Hi,
I am currently finishing a package for submission to Bioconductor 3.1
and, therefore, I am trying to make everything work on the latest
R-devel, but I have an issue with linking to Rsamtools. It seems that
Rsamtools installs the libraries libbam, libbcf, and libtabix to the
usrlib/x86_64/
Hi,
How could we mask the warnings when we check a package which imports on
BiocGenerics, AnnotationDbi and GenomeInfoDb.
The warning messages are:
Warning: multiple methods tables found for �species�
Warning: multiple methods tables found for �organism�
Yours Sincerely,
Jianhong Ou
TEL: 508-
On 16 March 2015 21:45, Hervé Pagès wrote:
> Hi Laurent,
>
> On 03/10/2015 07:28 AM, Laurent Gatto wrote:
>>
>> Dear all,
>>
>> Two possible candidates for BiocGenerics:
>>
>>> GenomeInfoDb::species
>> standardGeneric for "species" defined from package "GenomeInfoDb"
>>
>> function (x)
>> standar
Hi, Ulrich. I just built R-devel (on Ubuntu) from trunk and installed
Rsamtools using biocLite; the libraries ended up where I expect them:
> dir(system.file(package="Rsamtools", "usrlib"))
[1] "libbam.a" "libbcf.a" "libtabix.a"
> sessionInfo()
R Under development (unstable) (2015-03-19 r6803
Also, please consider developing your package against the new and
improved version of samtools, htslib, available via the Rhtslib package.
The samtools source in Rsamtools will eventually go away in favor of the
htslib library.
See announcement of Rhtslib:
https://stat.ethz.ch/pipermail/bioc-
This is done BTW.
Marc
On 02/27/2015 02:43 PM, Marc Carlson wrote:
Hi Sean,
This seems like a solid suggestion. I have put it into my queue.
Marc
On 02/27/2015 04:41 AM, Sean Davis wrote:
Hi, Marc.
Since Ensembl has switched to GRCh38 for their most recent builds, to
get
access to GR
On 03/16/2015 05:31 PM, Hervé Pagès wrote:
On 03/16/2015 04:06 PM, Michael Lawrence wrote:
On Mon, Mar 16, 2015 at 3:12 PM, Robert Castelo mailto:robert.cast...@upf.edu>> wrote:
+1 IMO BioC could adopt the zero-width ranges representation for
insertions, adapting readVcf(), writeVcf()
