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

. Raymond -------- Raymond Cavalcante, PhD Bioinformatics Analyst Epigenomics Core and Bioinformatics Core Biomedical Research Core Facilities University of Michigan Medical School rcava...@umich.edu rcava...@med.umich.edu On Fri, Feb 26, 2021 at 10:33 AM Nitesh Turaga wrote: > Yes, only one maintain

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

tesh > > On 2/25/21, 4:19 PM, "Bioc-devel on behalf of Raymond Cavalcante" < > bioc-devel-boun...@r-project.org on behalf of rcava...@umich.edu> wrote: > > Hello, > > Could we please change the maintainer of the chipenrich and > chipenrich.dat

[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

> wrote: > > On 10/23/2017 09:22 AM, Raymond Cavalcante wrote: >> Hello all, >> I’m getting some CHECK errors in the examples and tests for the annotatr >> package (http://bioconductor.org/checkResults/devel/bioc-LATEST/annotatr/ >> <http://bioconductor.org/chec

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

Hello all, I’m getting some CHECK errors in the examples and tests for the annotatr package (http://bioconductor.org/checkResults/devel/bioc-LATEST/annotatr/ ) that I cannot reproduce using the bioconductor/devel_core2 Docker

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

> wrote: > > 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” >

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

rg> wrote: > > Thanks for the report. It looks like the directory structure has > changed. I'll work on this tomorrow and will post back when it's fixed. > > Valerie > > >> On 01/25/2017 06:29 PM, Raymond Cavalcante wrote: >> Hello, >> >> I'

[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