I want to write an R function using R's C interface that takes a 2-column
matrix of increasing, non-overlapping integer intervals and returns a list
with those intervals plus some added intervals, such that there are no
gaps. For example, it should take the matrix rbind(c(5L, 6L), c(7L, 10L),
Hi all,
R-exts currently requests that package authors don't include copies of
standard licenses:
> Whereas you should feel free to include a license file in your source
> distribution, please do
> not arrange to install yet another copy of the GNU COPYING or COPYING.LIB
> files but
> refer to
bfcquery() just searches the cache, so if you've created two resources that
match the name then you end up with two rids
> xx = bfcnew(bfc, "foo")
> bfcquery(bfc, "foo", "rname")
# A tibble: 1 x 10
rid rname create_time access_time rpath rtype fpath last_modified_t… etag
I'm not a BiocFileCache expert, sorry. You will probably get better help
by opening a BiocFileCache issue on GitHub.
Cheers,
H.
On 9/11/20 12:00, Shraddha Pai wrote:
> Hi Herve,
> Sorry - hit shortcut to "send" by mistake.
>
> This is the code snippet that got cut off:
> if (length(rid)>1) {
I can compile a package under clang++ with -stdlib=libstdc++, but with
-stdlib=libc++ I get
"
In file included from
/home/jo/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/r/headers.h:67:
/home/jo/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp/platform/compiler.h:100:10:
fatal error:
Hi Karim,
On 11 September 2020 at 13:09, Karim Rahim wrote:
| Thanks for resolving this! It's been awhile since I've worked on this...
|
| So for dependencies, I'd like to keep it as simple as possible. I agree
| fftw3 may need to be updated.
|
| It's my understanding that if one were to
Hi Shraddha,
Seems to be a BiocFileCache issue.
On my laptop the following code (taken from your
Predict_CaseControl_from_CNV.Rnw vignette):
require(BiocFileCache)
geneURL <- paste("http://download.baderlab.org/netDx/;,
"supporting_data/refGene.hg18.bed",sep="")
cache <-
Hi Dirk,
Thanks for resolving this! It's been awhile since I've worked on this...
So for dependencies, I'd like to keep it as simple as possible. I agree
fftw3 may need to be updated.
It's my understanding that if one were to install the latest fftw (3.3.8)
from source then it would expose the
At the top of each build report page, e.g.,
http://bioconductor.org/checkResults/3.12/bioc-LATEST/netDx/malbec1-buildsrc.html
there's a link with title 'following settings' describing
build-system-specific settings. Does this help to reproduce the problem?
Martin
On 9/11/20, 11:52 AM,
Hello BioC-devel team,
Any idea why netDx 1.1.4 fails on the bioc devel build system?
This is the error:
--- re-building 'Predict_CaseControl_from_CNV.Rmd' using knitr
Quitting from lines 173-195 (Predict_CaseControl_from_CNV.Rmd)
Error: processing vignette 'Predict_CaseControl_from_CNV.Rmd'
On 10 September 2020 at 14:14, Marta Karaś wrote:
| Adding the following to .travis.yml:
|
| before_install:
| - if [ "$TRAVIS_OS_NAME" = "linux" ]; then sudo apt-get -y install
| libfftw3-dev ; fi
|
| did the trick!
I think that is an example of the issue discussed in this blog post:
E.g. in https://cran.r-project.org/bin/macosx/contrib/4.0/PACKAGES there is
Package: stringi
Version: 1.5.3
but there is no such binary at
https://cran.r-project.org/bin/macosx/contrib/4.0/
FYI, G.
__
R-devel@r-project.org mailing list
Abby, my answer was too concise. The thrust is that even if you define a method
for
"[<-" with signature x="matrix" and value ="Matrix", for example, it will never
be used since "matrix" is S3.
If instead x="someS4class" then the S4 method will be invoked.
There may be cases when changing the
If the current semantics is to be kept, one approach might be to insert in the
internal code of "[<-" something like the equivalent of
If(isS4(value))
value <- coreData(value)
with the contract that classes that wish to be treated as equivalent to basic
vector classes define suitable
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