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

[Martin Morgan]

maybe you are not using the 'devel' version of Bioconductor?

On 09/26/2018 03:48 PM, Bohdan Khomtchouk 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 
> <mailto: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 <mailto: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 <mailto: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 <mailto: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
>     <mailto: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}}
>      >>>>
>      >>>> _______________________________________________
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>      >>>>
>      >>>
>      >>>
>      >>> The information in this e-mail is intended only for
>     t...{{dropped:17}}
>      >
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