Right, match.fun() needs to be within the initial endoapply, not later.
Isn't the convention though to use `obeyQname<-` in this case? Or should
there be a convention?
On Wed, Nov 20, 2013 at 5:18 PM, Martin Morgan wrote:
> After this
>
> library(RNAseqData.HNRNPC.bam.chr14)
> library(T
After this
library(RNAseqData.HNRNPC.bam.chr14)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
fls <- RNAseqData.HNRNPC.bam.chr14_BAMFILES
exByGn <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, "gene")
Rsamtools is loaded but not attached; it's
summarizeOverlaps,GRanges,character-meth
- Original Message -
> From: "Li Shen"
> To: "Dan Tenenbaum"
> Cc: bioc-devel@r-project.org, "Kasper Daniel Hansen"
>
> Sent: Wednesday, November 20, 2013 1:28:54 PM
> Subject: Re: [Bioc-devel] Help: package builder error messages
>
>
> Thanks, Dan! Will you remove the error message
Hi Katsuhito,
I've cc'd your message to the Bioconductor mailing list. We have two
lists, one for general questions and the other for bug reports/feature
requests. Please post future questions to one of these lists instead of
sending them to a single person. The lists reach a wider audience an
Thanks, Dan! Will you remove the error message for me? Is there anything
else I need to do?
On Wed, Nov 20, 2013 at 4:14 PM, Dan Tenenbaum wrote:
>
>
> - Original Message -
> > From: "Li Shen"
> > To: "Kasper Daniel Hansen"
> > Cc: "Dan Tenenbaum" , bioc-devel@r-project.org
> > Sent:
- Original Message -
> From: "Li Shen"
> To: "Kasper Daniel Hansen"
> Cc: "Dan Tenenbaum" , bioc-devel@r-project.org
> Sent: Wednesday, November 20, 2013 1:06:47 PM
> Subject: Re: [Bioc-devel] Help: package builder error messages
>
>
> It looks like on my computer, if I remove
> "\bib
It looks like on my computer, if I remove "\bibliographystyle{apalike}",
the pdf simply cannot be built from Rnw. So I followed Dan's suggestion.
This time, I passed building on Mac but still failed Windows with the same
error message.
My understanding is that the pdf was not generated from the te
Excellent! Thank you Kasper.
On Wed, Nov 20, 2013 at 3:37 PM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:
> Ok, I analyzed the package using codetoolsBioC and there were a number of
> missing imports, including what Leonardo has described. I have fixed those
> in bumphunter 1.3.
Ok, I analyzed the package using codetoolsBioC and there were a number of
missing imports, including what Leonardo has described. I have fixed those
in bumphunter 1.3.3
Kasper
On Wed, Nov 20, 2013 at 3:28 PM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:
> I'll have a look.
>
> B
I'll have a look.
Basically, issues such as this is never the end-users problem and is likely
to either be caused by bumphunter not importing correctly (most likely) or
IRanges not exporting correctly.
Kasper
On Wed, Nov 20, 2013 at 3:02 PM, Leonardo Collado Torres wrote:
> Hello,
>
> Found h
Hello,
Found how to solve this. Basically, the NAMESPACE of the bumphunter package
is not complete (I think).
I downloaded
http://bioconductor.org/packages/release/bioc/src/contrib/bumphunter_1.2.0.tar.gz,
changed the version to 1.2.1 and added/modified the following lines to the
NAMESPACE:
impo
Hi Harris,
Answering your question from your first email, I do not think that it would
help if bumphunter exported matchGenes() or .matchGenes().
Currently by just importing annotateNearest(), R is correctly able to use
annotateNearest(), then .matchGenes(), and also nearestgene(). The problem
is
Assuming you have just copied the Sweave template from someone else, you
probably don't want to follow Dan's suggestion. Instead search for apalike
in the document and delete the line containing it. It is probably (from
memory)
\bibliographystyle{apalike}
Kasper
On Wed, Nov 20, 2013 at 2:05
- Original Message -
> From: "Li Shen"
> To: bioc-devel@r-project.org
> Sent: Wednesday, November 20, 2013 10:54:14 AM
> Subject: [Bioc-devel] Help: package builder error messages
>
> Hi,
>
> I'm trying to submit a new package to Bioc. Using the automated
> package
> builder, two out o
For the bibtex error you seem to be using two different styles files. I
think we need to see the preamble (header) of the vignette.
Inside BiocStyle there is a template_sweave.Rnw file which you could have a
look at.
Kasper
On Wed, Nov 20, 2013 at 1:54 PM, Li Shen wrote:
> Hi,
>
> I'm trying
Hi,
I'm trying to submit a new package to Bioc. Using the automated package
builder, two out of three machines did not finish nicely. More specific, my
package passed Linux but failed Windows and Mac.
Here is the error messages for Windows:
* checking for file 'Ge
Correction below.
On 11/20/2013 09:59 AM, Valerie Obenchain wrote:
Hi Delphine,
I've cc'd your message to the Bioconductor mailing list. We have two
lists, one for general questions and the other for bug reports/feature
requests. Please post future questions to one of these lists instead of
se
Hi Delphine,
I've cc'd your message to the Bioconductor mailing list. We have two
lists, one for general questions and the other for bug reports/feature
requests. Please post future questions to one of these lists instead of
sending them to a single person. The lists reach a wider audience and
Hi Jennifer,
I've cc'd your message to the Bioconductor mailing list. We have two
lists, one for general questions and the other for bug reports/feature
requests. Please post future questions to one of these lists instead of
sending them to a single person. The lists reach a wider audience and
Dear BioC-devel list,
I have what I hope is a simple problem. Basically, a function in my package
uses bumphunter::annotateNearest. This function in turn uses
IRanges::distance.
I would expect that using the following roxygen2 info would work:
#' @importMethodsFrom IRanges distance
#' @importFro
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