Installation issues

Common installation issues

This page lists issues when installing the cytomapper package on different operating systems.

Ubuntu 20.04

This section addresses installation issues on a clean ubuntu 20.04 system.

First, the newest R version needs to be installed (R v4.1 at the time of writing):

sudo apt-get update
sudo apt install dirmngr gnupg apt-transport-https ca-certificates software-properties-common
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
sudo apt install r-base

These instructions were taken from here.

Next, install the needed system libraries:

sudo apt-get install libfftw3-3 libfftw3-dev libtiff5-dev libfontconfig1-dev libcurl4-openssl-dev

Installing the release version

1. Install BiocManager

install.packages("BiocManager")

2. Install cytomapper

BiocManager::install("cytomapper")

Installing the development version

Installing from Bioconductor

1. Install BiocManager

install.packages("BiocManager")

2. Install the Bioconductor development branch

BiocManager::install(version = "devel")

3. Install cytomapper

BiocManager::install("cytomapper")

Installing from Github

Prior to installing cytomapper with building the vignettes, the following steps need to be taken:

1. Install system libraries

sudo apt-get install libssl-dev pandoc pandoc-citeproc

2. Install remotes

In a new R session, type:

install.packages("remotes")

3. Install cytomapper from Github

remotes::install_github("BodenmillerGroup/cytomapper", build_vignettes = TRUE, dependencies = TRUE)