[Bioc-devel] Issue with Bug fix push in devel branch

Hi all, I am just after pushing a bug fix to the current release branch (RELEASE_3_13) and the current devel branch for Bioconductor 3.14. A build was attempted for Bioc 3.14 for which the report is here: https://bioconductor.org/checkResults/3.14/bioc-LATEST/EWCE/riesling1-buildsrc.html. The

[Bioc-devel] Push bug fix to release branch

Hi, I have a package EWCE(https://github.com/NathanSkene/EWCE) that was newly published in Bioconductor in version 3.13. The release package version number is 1.0.0. However, I have identified a bug in the package and need to push the fix to the current release version and the devel version.

Re: [Bioc-devel] Add dockerhub push to github repository

_________ From: Nuno Agostinho Sent: 03 June 2021 20:15 To: Murphy, Alan E Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Add dockerhub push to github repository Hey Alan, is that installing the master branch or the current branch that has been pushed to? It is base

Re: [Bioc-devel] Add dockerhub push to github repository

cFlow package # Copy description WORKDIR scFlow ADD . . # Install R package from source RUN Rscript -e "remotes::install_local()" RUN rm -rf * Cheers, Alan. From: Nuno Agostinho Sent: 03 June 2021 11:57 To: Murphy, Alan E Cc: bioc-devel@r-project.org

[Bioc-devel] Add dockerhub push to github repository

Hi all, I'm working on developing an R package with the aim to eventually submit to Bioconductor. I would like to automatically create a new image and push to dockerhub with github actions when I push changes to the github repository. Does anyone have an example of this process in their

Re: [Bioc-devel] Bioconductor nightly build fail - ewceData not available for EWCE

and nebbiolo1, oddly riesling1 passed checks. If anyone knows why this could be happening or if it is likely to sort itself in the next build please let me know! Thanks, Alan. From: Murphy, Alan E Sent: 27 April 2021 10:23 To: bioc-devel@r-project.org Subject

[Bioc-devel] Bioconductor nightly build fail - ewceData not available for EWCE

Hi all, My recently accepted package EWCE(https://github.com/Bioconductor/Contributions/issues/1904) failed its first nightly build (https://bioconductor.org/checkResults/3.13/bioc-LATEST/EWCE/nebbiolo1-install.html) because the related data package ewceData, which was also recently accepted,

[Bioc-devel] Phase 3 1000 genomes reference genome

Hi all, I am looking for the 1000genomes Phase3 Reference Genome Sequence (equivalent to the Phase 2 version would be useful: BSgenome.Hsapiens.1000genomes.hs37d5 https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.1000genomes.hs37d5.html). The dataset I'm looking

[Bioc-devel] R CMD CHECK time out on Windows machine

Hi all, I am submitting [EWCE](https://github.com/NathanSkene/EWCE) to bioconductor and have been working to reduce the runtime of the R CMD Check which was causing issues. I have improved the run time and locally, on my mac, it is now running in 11m 56.5s. However, I still get a timeout error

Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor

. From: David Jimenez-Morales Sent: 06 April 2021 17:53 To: Andris Jankevics Cc: Murphy, Alan E ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor This email from biodavi...@gmail.com originates from outside Imperial

[Bioc-devel] Best practice use pkgdown, docker with Bioconductor

Hi all, I'm working on the development of (EWCE)[https://github.com/NathanSkene/EWCE] and have a question regarding a reviewer note. My package currently uses pkgdown to create a website through the master branch. I also create and push a new docker image from the main branch when the package

Re: [Bioc-devel] Package failed build on Windows - couldn't load related ExperimentHub dataset

that the check is more stringent on time than that of the Linux and Mac? Or what could be causing this? Kind regards, Alan. From: Herv� Pag�s Sent: 26 March 2021 16:13 To: Murphy, Alan E ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Package failed build on Windows

Re: [Bioc-devel] Package failed build on Windows - couldn't load related ExperimentHub dataset

4.34 0.256.11 Kind regards, Alan. From: Herv� Pag�s Sent: 25 March 2021 22:53 To: Murphy, Alan E ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Package failed build on Windows - couldn't load related ExperimentHub dataset *** This

[Bioc-devel] Package failed build on Windows - couldn't load related ExperimentHub dataset

Hi all, I am working on the development of [EWCE](https://github.com/NathanSkene/EWCE) which I am currently trying to get accepted to [Bioconductor](https://github.com/Bioconductor/Contributions/issues/1904#). Upon sumission checks, there still seems to be a Windows specific issue running

