We are getting hit hard by this in minfi as well, assuming this is fall out
from us using SummarizedExperiment.
Best,
Kasper
On Thu, Sep 12, 2013 at 7:16 AM, Stadler, Michael michael.stad...@fmi.chwrote:
Dear list and ShortRead maintainers,
Since I updated BioC 2.13 yesterday to the latest
The 'GroupedIRanges' error is related to some cleanup Herve is doing on
the subsetting code in IRanges/XVector. The error should be gone with
the most recent devel versions (IRanges 1.19.33, XVector 0.1.2,
GenomicRanges 1.13.42). These may take a day to propagate through
biocLite().
Valerie
Thanks Valerie and Herve for the fast fix - I can confirm that the problem is
gone with the versions below.
Michael
On Sep 12, 2013, at 11:50 AM, Valerie Obenchain voben...@fhcrc.org
wrote:
The 'GroupedIRanges' error is related to some cleanup Herve is doing on the
subsetting code in
Ok, sounds good.
This is especially nice to know for the annotation packages which are
hand created as opposed to being created by some script.
Kasper
On Thu, Sep 12, 2013 at 1:22 PM, Marc Carlson mcarl...@fhcrc.org wrote:
Hi Kasper,
You should get an email from me in the coming weeks with
Hi Kasper,
You should get an email from me in the coming weeks with instructions
regarding the upcoming release. If you need something changed before
then, please send me an email.
Marc
On 09/11/2013 06:17 PM, Dan Tenenbaum wrote:
Annotation packages are not in svn. Send your changes
I received the following email note re: the vcdExtra package
A vcd update has shown that packages TIMP and vcdExtra are not
declaring their dependence on colorspace/MASS: see
http://cran.r-project.org/web/checks/check_results_vcdExtra.html
But, I can't see what to do to avoid this, nor
Hi,
I am currently preparing a new version of my package papeR. When I run R CMD
check using the development version of R I get the following note:
Package in Depends field not imported from: ‘nlme’, ‘lme4’, ‘survival’
These packages needs to imported from for the case when
this namespace is
On 12/09/2013 9:38 AM, Michael Friendly wrote:
I received the following email note re: the vcdExtra package
A vcd update has shown that packages TIMP and vcdExtra are not
declaring their dependence on colorspace/MASS: see
http://cran.r-project.org/web/checks/check_results_vcdExtra.html
But,
Michael
(Several of us are struggling with these changes, so my comments are
from the newly initiated point of view, rather than the fully
knowledgeable.)
On 13-09-12 09:38 AM, Michael Friendly wrote:
I received the following email note re: the vcdExtra package
A vcd update has shown that
Just for the record, I did submit PR#15451:
'Bug 15451 - PATCH: namespaceImportFrom() not to warn when the
identical object is imported twice' on 2013-09-10
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15451
/Henrik
On Mon, Sep 9, 2013 at 2:37 PM, Henrik Bengtsson h...@biostat.ucsf.edu
On Thu, Sep 12, 2013 at 6:49 AM, Benjamin Hofner benjamin.hof...@fau.de wrote:
Hi,
I am currently preparing a new version of my package papeR. When I run R CMD
check using the development version of R I get the following note:
Package in Depends field not imported from: ‘nlme’, ‘lme4’,
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