Skip to content

Latest commit

 

History

History
62 lines (56 loc) · 3.18 KB

RequiredSoftware.md

File metadata and controls

62 lines (56 loc) · 3.18 KB
Raw

Required software

Here is a list of software that not everyone may have installed, but we are going to use, and that thus should be installed in advance. We can save a lot of time and trouble if you install this beforehand, often you will many programs installed already anyway. Also I am not sure how fast the connection will be if we all start downloading the first day.

Software to be installed in advance on your computer

  • Latest version of R (version 3.3.1)

  • Git

    • you will also need a github account

  • Decent text editor for R (Rstudio, Emacs + ESS)

  • LaTeX (Miktex on windows, package texlive on linux)

  • C/C++ compiler:

    • For windows, install Rtools
    • For mac, install XCode
    • For linux, everything should be up and running.

  • R Packages:

    • Essential for R package development, and for installing non-CRAN (Github) packages: devtools, testthat, maggrittr. You can install packages using the install.packages command inside R:
        install.packages(c("devtools", "testthat", "magrittr"))
    • Documentation (vignettes, practicals, tutorials): knitr
    • Plotting: ggplot2, rgl
    • phylogenetics: ape, phangorn, phytools, pegas, Rphylip, coalescentMCMC and some packages are hosted at the Biocoductor repository:
        source("https://bioconductor.org/biocLite.R")
    biocLite(pkgs=c("Biostrings", "seqLogo", "ggtree"))

    To automatically install all (most) phylogenetic packages on CRAN you can use the ctv package. This will take some time, so ensure you have a fast internet connection and your laptop is connected to power:

        install.packages("ctv")      
    library("ctv")      
    install.views("Phylogenetics")

    To check that you can install and compile programs you can try to install the latest phangorn version from github:

       devtools:::install_github("KlausVigo/phangorn")

    Some make users may encounter a problem installing phangorn from github. Apparently, Xcode does not install all the necessary Fortran libraries. So, if you receive the following error message:

        ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
    ld: library not found for -lgfortran
    clang: error: linker command failed with exit code 1 (use -v to see invocation)
    make: *** [phangorn.so] Error 1
    ERROR: compilation failed for package ‘phangorn’
    * removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/phangorn’
    Error: Command failed (1)

    You need to install Fortran. From the your terminal application, this can be done with the two following lines. Notice: you will need admin status to do it.

        curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
    sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /

    Now, when you try to reinstall phangorn again, you should success.