces using r-project.org> on behalf of Pages,
> Herve <hpages using fredhutch.org>
> Sent: Friday, November 2, 2018 6:08:13 PM
> To: bioc-devel using 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: hpages using fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
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