hi Martin,
On 10/06/2014 07:24 PM, Martin Morgan wrote:
[...]
There are two 'as.vector' generics, one defined in Matrix and one in
BiocGenerics (and made available via IRanges). These generics have
different methods
> showMethods(Matrix::as.vector)
Function: as.vector (package base)
x="abIndex
Sorry to re-open this thread, but it appears that this configuration
works with some builders but not others. There appear to be two
different failure modes:
Works with: oaxaca, perceval (OSX 10.6, 10.9)
Fails with: moscato1 (windows 2008)
InvalidUrlException
"D:%5Cpackagebuilder%5Cjobs%5CST
Dear all,
I would like to introduce a recent addition to Bioconductor.
I hope those of you working with transcriptomics data will find it useful
for their own work.
*GOexpress *is a package taking an *ExpressionSet *object minimally
including *assayData *and *phenoData* corresponding to either mi
Does that happen with the other methods or just "["? As a last resort, you
could just drop the import (because "[" is a primitive, it should just
work).
On Tue, Oct 7, 2014 at 3:08 AM, Robert Castelo
wrote:
> hi Martin,
>
> On 10/06/2014 07:24 PM, Martin Morgan wrote:
> [...]
>
> There are two
hi, it happens only with "[", that's why i'm puzzled.
it behaves as if you load a GRanges object 'x' and try to subset it
x[1]
without loading 'GenomicRanges' first.
robert.
On 10/07/2014 05:05 PM, Michael Lawrence wrote:
Does that happen with the other methods or just "["? As a last resort,
On 10/07/2014 08:15 AM, Robert Castelo wrote:
hi, it happens only with "[", that's why i'm puzzled.
it behaves as if you load a GRanges object 'x' and try to subset it
x[1]
without loading 'GenomicRanges' first.
Is there a reproducible example? I see in your code there are several places
wh
On Tue, Oct 7, 2014 at 8:54 AM, Martin Morgan wrote:
> On 10/07/2014 08:15 AM, Robert Castelo wrote:
>
>> hi, it happens only with "[", that's why i'm puzzled.
>>
>> it behaves as if you load a GRanges object 'x' and try to subset it
>>
>> x[1]
>>
>> without loading 'GenomicRanges' first.
>>
>
>
This is fixed now.
http://bioconductor.org/spb_reports/STATegRa_0.99.4_buildreport_20141007100210.html
Dan
- Original Message -
> From: "Gordon Ball"
> To: "Andrzej Oleś" , "Dan Tenenbaum"
>
> Cc: jmac...@u.washington.edu, bioc-devel@r-project.org, "david Gomez-Cabrero"
>
> Sent: T
Looks like we still have to move over the DataFrame, etc tests from IRanges?
Michael
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On 10/07/2014 10:35 AM, Michael Lawrence wrote:
Looks like we still have to move over the DataFrame, etc tests from IRanges?
Yes this and other leftovers.
H.
Michael
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Cool. We should consider moving some of the infrastructure pieces to the
github bridge.
I added a droplevels method for List that should take care of things.
On Mon, Oct 6, 2014 at 6:11 PM, Ryan C. Thompson
wrote:
> Hi,
>
> Yes, if something is on Github (or just any git/hg repo that I can clon
On behalf of a number of software developers, end-users, publishers
associated with the scientific analysis community, we would like to invite
all of you to review a document generated as a result of a NIH BD2K
supported meeting that focused on the opportunities and challenges of
developing a softw
On 10/07/2014 09:15 AM, Michael Lawrence wrote:
Probably in your code you do not actually want to require() ad hoc packages
and influence the user search path (and implicitly rely on search path order
for correct functionality), but rather to requireNamespace("foo");
foo::fun(...
The guidelines state :
Depends: is appropriate when a package is used in the example section of a man
page.
I think such packages should be in Suggests. In the example, the package should
be loaded by :
if(require(examplePackage))
{
exampleFunction(data)
}
--
I think the intent there is that if you virtually always need a package to
generate the input or analyze the output of a documented function, it
should be in Depends. If it's a package that is only useful for
demonstration, it should be in Suggests, and one should abide by the same
guidelines (requ
On 10/07/2014 07:05 PM, Michael Lawrence wrote:
I think the intent there is that if you virtually always need a package to
generate the input or analyze the output of a documented function, it
should be in Depends. If it's a package that is only useful for
demonstration, it should be in Suggests,
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