[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 [[al

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

eason. 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 > wrote: > >> On 10/15/2016 07:53 AM, Raym

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

at doesn't require an internet 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 documentatio

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

t 08:19, Vincent Carey wrote: > > sessionInfo()? > > On Thu, Nov 3, 2016 at 5:13 AM, Raymond Cavalcante <mailto:rcava...@umich.edu>> wrote: > Hello, > > Sometime yesterday calls like GenomeInfoDb::Seqinfo(genome = 'hg19') stopped > working with the error: >

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

s 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 >>> wrote: >>>> Hello, >>>> >>>> Somet

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

x27;https://ftp.ncbi.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() failing with 404 error

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'm suddenly encountering err

[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('ex

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 wrote: > > Hello

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

to > manage your packages) and report on whether this solves your problem. > > Martin > >> >> Thanks again, >> Raymond >> >>> On Feb 6, 2017, at 10:10 AM, Raymond Cavalcante wrote: >>> >>> Hello, >>> >>> Perha

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

the 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 [[alter

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

ta 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 wrote: > > Hello, > > I updated the devel version of chipenrich

[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 ima

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

017 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/checkResults/devel/bioc-LATEST/annotatr/&

[Bioc-devel] chipenrich bioc builds timeout not reproducible

particularly helpful. It seems to hang at vignette building. Any help would be appreciated, thanks, Raymond Cavalcante [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Duplicate commit error when pushing to annotatr upstream/master

github- <https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github->), but there is a note "This works only if you haven’t pushed the change causing the issue to the Bioconductor repository." I fall into this case. If anyone has any suggestio

[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

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

steps? 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 Caval

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

t; Nitesh > > 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 > chipenric

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

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 Biom