[Bioc-devel] namespace GenomicRanges

Hervé Pagès hpages at fredhutch.org
Wed Dec 2 23:10:43 CET 2015

Hi Karl,

On 12/02/2015 01:42 PM, Karl Stamm wrote:
> Happened to look if my package rgsepd was building correctly, and it
> seems as if some kind of change to a dependency is causing an
> installation error for me. I was explicitly importing and calling
> GenomicRanges::assay() for a year, and this month it is not exported.
> Error : object ‘assay’ is not exported by 'namespace:GenomicRanges'
> It appears to be fixed by removing the specification for that assay
> function, and now I'm using a generic, probably provided from another
> package. What happened here?

hpages at latitude:~/svn/bioconductor/Rpacks/rgsepd$ svn log -r 111129
r111129 | hpages at fhcrc.org | 2015-12-02 11:35:49 -0800 (Wed, 02 Dec 
2015) | 1 line

assay() has moved from GenomicRanges to SummarizedExperiment

Some background:

We're migrating the SummarizedExperiment class to its own package: the
SummarizedExperiment package. This process started a few months ago.
It's a long process but the good news is that we're almost done.

As part of this process I made some changes last week to
GenomicRanges/SummarizedExperiment in devel that broke a few packages.
I'm in the process of fixing them. I fixed rgsepd this morning
(commit 111129 above), at least I thought I fixed it. It seems that I
missed an instance of GenomicRanges::assay. I see that you just fixed
that (commit 111138). Thanks and sorry for the inconvenience.

> On a related note, should I be notified of a build error? When a similar
> problem occurred last month with biomart changing their interface, the
> build was failing for an unknown length of time. The fix was quick and easy
> but I didn't see the problem right away. Maybe I'm not on the correct RSS
> feeds, or how would a dev see his package having problems? Given the
> problem occurred by the build server updating a dependency, I wasn't
> actively working on anything.

Normally developers should get automatic notifications via email when
their package fails *in release*. The script in charge of sending these
notifications runs once a week only. I don't know why you didn't receive
anything but maybe Dan will be able to help when he's back from vacation
(tomorrow I think).


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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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