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@latitude:~/svn/bioconductor/Rpacks/rgsepd$ svn log -r 111129
------------------------------------------------------------------------
r111129 | hpa...@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).
Cheers,
H.
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
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://stat.ethz.ch/mailman/listinfo/bioc-devel