Skip to content

Latest commit

 

History

History
87 lines (62 loc) · 2.91 KB

faqs.md

File metadata and controls

87 lines (62 loc) · 2.91 KB
layout title
default
FAQs

{::options parse_block_html="true" /}

<style> h1, .h1, h2, .h2, h3, .h3, h4, .h4 { margin-top: 50px } p.caption {font-size: 0.9em;font-style: italic;color: grey;margin-right: 10%;margin-left: 10%;text-align: justify} </style>

Frequently asked questions

We recommend that you follow the pre-course installation instructions, which should avoid most bugs. As the tutorial is time limited, we will not be able to assist you in debugging your installations during the hands-on sessions.

Bugs and potential solutions

`> I've installed everything through conda. Should I install instead the docker containers?`

Yes, this is strongly recommended as it will avoid many bugs.

`> But I'd like to keep using conda. What are common ways to solve most bugs?`

Here are some helpful tips that may assist in solving installation problems or package-related bugs:

  • deactivate the environment if applicable;
  • clean cache with conda clean -a -y;
  • re-install the specific environment;
  • if the problem persists, consider installing the problematic package reported in the bug from terminal with mamba install -c conda-forge [package name] --force-reinstall. If you get an error Problem: nothing provides requested [package name please search for it in anaconda cloud and change the channel accordingly (e.g. one of -c [bioconda | r | rdonnelly ]);
  • if the problem still persists, consider installing it manually within R from CRAN or bioconductor. You'll find all packages used at the end of each notebook and html file.
`> Command line developer tools not found (OSX)`

If you don't yet have Mac OSX command line developer tools, please install it using:

xcode-select --install
`> rstudio crashes upon opening`

In terminal try to open R by typing: r. Examine the returned error.

`> unable to load shared object '.../R/library/igraph/libs/igraph.dylib'`

In terminal, run

mamba install -c conda-forge igraph --force-reinstall
`> dyld: Library not loaded: @rpath/libncurses.6.dylib`

In terminal run

mamba install conda-forge::ncurses
`> mofapy package not found.`

Please install it from R with

library(reticulate)
use_condaenv(condaenv='ismb_dr_ui_na')
`> MOFA bugs`

Refer to the MOFA repository.