[Bioc-devel] ExperimentHub packages offline

2024-03-16 Thread Laurent Gatto via Bioc-devel
Packages that use ExperimentHub to distribute date can use createHubAccessors() - here's the relevant section from `?createHubAccessors`: ‘createHubAccessors(pkgname, titles): ’ This helper is intended to be used by ExperimentHub package developers in their .onLoad() function in zz

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

2024-05-22 Thread Laurent Gatto via Bioc-devel
Dear Vilhelm, If you need to use/share (reasonably large) MS data, you could consider contributing data to the MsDataHub package [1], that is superseding msdata and makes use of ExperimentHub. Feel free to get in touch (ideally opening a GitHub) if this is of interest to you. Best wishes, Lau

[Bioc-devel] Package with restrictive licenses, not suitable for Bioconductor

2024-06-30 Thread Laurent Gatto via Bioc-devel
The Bioconductor contributions guide says: > Licenses restricting use, e.g., to academic or non-profit > researchers, are not suitable for Bioconductor. but we have several packages with restrictive licenses: - RankProd: free for non-commercial users. Non-academic users MUST have requested fro

[Bioc-devel] ExperimentHub ft resource with password

2025-02-06 Thread Laurent Gatto via Bioc-devel
Dear hub developers, dear Lori, Section 7.1 'Hosting Data on a Publicly Accessible Site' from the 'Creating A Hub Package' vignette (HubPub package) [1] describes how to define resources stored on ftp servers. Is there a way to specify a password to download such a resource? The data I would

[Bioc-devel] ExpData in SummarizedExperiment

2025-05-05 Thread Laurent Gatto via Bioc-devel
Dear Hervé, dear maintainers We are bitten by the following issue related to SE and SCE: Using version 1.38.0: ## BiocManager::install("Bioconductor/SummarizedExperiment", ## ref = "a320baea6278ba6d7e6c646f5576ea6e8b6cd732", ## force = TRUE) ## version 1

[Bioc-devel] S4Vectors installation error: no setequal S4 generic

2025-03-05 Thread Laurent Gatto via Bioc-devel
Dear all I am trying to install S4Vectors in a clean R 4.4.3 and 4.4.1 and hit the same issue. Dependencies BiocVersion 3.20.0 and BiocGenerics 0.52.0 install as expected, but S4Vectors 0.44.0 fails with the following error: ** testing if installed package can be loaded from final location Er