Ah, that makes sense. I was setting up R on a computer that hadn't been
used in a while, and it had a bunch of packages installed in /usr/local,
including an old version of BioC that was preventing an upgrade. So I
removed the R site-packages directory in /usr/local and started over.
Somehow di
On 08/07/2015 04:31 PM, Dan Tenenbaum wrote:
- Original Message -
From: "Ryan C. Thompson"
To: bioc-devel@r-project.org
Sent: Friday, August 7, 2015 4:27:57 PM
Subject: [Bioc-devel] bumphunter package has unstated dependency on digest
package?
Konsole output Hello,
I was recen
- Original Message -
> From: "Ryan C. Thompson"
> To: bioc-devel@r-project.org
> Sent: Friday, August 7, 2015 4:27:57 PM
> Subject: [Bioc-devel] bumphunter package has unstated dependency on digest
> package?
>
> Konsole output Hello,
>
> I was recently setting up the latest versio
Konsole output Hello,
I was recently setting up the latest version of R & Bioc on a system,
installing all packages from scratch, and I ran into an error while
installing bumphunter. It failed to install because it couldn't load the
"digest" package. After installing this package manually, bump
Thanks for the report and reproducible example. Now fixed in 1.14.8 and
1.15.22.
Valerie
On 08/07/2015 07:25 AM, Julian Gehring wrote:
Hi,
When I use the 'filterVcf' function to process a VCF file in chunks, the
output file contains as many copies of the header as there are
chunks. Consider
Hi,
When I use the 'filterVcf' function to process a VCF file in chunks, the
output file contains as many copies of the header as there are
chunks. Consider the example, adapted from the 'filterVcf' man page:
library(VariantAnnotation)
fl <- system.file(package = "VariantAnnotation", "extdat
