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cellgeni / schard

reticulate-free single cell format conversion
GNU General Public License v3.0
49 stars 3 forks source link

rhdf5 not available #5

Closed derrik-gratz closed 2 months ago

derrik-gratz commented 2 months ago

Hello, I'm trying to install this package to convert h5ad, but I cannot complete the install as one of the specified dependencies rhdf5 is unavailable. Even if I install it manually prior to installing the package it still cannot install. I created a pull request to resolve the dependency issue via biocviews specification in the description

4

install.packages("bioc::rhdf5")
# Downloading packages -------------------------------------------------------
- Downloading rhdf5 from BioCsoft ...           OK [1.2 Mb in 0.13s]
Successfully downloaded 1 package in 0.33 seconds.

The following package(s) will be installed:
- rhdf5 [2.46.1]
These packages will be installed into "/yerkes-cifs/runs/Analysis/2024_Analyses/p00000_Zachary/analysis/renv/library/R-4.3/x86_64-pc-linux-gnu".

Do you want to proceed? [Y/n]: 
# Installing packages --------------------------------------------------------
- Installing rhdf5 ...                          OK [built from source and cached in 12s]
Successfully installed 1 package in 13 seconds.
> install.packages("cellgeni/schard")
# Downloading packages -------------------------------------------------------
- Downloading schard from GitHub ...            OK [7.6 Kb in 0.58s]
Error: package 'rhdf5' is not available

> install.packages("derrik-gratz/schard")
# Downloading packages -------------------------------------------------------
- Downloading schard from GitHub ...            OK [7.6 Kb in 0.5s]
Successfully downloaded 1 package in 1.6 seconds.

The following package(s) will be installed:
- schard [derrik-gratz/schard@main]
These packages will be installed into "/yerkes-cifs/runs/Analysis/2024_Analyses/p00000_Zachary/analysis/renv/library/R-4.3/x86_64-pc-linux-gnu".

Do you want to proceed? [Y/n]: 
# Installing packages --------------------------------------------------------
- Installing schard ...                         OK [built from source and cached in 4.6s]
Successfully installed 1 package in 4.6 seconds.
iaaka commented 2 months ago

Hi @derrik-gratz, thank you for pointing this out. Indeed bioc instruction didn't work as intended. I replaced it with biocViews according to your suggestions. I committed it along side with some other rearrangements of dependences, so the latest commit include it. So, for simplicity I'll decline your pull request (since it is implemented now) but I'm fully appreciate your help!