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

2018-09-26 Thread Bohdan Khomtchouk
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

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

2018-09-26 Thread 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

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

2018-09-26 Thread 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 wrote: > your annotation hub is out of date. run hub = AnnotationHub() and try > again > > On Wed, Sep 26, 2018 at 3:48 PM,

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

2018-09-26 Thread 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your annotation hub is out of date.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 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

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

2018-09-26 Thread 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): >

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

2018-09-26 Thread Tim Triche, Jr.
hmm, does it make sense to submit the hg19, hg38, and mm10 HMM CpG island predictions to AnnotationHub? R> qhs <- query(ah, "island" ) R> qhs AnnotationHub with 4 records # snapshotDate(): 2018-08-20 # $dataprovider: UCSC # $species: Homo sapiens # $rdataclass: GRanges # additional mcols():

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

2018-09-25 Thread Martin Morgan
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

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

2018-09-25 Thread Bohdan Khomtchouk
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 wrote: > Here it is: >

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

2018-09-25 Thread Bohdan Khomtchouk
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 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

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

2018-09-25 Thread Vincent Carey
(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 wrote: > I need to

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

2018-09-25 Thread Bohdan Khomtchouk
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