[Bioc-devel] Bioc-devel Digest, Vol 152, Issue 10

[calogero UNITO]

Hi Dario,
I am the maintainer of chimera package
thank for the info I am going to check which is the problem in 
importFusionData.
There is only one example of data import, because of limits in package size.
An other example can be retrieved from:
download.file("http://sourceforge.net/projects/ochguiextras/files/chimera/Chimeric.out.junction.zip/download", 
"Chimeric.out.junction.zip", mode="wb")

I check the example:
tmp <- importFusionData("fusionmap", 
paste(find.package(package="chimera"),"/examples/mcf7.FMFusionReport", 
sep=""), org="hg19")
and it seems to import correctly the fusionmap data.

Same  happens with:
download.file("http://sourceforge.net/projects/ochguiextras/files/chimera/Chimeric.out.junction.zip/download", 
"Chimeric.out.junction.zip", mode="wb")
unzip("Chimeric.out.junction.zip")
tmp <- importFusionData("star", "Chimeric.out.junction", org="hg19", 
min.support=100)

Could please send me the code you have run and could you please describe 
the issue you encountered?
Cheers
Raf

  Today's Topics:
>     1. Re: chimera Attempts to Open Non-existent File (Dario Strbenac)
>     
> Message: 1
> Date: Sun, 6 Nov 2016 11:00:07 +0000
> From: Dario Strbenac <dstr7320 at uni.sydney.edu.au>
> To: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
> Subject: Re: [Bioc-devel] chimera Attempts to Open Non-existent File
> Message-ID:
> 	<MWHPR01MB27010078D6700175272F5A9CCDA30 at MWHPR01MB2701.prod.exchangelabs.com>
> 	
> Content-Type: text/plain; charset="us-ascii"
>
> Good day,
>
> The examples section of importFusionData is almost entirely commented out, so it's unclear whether it works. Since a lot of the package code is never run by R CMD check and the test coverage is 0%, it's plausibly a package development issue.
>
> -------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
>
>

-- 
----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
MBC Centro di Biotecnologie Molecolari
Via Nizza 52, Torino 10126
Tel.   ++39 0116706454
Fax    ++39 0112366457
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
        raffaele.calogero at gmail.com
www:   http://www.bioinformatica.unito.it