Thanks, Sean and all, for the fix. I have updated both devel and release
versions. Hopefully, the error will be gone in the next build process.
Best,
Jack Zhu
From: Sean Davis
Date: Tuesday, December 3, 2024 at 11:36 AM
To: Kern, Lori
Cc: bioc-devel@r-project.org , Zhu, Jack (NIH/NCI)
[E]
Hi Pariksheet,
Thanks for pointing this out.
I have created an issue regarding this scenario here:
https://github.com/Bioconductor/pkgrevdocs/issues/130
and we will add more details at https://contributions.bioconductor.org
To answer your question, yes, the package should be updated in the
rele
Hi Tulip,
I'm glad you are maintaining groHMM; I previously had not got much response
from contributing bug fixes, so you may be interested in looking at and maybe
integrating my fork: https://github.com/coregenomics/groHMM where the NEWS file
summarizes the changes. There is also a test suite
You need to commit your changes to g...@git.bioconductor.org, which you
apparently have not done as yet (you should have g...@git.bioconductor.org set
up as a remote which you can see by doing git remote -v). The last commit is
Jennifer Wokaty bumping the version for the last release:
/groHMM$
Hi,
I edited the file based on Mike' s suggestion on the git page (image1) but
doesn't seem to reflect when I clone the file using the git clone bioconductor
package yet. Can someone confirm it will be done and nothing else I have to do
from my end.
Let me know.
Regards,
Tulip.
___
Dear Bioc team,
I am seeing check errors on nebbiolo1 and palomino7 and build and install
error on kunpeng2 for my package "seqArchR". The check errors are due to
the missing Python module scikit-learn, and others are due to dependencies
not being available. I believe this is being looked into by
Sorry, all, for not getting to this sooner.
R.utils::gunzip() is a replacement. I created PRs for those changes, but I
didn't test them. Let me know how it goes.
Sean
On Tue, Dec 3, 2024 at 10:31 AM Kern, Lori via Bioc-devel <
bioc-devel@r-project.org> wrote:
> gunzip function was removed from
You could just grab Sean's version from his GEOquery GitHub and put the
function in your package.
https://github.com/seandavi/GEOquery/commit/b3f81349f937870ae030757b454a02fa759b4da7
Best,
Jim
-Original Message-
From: Bioc-devel On Behalf Of Zhu, Jack
(NIH/NCI) [E] via Bioc-devel
Se
Thanks, Lori. I will work on it. Any suggestions from others will be
appreciated.
Best,
Jack Zhu
From: Kern, Lori
Date: Tuesday, December 3, 2024 at 10:30 AM
To: bioc-devel@r-project.org , Zhu, Jack (NIH/NCI)
[E]
Subject: Re: [EXTERNAL] SRAdb problems reported in the Multiple platform
bui
gunzip function was removed from GEOquery. See
https://code.bioconductor.org/browse/GEOquery/commit/b3f81349f937870ae030757b454a02fa759b4da7
So you will either have to find a replacement function or implement your own.
Lori Shepherd - Kern
Bioconductor Core Team
Roswell Park Comprehensive Can
Hi,
I have been trying to fix the following error from the SRAdb building process
at Bioconductor servers:
* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘SRAdb’ ...
** using staged installation
** R
** inst
** byte-compile and prepare packag
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