[Rd] Why does lm() with the subset argument give a different answer than subsetting in advance?

dataset? This feels like a serous leak of information when evaluating train and test datasets in a statistical learning framework. Ray Raymond R. Balise, PhD Assistant Professor Department of Public Health Sciences, Biostatistics University of Miami, Miller School of Medicine 1120 N.W. 14th

Re: [Bioc-devel] Please change maintainer of chipenrich and chipenrich.data packages

Hi Nitesh, To echo Kai's response, I don't have a problem either. Again, sorry for the confusion, I didn't realize I'd retain my access. Thanks, Raymond Raymond Cavalcante, PhD Bioinformatics Analyst Epigenomics Core and Bioinformatics Core Biomedical Research Core

Re: [Bioc-devel] Please change maintainer of chipenrich and chipenrich.data packages

was that both Kai Wang and myself would be both be able to push upstream, and in effect be maintainers. With that in mind, with Kai Wang changed to be the "Maintainer of record", may I retain my ability to push upstream to the repo as well? Thanks, and sorry for any confusion

Re: [Bioc-devel] Please change maintainer of chipenrich and chipenrich.data packages

Thank you. I have one last question: Could we make Kai a co-maintainer, rather than replacing me? Sorry for the mix-up, I was under the impression that only one maintainer was allowed. Thanks again, Raymond On Fri, Feb 26, 2021 at 10:23 AM Nitesh Turaga wrote: > Hi, > > I've

[Bioc-devel] Please change maintainer of chipenrich and chipenrich.data packages

? FWIW, at this page https://bioconductor.org/developers/how-to/git/change-maintainer/ there is a reference to maintai...@bioconductor.org. This was the first addressed I tried, but got various bounce backs. Perhaps the change maintainer page should be updated? Thanks, Raymond Cavalcante

[Bioc-devel] GenomicRanges distanceToNearest() causing issues

Bioconductor team members have any news as to the status of this problem? Thanks, Raymond Cavalcante ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Cannot reproduce Bioc build server errors for annotatr package

Hi Martin, A ha! Thank you for pointing that out. Not sure how that space got in there, but I’ll remove it and hopefully it’ll clear the error. Odd about the reproducibility though… Thanks again, Raymond > On Oct 26, 2017, at 17:34, Martin Morgan <martin.mor...@roswellpark.org>

[Bioc-devel] Cannot reproduce Bioc build server errors for annotatr package

for the Docker image based on the https://hub.docker.com/r/bioconductor/devel_core2/ <https://hub.docker.com/r/bioconductor/devel_core2/> image. I suppose I could change all of my example data to use '*' for the strand, but many peak callers (macs2 being one of the most popular) use the

Re: [Bioc-devel] Devel landing page version not updated after successful build

is being used. Orthogonally, the Travis builds that I have setup for these packages using Rdevel appear to be fine. Thanks for any advice, Raymond Cavalcante > On Apr 11, 2017, at 10:32 AM, Raymond Cavalcante <rcava...@umich.edu> wrote: > > Hello, > > I updated the devel versi

[Bioc-devel] Devel landing page version not updated after successful build

landing page being quicker to update after a successful build, so I wanted to check in to see if I should be patient, if I've made a mistake, or there is something in the background that I need someone's help to fix. Thanks! Raymond Cavalcante [[alternative HTML ver

Re: [Bioc-devel] rtracklayer::import() fails when genome parameter is used

version was installed to test if an update from Friday had fixed the problem. Turns out that problem is still present, but a thread for that is ongoing. In any event, thanks for the quick reply, Raymond > On Feb 6, 2017, at 11:23 AM, Martin Morgan <martin.mor...@roswellpark.org>

Re: [Bioc-devel] rtracklayer::import() fails when genome parameter is used

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 <rcava...@umich.edu> wrote: &

[Bioc-devel] rtracklayer::import() fails when genome parameter is used

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

Re: [Bioc-devel] GenomeInfoDb::Seqinfo() failing with 404 error

Hello, I was wondering if any progress has been made on fixing this? I looked through recent commits for GenomeInfoDb, but there didn't seem to be anything related to this problem. Thanks, Raymond > On Jan 25, 2017, at 23:01, Obenchain, Valerie > <valerie.obench...@roswellpark.o

[Bioc-devel] GenomeInfoDb::Seqinfo() failing with 404 error

.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_01405.13.assembly.txt': > status was '404 Not Found' I'm not sure how to fix this issue, as it seems to be more of an NCBI problem. Any help would be greatly appreciated. Thanks, Raymond Cavalcante ___

Re: [Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?

so queries NCBI to get the mappings to the NCBI >>> seqlevels. Does that really need to happen when only getting the >>> Seqinfo? >>> >>> >>> On Thu, Nov 3, 2016 at 5:13 AM, Raymond Cavalcante >>> <rcava...@umich.edu> wrote: >>>> Hello,

Re: [Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?

, Vincent Carey <st...@channing.harvard.edu> wrote: > > sessionInfo()? > > On Thu, Nov 3, 2016 at 5:13 AM, Raymond Cavalcante <rcava...@umich.edu > <mailto:rcava...@umich.edu>> wrote: > Hello, > > Sometime yesterday calls like GenomeInfoDb::Seqinfo(genome = 'hg19') stop

[Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?

ernet connection (other than to download the package)? BSgenome is too large to require of users just for chromosome lengths. The org.db packages have chromosome lengths, but only with respect to one genome version for that organism, and from the documentation it isn't clear which version

Re: [Bioc-devel] Version on GitHub mirror different than Bioconductor

. There actually some other changes from the acc43cb commit that didn't migrate to Bioc. Sorry for the trouble, but what's the easiest way to fix this? Thanks, Raymond Cavalcante > On Oct 15, 2016, at 08:21, Martin Morgan <martin.mor...@roswellpark.org> > wrote: > >> On 10/15/2

[Bioc-devel] Version on GitHub mirror different than Bioconductor

.99.19 https://bioconductor.org/packages/devel/bioc/html/annotatr.html <https://bioconductor.org/packages/devel/bioc/html/annotatr.html>). I'm not sure what I could do from my end to help solve this, so I'm hoping someone can help me. Thanks, Raymond Cavalcante [[alternative

Re: [Rd] Use GPU in R with .Call

Thank you--Brian for your reponse. I am really curious about how to compile GPU with R. I know it can be hard to learn, but still I want to program it by myself. -- View this message in context: http://r.789695.n4.nabble.com/Use-GPU-in-R-with-Call-tp4637333p4637356.html Sent

[Rd] Use GPU in R with .Call

Hi All, I am a newbie to GPU programming. I wonder if anyone can help me with using GPU in .Call in R. Basically, I want to write a function that calcuates the sum of two double type vectors and implement this using GPU. My final goal is to make such an implementation callable from

Re: [Rd] .Call in R

I agree with Martin that this might not be suitable for a C solution. -- View this message in context: http://r.789695.n4.nabble.com/Call-in-R-tp4080721p4087141.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org

[Rd] .Call in R

Hi R developers, I am new to this forum and hope someone can help me with .Call in R. Greatly appreciate any help! Say, I have a vector called vecA of length 1, I generate a vector called vecR with elements randomly generated from Uniform[0,1]. Both vecA and vecR are of double type.