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aertslab / SCopeLoomR

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...
MIT License
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Installation error #2

Closed abhisheksinghnl closed 5 years ago

abhisheksinghnl commented 5 years ago

Hi,

I am working on aws and I was trying to install the package. I followed everything as mentioned in the installation steps. I get the following error on the last step:

> install_github("aertslab/SCopeLoomR")
Downloading GitHub repo aertslab/SCopeLoomR@master
Installing 2 packages: hdf5r, rlist
Installing packages into ‘/home/asingh74/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Error: (converted from warning) unable to access index for repository http://www.bioconductor.org/packages/3.6/extra/src/contrib:
  cannot open URL 'http://www.bioconductor.org/packages/3.6/extra/src/contrib/PACKAGES'

How can I fix this error? Please let me now.

dweemx commented 5 years ago

Which R version are you running?

abhisheksinghnl commented 5 years ago

R 3.4.2

dweemx commented 5 years ago

I don't know why it's trying to accessing BioC extra page from Bioconductor 3.6 which is weird because it has been removed from this version. Maybe try to reinstall Bioconductor?

abhisheksinghnl commented 5 years ago

The new BiocManager is available for R3.5 version, till 3.4 biocLite was used. If that is what the problem is?

abhisheksinghnl commented 5 years ago

I solved it by installing it like this

install_github("aertslab/SCopeLoomR", repos = c(CRAN = "https://cran.cnr.berkeley.edu/"))

dweemx commented 5 years ago

Great!