BiostatR Blog

In terminal: sudo apt-get install libfribidi-dev sudo apt-get install libharfbuzz-dev Then in R install.packages("pkgdown")

# update indices sudo apt update -qq # install two helper packages we need sudo apt install --no-install-recommends software-properties-common dirmngr # import the signing key (by Michael Rutter) for these repo sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 # add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" Here we use lsb_release -cs to access which Ubuntu flavor you run: one of “hirsuite”, “groovy”, “focal”, “bionic”, … Then run sudo apt install --no-install-recommends r-base See:  https://cran.r-project.org/bin/linux/ubuntu/ pkgs <- as.data.frame(installed.packages(), stringsAsFactors = FALSE, row.names = FALSE) pkgs[, c("Package", "Version", "Built")] Will list the packages with their built version. Then you can do: update.packag...

In terminal. You must have MacBrew installed. If not, use: Install macbrew via: /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" Then brew install proj brew install gdal brew install geos sudo R Then in R: library("devtools") install_github("r-spatial/sf", build_opts = c("--with-proj-include=/usr/local/include",                                                "--with-proj-lib=/usr/local/lib"), force=TRUE) And... > packageVersion("sf") [1] ‘0.9.9’

Informations are available here  https://bitbucket.org/nygcresearch/treemix/downloads/ In terminal, enter for  Ubuntu 20.04: wget https://bitbucket.org/nygcresearch/treemix/downloads/treemix-1.13.tar.gz tar -xvf treemix-1.13.tar.gz sudo apt-get install libgsl-dev sudo apt install libboost-dev sudo apt install libboost-all-dev cd treemix-1.13/ ./configure make sudo make install And it works: $ treemix TreeMix v. 1.13 $Revision: 231 $ Options: -h display this help -i [file name] input file -o [stem] output stem (will be [stem].treeout.gz, [stem].cov.gz, [stem].modelcov.gz) -k [int] number of SNPs per block for estimation of covariance matrix (1) -global Do a round of global rearrangements after adding all populations -tf [file name] Read the tree topology from a file, rather than estimating it -m [int] number of migration edges to add (0) -root [string] comma-delimited list of populations to set on one side of the root (for migration) -g [vertices file name] [edges file na...