Hi Michael,
Thanks for the fast patching. However, going a step further and trying
to read the VCF again fails (with VariantAnnotation_1.9.35
). I'm not sure if this is related to the same issue.
#+BEGIN_SRC R
library(VariantAnnotation)
example(VRanges)
writeVcf(vr, out.vcf) ## works
Hi Julian,
Thanks for this one. It was a bug in Rsamtools, now fixed in devel, version
1.15.27. I'll leave it to Martin/Val to OK it and push to release.
Michael
On Thu, Feb 6, 2014 at 1:46 AM, Julian Gehring julian.gehr...@embl.dewrote:
Hi Michael,
Thanks for the fast patching. However,
Dear list,
Just upgraded to MacOS Mavericks, fresh install of R 3.0.2 and trying to
install a previous version of my QCA package (the most recent one source
file, which passed the R CMD check --as-cran with R 3.0.1)
I seem to have some difficulties in the C code, apparently it doesn't find
some
This is an R-sig-mac issue, so Cc:ed there.
I have seen this after an upgrade to Mavericks: you have a partial
installation of the pre-Mavericks Xcode Command Line Tools after the
upgrade (which removed some of it).
See the current R-admin manual for how to use the CRAN binary of R 3.0.2
I went through this pain two days ago, but I managed both building R
from source and my own packages by following Brian Ripley excellent (as
always) pointers on the r-sig-mac mailing list (around october 2013).
Look there, and ask further questions on that list.
Göran Broström
On 02/06/2014
I suggest that there be an additional sentence
in the explanation for the 'repos' argument in
the help file for 'install.packages':
If the repository is on a local drive, then the
string should begin with \code{file:}, e.g.,
\code{file:J:/Rrepos}.
Perhaps I'm missing some subtlety, but it
First, let me apologize in advance if this is the wrong place to submit
a suggestion for a change to functions in the base-R package. It never
really occurred to me that I'd have an idea worthy of such a change.
My idea is to provide an upgrade to all the sets tools (intersect,
union,
