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

[Bohdan Khomtchouk]

Just did, same result:

> hub = AnnotationHub()
snapshotDate(): 2018-04-30

I re-installed AnnotationHub package as well.


On Wed, Sep 26, 2018 at 1:16 PM Vincent Carey <stvjc using channing.harvard.edu>
wrote:

> your annotation hub is out of date.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
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>>> >
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>>
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