Re: [Bioc-devel] Methods to speed up R CMD Check

Kind regards, Alan. ________ From: Herv� Pag�s Sent: 23 March 2021 19:08 To: Murphy, Alan E ; Martin Morgan ; Kern, Lori ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Methods to speed up R CMD Check Doesn't really matter where you put them but .my_intern

Re: [Bioc-devel] Methods to speed up R CMD Check

_ From: Herv� Pag�s Sent: 23 March 2021 17:31 To: Murphy, Alan E ; Martin Morgan ; Kern, Lori ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Methods to speed up R CMD Check 3 ways to do this, one that doesn't work, and two that work ;-) 1. Simple way that doesn't work:

Re: [Bioc-devel] Methods to speed up R CMD Check

ons, examples, tests and the vignette so eh it would need to be available to all. Sorry I don't have much experience using experiment datasets. Kind regards, Alan. From: Herv� Pag�s Sent: 23 March 2021 16:46 To: Murphy, Alan E ; Martin Morgan ; Kern, Lori ; bioc-deve

Re: [Bioc-devel] Methods to speed up R CMD Check

__________ From: Martin Morgan Sent: 22 March 2021 18:17 To: Kern, Lori ; Murphy, Alan E ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Methods to speed up R CMD Check (sticking bioc-devel back in the recipient list so others can learn / improve / disagree with this suggestion.) my

[Bioc-devel] Methods to speed up R CMD Check

Hi all, I am working on the development of [EWCE](https://github.com/NathanSkene/EWCE) but have hit an issue with R CMD check's runtime. I have been informed this test needs to be completed in 15 minutes but mine is currently running in ~24 minutes and I am looking for methods to speed this

Re: [Bioc-devel] Removal of large items in git history - BiocCheck warning

Hey Mike, Thank you very much for the suggestion, this worked perfectly. I'll definitely be stealing this code for future reference. Kind regards, Alan. From: Mike Smith Sent: 09 March 2021 11:14 To: Murphy, Alan E Cc: bioc-devel@r-project.org Subject: Re

Re: [Bioc-devel] Removal of large items in git history - BiocCheck warning

t; how would I go about checking (and removing?) hidden files from the .git/objects/pack history? Kind regards, Alan. From: stefano Sent: 08 March 2021 22:18 To: Nitesh Turaga Cc: Murphy, Alan E ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Removal of

[Bioc-devel] Removal of large items in git history - BiocCheck warning

Hi all, I am working on the development of EWCE for submission to Bioconductor. I have removed some large objects from the package and moved them to a separate ExperimentHub package however, after their removal, I got a BiocCheck large file warning. To

Re: [Bioc-devel] ExperimentHub package development - Windows OS specific error

. From: Gavin Lloyd Sent: 03 March 2021 09:35 To: Murphy, Alan E ; bioc-devel@r-project.org Subject: Re: ExperimentHub package development - Windows OS specific error I did not get this error on my Windows machine; ExperimentHub can find the alzzh_gwas_top100 dataset

Re: [Bioc-devel] ExperimentHub package development - Windows OS specific error

sign(xx, func, envir=ns) namespaceExport(ns, xx) }) I checked and objs does contain the correct list of titles so the issue isn't there. Sorry about the continuation in the question but does anyone know why this could be happening? Kind regards, Alan.

[Bioc-devel] ExperimentHub package development - Windows OS specific error

Hi all, My apologies, I have emailed before on a related issue but now think I have found a potential cause of the issue I am having but can't seem to find a fix. I am working on an ExperimentHub data package; ewceData, which fails checks on Windows

[Bioc-devel] Formatting of ExperimentHub Data in package

Hi all, I am trying to format my data.R file in an ExperimentHub package but have ran into issues when running checks. Note that my data package has a load function; zzz.r, so datasets can be called as such dataset_name(). An example of one dataset in my data.R file is ``` #' All MGI gene

[Bioc-devel] Issue removing large data files from git history

Hi, I have recently moved my data to an ExperimentHub package and thus need to clean my statistical package's git history. I followed the guides from both the Bioconductor help page and BFG cleaner pages: https://bioconductor.org/developers/how-to/git/remove-large-data/

[Bioc-devel] Reference ExperimentHub package in statistical package

Hi, I have submitted an ExperimentHub package ewceData to Bioconductor's Github for consideration here. I am next going to append a link to my statistical package repository once the status is updated to 'review in progress'. I am

[Bioc-devel] EWCE Bioconductor package

Hi all, My apologies in advance if this is not the correct mailing list for this question, regarding development to the EWCE Bioconductor package. I work as part of Dr. Nathan Skene's group who submitted the package EWCE to