Closed iscastanho closed 2 years ago
Hey,
The q-values are available in 1.4.0 which is released in the bioconductor current branch so try installing with
BiocManager::install("EWCE")
rather than from github. This is available for R 4.1 so should work with your set-up and not installing from github may reduce issues. If this doesn't work I think something else is the issue with your set-up which isn't specific to the package (EWCE installs cleanly on windows mac and linux, this is checked by bioconductor). Have a look at your error message to try and solve this like:
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
So try and install nloptr
prior to installing EWCE. Do this for all dependencies that failed.
The other option is to use a docker image with EWCE installed which we have available here: https://hub.docker.com/r/neurogenomicslab/ewce/tags, The different tags align with the package version.
@iscastanho Conda doesn't have R4.2 yet (it's rather behind), so if you want to use an env I would use the Docker container: https://nathanskene.github.io/EWCE/articles/EWCE.html#docker
As a side note, please use the Issues template when submitting Issues.
Thank you @Al-Murphy for the patience and replies. I solved it by downloading manually from Bioconductor and installing manually using install.packages() in R.
Thank you @bschilder for the suggestion but unfortunately Docker is not an option in the server I am using. I apologize for missing the template, but I initially posted this as a reply to a closed issue and then realized that I should post it as a new issue, and when I used the option "Reference in new issue" no template was shown. I will keep it in mind for future reference. Thank you for pointing this out.
@iscastanho If your server doesn't allow Docker, the same vignette shows how to create a Singularity container (which doesn't have the same security concerns as Docker).
I'm starting a new thread since this is a new issue.
I was missing q-values in
full_results$results
and EWCE functions until I realized that I have been using EWCE 1.2, which I hadn't noticed before because I installed EWCE recently and assumed that a recent version had been installed. I am using conda environments and with R 4.1 I can only seem to be able to install EWCE 1.2. I've created a conda environment with R 4.2 but I sill can't manage to install EWCE 1.4+. If I useconda install -c r bioconductor-ewce
it asks me if I want to revert to R 4.1 (-c bioconda
doesn't seem to have R 4.2 yet, so that obviously didn't work either). if I try to install EWCE in an R session usingBiocManager::install("EWCE")
the installation is not successful and I get similar errors to when I try the GitHub version using devtools that I show below.Originally posted by @iscastanho in https://github.com/NathanSkene/EWCE/issues/44#issuecomment-1172591634