Hi Yu,
On 09/22/2016 02:15 PM, Yu Kong wrote:
Dear BioConductor community,
My package (MADSEQ) passed the build on Linux (*malbec1*) and Mac (*morelia*)
build servers. However it fails on Windows (tokay1) server for multiple
days. Our package is a Bayesian model depends on JAGS sampler. The err
Yes, that was the strange thing (for me at least): some packages showed
"all" and some showed "some" and a cursory look did not reveal any pattern.
R.
On Fri, 23-09-2016, at 08:26, Hervé Pagès wrote:
> On 09/22/2016 11:09 PM, Ramon Diaz-Uriarte wrote:
>> Hi Hervé,
>>
>> Thanks for the clarificat
Dear Bioc Team,
First of all thanks a lot again for all the time you spend developing and
maintaining the Bioc repository.
I recently added 'Biobase' as "suggests" in the 'biosigner' package in order to
have the biosign method work on 'ExpressionSet' objects (devel version of
'biosigner').
Si
In general you can assume this to be the case for core functionality like
the stuff in Biobase.
What you should do however, since combine() is an S4 method, is import the
S4 method from BiocGenerics. In fact, it is a good idea to check which
generics are defined in BiocGenerics and consider wheth
You'll need to either `importFrom(Biobase, only, the, symbols,
needed)` or use the `except="combine"` argument to `import()`.
On Fri, Sep 23, 2016 at 4:59 AM, THEVENOT Etienne 207099
wrote:
> Dear Bioc Team,
>
> First of all thanks a lot again for all the time you spend developing and
> maintain
Hi Hervé,
Thank you so much for help. My package uses JAGS thru the rjags package.
Thanks,
Yu
On Fri, Sep 23, 2016 at 2:59 AM, Hervé Pagès wrote:
> Hi Yu,
>
> On 09/22/2016 02:15 PM, Yu Kong wrote:
>
>> Dear BioConductor community,
>>
>> My package (MADSEQ) passed the build on Linux (*malbec1*
Hi Yu,
On 09/23/2016 06:57 AM, Yu Kong wrote:
Hi Hervé,
Thank you so much for help. My package uses JAGS thru the rjags package.
Good. Thanks for clarifying. So can you please remove the
SystemRequirements line from the DESCRIPTION file of your
package?
I just installed JAGS on tokay1.
Ch
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On 09/23/2016 12:15 PM, Martin Morgan wrote:
Bioc Developers!
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Hi everyone—
I’m working with a team that’s generating single cell ATAC data in large
amounts and am designing the framework of an S4 object to facilitate analyses
in R. I have a couple of high-level questions that I wanted to pose early to
hopefully attain some community guidance in the implem
Hi Caleb,
Per your question on sparse on-disk matrices: is your experimental data coming
in some pre-defined text or binary file format, or are you looking to convert
to a new, custom format to take advantage of the sparsity?
I need to start working on an on-disk sparse matrix implementation so
Hi Caleb,
Hopefully Herve will chime in regarding SummarizedExperiment, but yes, I
think you can and should inherit from that. The `assays` slot must be an
object of type `Assays`, but that does appear to include a sparse Matrix.
See the comments at the top of Assays-class.R in the tarball for
Summ
Hi,
Yes, I would also encourage you to explore the SummarizedExperiment
route rather than ExpressionSet one. To be more precise,
RangedSummarizedExperiment is probably what you need: you can put
a GRanges object along the 1st dimension to describe your peaks and
a DataFrame object along the 2nd d
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