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

Pages, Herve hp@ge@ @ending from fredhutch@org
Tue Nov 13 21:33:31 CET 2018 

I'm going to try to provide some details, at the risk to confuse you even more.


In BioC 3.8 / R 3.5 base::lengths() was not just slow on some Bioconductor objects like IRanges or GRanges, it didn't work:


  > ir <- IRanges(1:21, 20)
  > base::lengths(ir)
  Error in getListElement(x, i, ...) :
    IRanges objects don't support [[, as.list(), lapply(), or unlist() at
    the moment


Now it works (in BioC 3.9 / R 3.6):


  > ir <- IRanges(1:21, 20)
  > base::lengths(ir)
   [1] 20 19 18 17 16 15 14 13 12 11 10  9  8  7  6  5  4  3  2  1  0


The change I announced in my original post is about base::lengths() being now an S4 generic. A standard S4 generic like BiocGenerics::lengths() or base::lengths() doesn't do any work beyond dispatching to the right method. What happened in R 3.6 is that base::lengths() is now an S4 generic. This means that it knows how to take care of dispatching to the right method. The various "lengths" methods defined in Bioconductor are the ones doing the real work and they are fast. They have not changed and their speed should not be affected by this change in base::lengths().


Furthermore: in R 3.6, even though you can't see it, there is a default "lengths" method defined in base (it's used as a fallback when no other method applies). In my 1st code chunk above (i.e. when base::lengths() was not a generic), I'm calling directly this default method (note that this was the default method of the BiocGenerics::lengths() generic). This default method is indeed slow or doesn't work on Bioconductor objects. By calling BiocGenerics::lengths() (in BioC 3.8) or base::lengths() (in BioC 3.9), dispatch selects the fast method so nothing has changed from that perspective.


Hope this helps,

H.


On 11/13/18 08:59, H�kon Tjeldnes wrote:
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><mailto:lawrence.michael using gene.com>
Sendt: fredag 2. november 2018 23.50
Til: hauken_heyken using hotmail.com<mailto: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
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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<mailto:hpages using fredhutch.org>
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