Hi Raymond,
This should be fixed now in GenomeInfoDb 1.10.3 (release) and 1.11.8
(devel). Both packages should become available via biocLite() in the
next 24 hours or so.
Thanks again for reporting the issue and for your patience.
Cheers,
H.
On 02/01/2017 12:32 PM, Hervé Pagès wrote:
Hi Raymo
Hello,
After reverting to the release version of GenomeInfoDb (1.10.2) the error
disappears.
In my defense, disaster is overstating it a bit, especially given the context.
GenomeInfoDb::Seqinfo() has been failing because of changes to the NCBI servers
(and still continues to fail). The devel v
For what it's worth, the Rcpp team is aware that CRAN will soon be emitting
NOTEs for packages not registering native routines as well -- it's
currently tracked at
https://github.com/RcppCore/Rcpp/issues/636
The main difficulty on the Rcpp side is ensuring that we play well with
users who already
On 02/06/2017 10:13 AM, Raymond Cavalcante wrote:
Oops, I got so caught up in the setting up the code I forgot to say what the
error was:
Error in match.arg(pruning.mode) :
'arg' should be one of “error”, “coarse”, “fine”, “tidy”
you have a mixture of 'release' (even-numbered y in x.y.z) an
Autogeneration of registration code seems tractable and probably worth an
investment.
https://github.com/kevinushey/Kmisc/blob/master/R/registerFunctions.R
appears to be exported at this time.
On Mon, Feb 6, 2017 at 10:22 AM, Peter Hickey
wrote:
> FWIW I've had some success registering Rcpp-ba
FWIW I've had some success registering Rcpp-based native routines
using Kmisc:::registerFunctions() by Kevin Ushey
(https://cran.r-project.org/web/packages/Kmisc/index.html). Note this
is a non-exported function and from memory it required a little bit of
post-processing, but it got me most of the
Might be worth it to take this one over to Rcpp-devel and get some feedback
there?
Best,
Kasper
On Mon, Feb 6, 2017 at 5:22 AM, Aaron Taudt wrote:
> Dear all,
>
> I am trying to register the native routines in my package as recommended by
> BiocCheck. I have done this previously for a package u
Oops, I got so caught up in the setting up the code I forgot to say what the
error was:
Error in match.arg(pruning.mode) :
'arg' should be one of “error”, “coarse”, “fine”, “tidy”
Thanks again,
Raymond
> On Feb 6, 2017, at 10:10 AM, Raymond Cavalcante wrote:
>
> Hello,
>
> Perhaps this is
Hello,
Perhaps this is related to problems in GenomeInfoDb::Seqinfo() and NCBI server
file structure changes, but rtracklayer::import() is failing when I specify a
genome.
See below for example code.
Thanks,
Raymond Cavalcante
library(annotatr)
# These fail
file = system.file('extdata', 'tes
On 02/06/2017 05:22 AM, Aaron Taudt wrote:
Dear all,
I am trying to register the native routines in my package as recommended by
BiocCheck. I have done this previously for a package using C++ code.
However, for this package I am using Rcpp and I cannot figure out how to
register my native routin
Dear all,
I am trying to register the native routines in my package as recommended by
BiocCheck. I have done this previously for a package using C++ code.
However, for this package I am using Rcpp and I cannot figure out how to
register my native routines.
My first problem is that I don't know wh
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