Perhaps a buglet in the build system / the website code? --
When I follow the link to “R Script” on the page
http://www.bioconductor.org/packages/devel/bioc/html/DESeq2.html
(i.e.
http://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.R
) the result is a nearly empty
I think the more clean solution for Davide (if he inists on having separate
objects; I decided against it in minfi) is to extend the class to allow
this.
Kasper
On Thu, Jun 18, 2015 at 12:25 AM, Ryan r...@thompsonclan.org wrote:
Oh wow, I didn't know you could put a DataFrame into a single
yes, if a formal extension is warranted. the metadata slot could also be
used.
On Thu, Jun 18, 2015 at 2:59 PM, Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
I think the more clean solution for Davide (if he inists on having separate
objects; I decided against it in minfi) is to
Let the record show that it was relatively trivial to add a generic
function called update() to fix the broken serialized instances of the
older SE-descendant classes that now inherit from RSE...
Although it was a drag until I got around to writing those.
I'll try to put together a decently
Elena,
On 06/18/2015 10:48 AM, Elena Grassi wrote:
Hi Hervé,
thanks for your kind answer - refactoring is always good, I've lagged
behind in the last months not following the novelties so to be
truthful it has been my fault and today I was in a bit of a hurry for
other reasons.
I'm in the
On 06/18/2015 05:53 PM, Tim Triche, Jr. wrote:
Let the record show that it was relatively trivial to add a generic
function called update() to fix the broken serialized instances of the
older SE-descendant classes that now inherit from RSE...
Although it was a drag until I got around to writing
Hey since the refactoring is already breaking stuff willy nilly, can I make a
few suggestions?
1) please for the love of all that is holy have backwards compatible methods
for RSEs. It's excruciating to have RSE as the target class, supporting
RELEASE users with SE, and have to do endless
Dear All,
A package of mine is generating a NOTE about the vignette (a long 80 pages
document) saying
consider running tools::compactPDF() on these files
(http://www.bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/zin1-checksrc.html
---yes, there is also a WARNING and it fails on
you can just implement this by having reserved column names in the colData
slot; that will work and will take appr. 23 seconds to implement. I agree
it is not as clean from a design perspective, but you get 100% of the
functionality and you can write a separate checker for the colData argument.
Thanks Dan.
Best,
R.
On Thu, 18-06-2015, at 20:10, Dan Tenenbaum dtene...@fredhutch.org wrote:
- Original Message -
From: Ramon Diaz-Uriarte rdia...@gmail.com
To: bioc-devel@r-project.org
Cc: ramon diaz ramon.d...@iib.uam.es
Sent: Thursday, June 18, 2015 11:00:51 AM
Subject:
I agree 100%: It would be wonderful to have a roadmap and (perhaps) some
high level discussion of what should be done for various things. Things
are breaking right and left and we don't want to have to deal with this
again in 6 months, so why don't we make sure the design has been looked at
with
Hi Tim,
On 06/18/2015 10:48 AM, Tim Triche, Jr. wrote:
Hey since the refactoring is already breaking stuff willy nilly, can I make a
few suggestions?
1) please for the love of all that is holy have backwards compatible methods
for RSEs. It's excruciating to have RSE as the target class,
Thanks Kasper,
I think that's a good solution.
Best,
Davide
On Thu, Jun 18, 2015 at 11:51 AM Kasper Daniel Hansen
kasperdanielhan...@gmail.com wrote:
you can just implement this by having reserved column names in the colData
slot; that will work and will take appr. 23 seconds to implement.
Thank you all for the responses.
I didn't think about the nested DataFrame solution. It should work.
I agree that an extension might be cleaner, but I clearly need to give it
more thought.
One of the reasons I wanted to have quality and metadata as separate slots
is that one could enforce that
- Original Message -
From: Wolfgang Huber whu...@embl.de
To: bioc-devel@r-project.org
Sent: Thursday, June 18, 2015 5:47:27 AM
Subject: [Bioc-devel] Rendering of vignette R code on the website
Perhaps a buglet in the build system / the website code? --
When I follow the link to
I'm sorry I was not expecting other developers to fix my package for every
mods to base packages that's why I asked...I'm still new to this world and
I decided to ask before fixing too soon or making further structural errors
- I usually like the gory details but unfortunately lack time to follow
Hi Michael, Herve,
On 6/17/2015 9:43 PM, Hervé Pagès wrote:
Hi Michael,
On 06/17/2015 12:35 AM, Michael Love wrote:
Background:
With previous approaches that I would recommend to users for building
txdb along the way of making count tables, it was desirable that the
GTF release information
that's great Hervé and Sonali!
thanks for the quick response.
best, m
On Thu, Jun 18, 2015 at 10:07 AM, Sonali Arora sar...@fredhutch.org wrote:
Hi Michael, Herve,
On 6/17/2015 9:43 PM, Hervé Pagès wrote:
Hi Michael,
On 06/17/2015 12:35 AM, Michael Love wrote:
Background:
With
Hello,
I'm writing as long as I am struggling a bit to keep the pace of
RangedSummarizedExperiment in my package roar, whose main class
contains RangedSummarizedExperiment to hold some of the data.
Sometimes the developers fix issues for me but I would like to ease
their work as much as possible
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