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

[Bohdan Khomtchouk]

Martin, I don't see it unfortunately:

> query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
AnnotationHub with 0 records
# snapshotDate(): 2018-04-30

But perhaps it needs to be added to AnnotationHub, because I see other
.chr.gtf files that go up to 86 (while I'm using 93 in this original post):

> query(hub, c("GTF", "Mus musculus", ".chr.gtf"))
AnnotationHub with 112 records
# snapshotDate(): 2018-04-30
# $dataprovider: Ensembl
# $species: Mus musculus
# $rdataclass: GRanges
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
#   tags, rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH50868"]]'

            title
  AH50868 | Mus_musculus.GRCm38.84.chr.gtf
  AH51038 | Mus_musculus.GRCm38.85.chr.gtf
  AH51979 | Mus_musculus.GRCm38.86.chr.gtf
  AH51983 | Mus_musculus_129s1svimj.129S1_SvImJ_v1.86.chr.gtf
  AH51986 | Mus_musculus_aj.A_J_v1.86.chr.gtf
  ...       ...
  AH61202 | Mus_musculus_lpj.LP_J_v1.92.chr.gtf
  AH61205 | Mus_musculus_nodshiltj.NOD_ShiLtJ_v1.92.chr.gtf
  AH61208 | Mus_musculus_nzohlltj.NZO_HlLtJ_v1.92.chr.gtf
  AH61211 | Mus_musculus_pwkphj.PWK_PhJ_v1.92.chr.gtf
  AH61214 | Mus_musculus_wsbeij.WSB_EiJ_v1.92.chr.gtf

So it looks like "AH51979 | Mus_musculus.GRCm38.86.chr.gtf" is the latest
one available in AnnotationHub right now.


On Tue, Sep 25, 2018 at 10:35 PM 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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