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

[Håkon Tjeldnes]

Just to be sure, you are saying that now base::lengths is as fast as BiocGenerics::lengths was ? Else we would still need the Bioc version. Because the old base implementation was terrible, I will try to verify this if you are unsure.
________________________________
Fra: Michael Lawrence <lawrence.michael using gene.com>
Sendt: fredag 2. november 2018 23.50
Til: hauken_heyken using hotmail.com
Kopi: bioc-devel; Herv� Pag�s
Emne: Re: [Bioc-devel] Error : object 'lengths' is not exported by 'namespace:BiocGenerics'

Yes, please follow Herv�'s instructions.

On Fri, Nov 2, 2018 at 3:41 PM H�kon Tjeldnes <hauken_heyken using hotmail.com<mailto: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 ?

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From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Pages, Herve <hpages using fredhutch.org<mailto:hpages using fredhutch.org>>
Sent: Friday, November 2, 2018 6:08:13 PM
To: bioc-devel using r-project.org<mailto: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.

--
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

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