[Bioc-devel] Error: file larger than 5 Mb.

[Tim Triche, Jr.]

hmm, does it make sense to submit the hg19, hg38, and mm10 HMM CpG island
predictions to AnnotationHub?

R> qhs <- query(ah, "island" )
R> qhs
AnnotationHub with 4 records
# snapshotDate(): 2018-08-20
# $dataprovider: UCSC
# $species: Homo sapiens
# $rdataclass: GRanges
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH5086"]]'

           title
  AH5086 | CpG Islands
  AH5204 | CpG Islands
  AH5344 | CpG Islands
  AH5463 | CpG Islands
R> qhs$title
[1] "CpG Islands" "CpG Islands" "CpG Islands" "CpG Islands"
R> qhs$dataprovider
[1] "UCSC" "UCSC" "UCSC" "UCSC"


There's rather a lot of items that might belong in AnnotationHub (and not
any package) now that I think about it.

Does each type of data need to go through
https://www.bioconductor.org/packages/devel/bioc/vignettes/AnnotationHub/inst/doc/CreateAnAnnotationPackage.html
or can items be submitted directly?

Thanks,

--t


On Wed, Sep 26, 2018 at 1:35 AM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:

> Good news, the file is in AnnotationHub and can be used from there.
> There is a download cost the first time but not subsequently.
>
> library(AnnotationHub)
> hub = AnnotationHub()
> query(hub, "Mus_musculus.GRCm38.93.chr.gtf.gz")
>
> ## note 'AH' number, then...
> gtf = hub[["AH63797"]]
>
> Need the path rather than the imported path? use cache(hub["AH63797"])
> instead.
>
> Martin
>
> On 09/25/2018 09:59 PM, Bohdan Khomtchouk wrote:
> > To generate mouse.rda, I used:
> >
> > library(rtracklayer)
> > mouse <- readGFF("
> >
> ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.chr.gtf.gz
> > ")
> >
> > And then I saved the object as mouse.rda
> >
> >
> > On Tue, Sep 25, 2018 at 6:33 PM Bohdan Khomtchouk <
> khomtchoukmed using gmail.com>
> > wrote:
> >
> >> Here it is:
> >>
> https://github.com/Bohdan-Khomtchouk/geneXtendeR/blob/master/data/mouse.rda
> >>
> >>
> >> On Tue, Sep 25, 2018 at 6:23 PM Vincent Carey <
> stvjc using channing.harvard.edu>
> >> wrote:
> >>
> >>> (resending with reply all -- please reply to this one)
> >>>
> >>> Can you say some more about the content of the file?  Perhaps it can be
> >>> placed in ExperimentHub.  "mouse.rda" is not very descriptive.  is it
> >>> in your github repo?
> >>>
> >>>
> >>> On Tue, Sep 25, 2018 at 6:25 PM, Bohdan Khomtchouk <
> >>> khomtchoukmed using gmail.com> wrote:
> >>>
> >>>> I need to include an important .rda file in the /data folder of my
> >>>> Bioconductor package.  However, this .rda file exceeds 5 Mb in size.
> Do
> >>>> I
> >>>> have any other options besides for deleting it?
> >>>>
> >>>> bohdankhomtchouk$ git push origin master
> >>>>
> >>>> Counting objects: 65, done.
> >>>>
> >>>> Delta compression using up to 8 threads.
> >>>>
> >>>> Compressing objects: 100% (65/65), done.
> >>>>
> >>>> Writing objects: 100% (65/65), 13.79 MiB | 7.62 MiB/s, done.
> >>>>
> >>>> Total 65 (delta 30), reused 0 (delta 0)
> >>>>
> >>>> remote: Error: file larger than 5 Mb.
> >>>>
> >>>> remote:
> >>>>
> >>>> remote:     File name: 'data/mouse.rda'
> >>>>
> >>>> remote:     File size: 12.9 Mb
> >>>>
> >>>> remote:
> >>>>
> >>>> remote: Please see Biocondcutor guidelines
> >>>>
> >>>> remote: https://bioconductor.org/developers/package-guidelines/
> >>>>
> >>>> remote:
> >>>>
> >>>> To git.bioconductor.org:packages/geneXtendeR
> >>>>
> >>>>   ! [remote rejected] master -> master (pre-receive hook declined)
> >>>>
> >>>> error: failed to push some refs to 'git using git.bioconductor.org:
> >>>> packages/geneXtendeR'
> >>>>
> >>>> --
> >>>> Bohdan Khomtchouk, Ph.D.
> >>>> AHA Postdoctoral Fellow, Gozani & Assimes Labs
> >>>> Department of Biology & Department of Medicine
> >>>> Division of Cardiovascular Medicine
> >>>> Stanford University
> >>>> Stanford, CA 94305
> >>>> https://profiles.stanford.edu/bohdan-khomtchouk
> >>>>
> >>>>
> >>>> CONFIDENTIALITY NOTICE: Information contained in this
> me...{{dropped:9}}
> >>>>
> >>>> _______________________________________________
> >>>> Bioc-devel using r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>
> >>>
> >>>
> >>> The information in this e-mail is intended only for t...{{dropped:17}}
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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