Sorry, indeed you have most of the information that I found through
trial-error-stackoverflow already. Some of these lines when missed cause a lot
of headache. Thanks for pointing again!
Best regards,
Jelena Čuklina.
On 15 Oct 2019, 15:46 +0200, Shepherd, Lori ,
wrote:
Have you looked at the
Have you looked at the extensive git documentation and the FAQ we already have
for reference:
http://bioconductor.org/developers/how-to/git/
There is a page dedicated to BFG:
http://bioconductor.org/developers/how-to/git/remove-large-data/
Nitesh and Herve also commented relating to this back
Thank you Herve,
I finally was able to reproduce the error and solve it. You are right, it was
most probably due to the data.table package.
Interestingly, the problem occurs randomly, with different error messages
(sometimes it is complaining about negative vector size...). I will open an
Thankyou Lori,
Cheers,
Aditya
From: Shepherd, Lori [lori.sheph...@roswellpark.org]
Sent: Tuesday, October 15, 2019 2:22 PM
To: Bhagwat, Aditya; bioc-devel@r-project.org
Subject: Re: Converting gene ids to GRanges - ensembl centric TxDb missing for
human
Again
Tonight is expected to be the last build of the RELEASE_3_9 release branch.
We will be freezing commits to this branch at 3 PM EST today.
Cheers,
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton
Again we would not recommend posting these types of questions to both the
mailing list and the support site.
Since this is not a developer question - the support site was the appropriate
place -
https://support.bioconductor.org/p/125609/
We have members of the team working on developing the
Dear BioC devel,
I want to convert geneids to GRanges by doing:
GenomicFeatures::genes(txdb)[geneids]
Works wonderfully for mouse, with entrezgene as well ensemblgene-centric TxDbs:
txdb <-
TxDb.Mmusculus.UCSC.mm10.knownGene::TxDb.Mmusculus.UCSC.mm10.knownGene
There is no RELEASE_3_10 branch yet. The master branch is the devel 3.10
branch. Once we make that branch we will announce it.
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New
Dear Bioconductor team,
my submission to Release_3_10 branch is declined. Could you please tell why is
that? I can’t submit to master as I need repo reset due to large file cleaning
and history re-writing, is this issue related? Or is it the deadline missed?
Error message:
! [remote rejected]
