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

Bohdan Khomtchouk khomtchoukmed @ending from gm@il@com
Thu Sep 27 00:12:08 CEST 2018 

Looks like that was the issue, thanks Vincent & Martin!

> hub = AnnotationHub()
snapshotDate(): 2018-08-20
> isDevel()
[1] TRUE

> query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
AnnotationHub with 1 record
# snapshotDate(): 2018-08-20
# names(): AH63797
# $dataprovider: Ensembl
# $species: Mus musculus
# $rdataclass: GRanges
# $rdatadateadded: 2018-07-31
# $title: Mus_musculus.GRCm38.93.chr.gtf
# $description: Gene Annotation for Mus musculus
# $taxonomyid: 10090
# $genome: GRCm38
# $sourcetype: GTF
# $sourceurl: ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus...
# $sourcesize: 29183870
# $tags: c("GTF", "ensembl", "Gene", "Transcript", "Annotation")
# retrieve record with 'object[["AH63797"]]'


On Wed, Sep 26, 2018 at 2:01 PM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:

> 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}}
> >      >>>>
> >      >>>> _______________________________________________
> >      >>>> Bioc-devel using r-project.org <mailto: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 <mailto:Bioc-devel using r-project.org>
> >     mailing list
> >      > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >      >
> >
>

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