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

[Vincent Carey]

your annotation hub is out of date.  run hub = AnnotationHub() and try again

On Wed, Sep 26, 2018 at 3:48 PM, Bohdan Khomtchouk <khomtchoukmed using gmail.com>
wrote:

> 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}}
>> >
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>> >
>>
>

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