TL;DR

First consulted this page

I have R-4.0.5 with Bioconductor 3.12(4.0), use the latest scripts for installation.

In Rstudio:

> if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
> BiocManager::version()
> # If your bioconductor version is previous to 4.0, see the section bellow
> 
> ## Required
> BiocManager::install(c("AUCell", "RcisTarget"))
> BiocManager::install(c("GENIE3")) # Optional. Can be replaced by GRNBoost
> 
> ## Optional (but highly recommended):
> # To score the network on cells (i.e. run AUCell):
> BiocManager::install(c("zoo", "mixtools", "rbokeh"))
> # For various visualizations and perform t-SNEs:
> BiocManager::install(c("DT", "NMF", "ComplexHeatmap", "R2HTML", "Rtsne"))
> # To support paralell execution (not available in Windows):
> BiocManager::install(c("doMC", "doRNG"))
> > # To export/visualize in http://scope.aertslab.org
> if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
> devtools::install_github("aertslab/SCopeLoomR", build_vignettes = TRUE)

These worked fine.

Then, when installing SCENIC using devtools:

> if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
> devtools::install_github("aertslab/SCENIC") 
Downloading GitHub repo aertslab/SCENIC@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  download from 'https://api.github.com/repos/aertslab/SCENIC/tarball/HEAD' failed

Tried several times with no success.

There are some discussions on this behavior with devtools and remotes, for example this issue, but I find it un-straightforward.

Instead, I decided to switch to SCENIC(R) github page and install directly from there. First tried directly cloning the repo:

$ git clone https://github.com/aertslab/SCENIC.git
Cloning into 'SCENIC'...
fatal: unable to access 'https://github.com/aertslab/SCENIC.git/': Could not resolve host: github.com

This also failed!

Then tried Download ZIP to local and unzip SCENIC-master.zip. Create a new project in Rstudio from the directory containing SCENIC build and hit the Install and Restart button.

This also failed because of an error of the sort “Dependency ‘dynamicTreeCut’ not available”, but this won’t be very difficult to solve.

Install dynamicTreeCut manually:

> install.packages("dynamicTreeCut")
Warning in install.packages :
  unable to access index for repository https://cran.rstudio.com/src/contrib:
  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Installing package into ‘/home/luolab/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
Warning in install.packages :
  unable to access index for repository https://cran.rstudio.com/src/contrib:
  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning in install.packages :
  package ‘dynamicTreeCut’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

To fix this, in Rstudio go to Tools > Global Options > Packages and Uncheck Use secure download method for HTTP. Then:

> install.packages("dynamicTreeCut")
Installing package into ‘/home/luolab/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/dynamicTreeCut_1.63-1.tar.gz'
Content type 'application/x-gzip' length 24027 bytes (23 KB)
==================================================
downloaded 23 KB

* installing *source* package ‘dynamicTreeCut’ ...
** package ‘dynamicTreeCut’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dynamicTreeCut)

The downloaded source packages are in
	‘/tmp/RtmpgfV9Bj/downloaded_packages’

Success!

Now Install and Restart SCENIC again and everything worked.

Next job is to import pySCENIC results to R SCENIC, consult the followings:

P.S.

When trying to push this post to github remote, failed again…

$ git push -u --all
fatal: unable to access 'https://github.com/RuiyuRayWang/blog.git/': Could not resolve host: github.com

Looks like we’re having a bad day with github server…

Last modified on 2021-12-22