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carmonalab / ProjecTILs

Interpretation of cell states using reference single-cell maps
GNU General Public License v3.0
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struggling to load dependencies UCell and scGate #31

Closed ncedi12 closed 2 years ago

ncedi12 commented 2 years ago

Hi all, might I get assistance in troubleshooting the recurrent error I'm getting that prevents me from downloading the dependencies for ProjectTILs

I follow the vignette guideif (!requireNamespace("renv")) install.packages("renv") library(renv) renv::restore() remotes::install_github("carmonalab/UCell") remotes::install_github("carmonalab/scGate") remotes::install_github("carmonalab/ProjecTILs")

remotes::install_github("carmonalab/UCell", ref="v1.3") remotes::install_github("carmonalab/scGate")

I seem to be able to get 'renv

if (!requireNamespace("renv"))

  • install.packages("renv") library(renv) renv::restore()
  • The library is already synchronized with the lockfile.

  • My errors are as follows

Error in file(filename, "r", encoding = encoding) : cannot open the connection Calls: source -> file In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file 'renv/activate.R': No such file or directory Execution halted ERROR: lazy loading failed for package 'UCell' arning messages: 1: In .inet_warning(msg) : package ‘UCell’ is not available for Bioconductor version '3.14'

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 2: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘commonmark’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘maptools’ had non-zero exit status

This is my r version

sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.2.1

mass-a commented 2 years ago

Hello and thanks for reporting this.

Currently UCell is being reviewed to go into Bioconductor, so the installation of the HEAD version may be unstable. In the interim, I suggest you install UCell using a tagged version:

remotes::install_github("carmonalab/UCell", ref="v1.3")

The renv commands are only relevant if you clone the demo repository into your machine, otherwise you can skip those and install the required packages manually.