[Bioc-devel] ExperimentHub with AWS

Hi all, I am maintaining a newly added package on Bioconductor (preciseTAD). I am interested in having an accompanying experiment data package where I will be storing approximately ~5gb worth of rds (or Rda) objects. They are currently being stored on a google drive but I would prefer them to be

Re: [Bioc-devel] Git pack file greater than 5MB

Hi all, Thank you all for taking the time to discuss this issue. While the package does have a fairly long history with multiple authors, I am currently the only active developer on the project. So, if it preferable from Bioconductor’s perspective, I will rewrite the repository's history. I

Re: [Bioc-devel] Updating to Python 3: Problem with Importlib library

The script is currently in the root directory of the package ~/b/git$ ls seq2pathway/scripts/ Function_PeakMutationAnnotation_GENCODE_05182015.py Function_PeakMutationAnnotation_GENCODE_08182020.py but needs to be in inst/scripts folder like the earlier version ~/b/git$ ls

Re: [Bioc-devel] Git pack file greater than 5MB

yes Hervé has made this point too -- mucking with the history of the package, potentially breaking historical checkouts (when large files are deleted from the history, too). It's relevant because when a package is added to our repository we do a full clone of the master branch; an alternative

[Bioc-devel] Updating to Python 3: Problem with Importlib library

Hi, I am writing on behalf of the development team for the package seq2pathway. After updating to python 3 and replacing the deprecated imp library with importlib library, we encountered the following problem. Our python code is included in the file

Re: [Bioc-devel] Git pack file greater than 5MB

I understood that it's a submission. Just wanted to make sure that it's clear there might be side effects, e.g. people clone and collaborate also before submitting to Bioc and a rewrite might surprise existing collaborators etc. /H On Thu, Oct 1, 2020, 09:04 Nitesh Turaga wrote: > This package

Re: [Bioc-devel] Git pack file greater than 5MB

This package isn’t yet a Bioconductor package Henrik. It will break other forks most likely. This package hasn’t been submitted to the Contributions either to be reviewed. So this is the time to break what needs to be broken before it’s submitted to Bioconductor and gets into the Bioconductor

Re: [Bioc-devel] Git pack file greater than 5MB

Doesn't a git rewrite break all existing clones, forks out there? I'm happy to be corrected, if this is not the case. /Henrik On Thu, Oct 1, 2020, 08:16 Nitesh Turaga wrote: > Hi, > > The BiocCheck will complain on the build system about the > 5MB package > size. > > The rewrite of the history

Re: [Bioc-devel] Git pack file greater than 5MB

Hi, The BiocCheck will complain on the build system about the > 5MB package size. The rewrite of the history with BFG cleaner (https://rtyley.github.io/bfg-repo-cleaner/ ) is not as severe as you think it is to be honest. It is just removing these

Re: [Bioc-devel] Issue with connecting to 'git.bioconductor.org' during git fetch --all

Most people don’t use passphrase for SSH keys on Bioconductor. But it seems like you do have one or your permissions for the SSH key pair you have are wrong. 1. If you have a passphrase and forgot it, just make a new SSH key and add it to your BiocCredentials account. 2. If it’s a

Re: [Bioc-devel] EXTERNAL: Publickey permission denied

Hello, It was resolved, thank you! I fixed the error on first build report by removing lines causing it. Regards, Émilie Le jeu. 1 oct. 2020 à 14:37, Interdonato, Kayla < kayla.morr...@roswellpark.org> a écrit : > Hello, > > I am assigned as the reviewer for this package. I see a valid push on

Re: [Bioc-devel] EXTERNAL: Publickey permission denied

Hello, I am assigned as the reviewer for this package. I see a valid push on the issue and a build report was produced. Is it safe to assume this was resolved or are you still experiencing issues? If you want to comment on the issue directly I'd be happy to help you with any further problems

[Bioc-devel] Issue with connecting to 'git.bioconductor.org' during git fetch --all

Hi Bioconductor, Wanted to clarify a small issue before continuing with a package update. I just added a new SSH key to biocredentials and my github account. It seems to have worked fine, but I got a warning when I tried to fetch. I have copied the output from git remove -v and git fetch --all

Re: [Bioc-devel] SSL error on Ubuntu 20.04

Hi Lara, I've encountered this issue with biomaRt too. I found I could get the connection to work with the following: library(httr) url <- "https://www.ensembl.org/; httr_config <- config(ssl_cipher_list = "DEFAULT@SECLEVEL=1") res <- with_config(config = httr_config, GET(url)) I haven't

[Bioc-devel] Publickey permission denied

Hello, I submitted my package to Bioconductor yesterday. I had an error to fix, once fixed I wanted to push the updated package to g...@git.bioconductor.org: packages/famat. So i used these command lines (which both worked) : - git remote add upstream g...@git.bioconductor.org:packages/famat.git