RADseq Genomics in R

Time to allow: ETA ~30-45 min for experience users, 1h-2h for novices

This vignette purposes is to show users how to setup their computers for RADseq genomic analysis inside R. It targets users of my packages or workshops.

The vignette as an Installation problems section, browse through it if your experiencing installation issues.

The vignette is also usefull if your:

conducting imputations
using simulations with grur and it’s dependencies or simulations with strataG.
specific installation instructions for:
rmetasim
XGBoost
LightGBM
randomForestSRC
ranger
missRanger
pcaMethods
how to have OpenMP enabled specific packages. R packages that requires to run in parallel for the imputations (e.g. fstcore, fst, data.table).

I’m currently merging information also found in this tutorial

macOS

Warning: package management software Homebrew and/or MacPorts :

My experience with these packages is that at some point they will be unreliable with genomic software installation. It might do the trick for some software, but eventually you will lose a lot of time trying to figure out what’s your problem.

In this vignette I present brewless options only.

Update your OS

the current version is macOS Sequoia 15.1
how to update

Get administrator and root user access

Make sure you have administrator and root user access to your computer how.

Apple’s Command Line Tools

Make sure it’s installed…if not, follow instructions. Although the prompt message may be a bit confusing, just click install.

xcode-select --install

Notes:

If command line tools is already installed you’ll get this message xcode-select: error: command line tools are already installed, use "Software Update" to install updates
to test if you have a compiler, you can also type: make in the terminal, if it’s installed you will have something similar to this *** No targets specified and no makefile found. Stop.

Terminology:

Reading: to understand the basic steps to install software with the terminal (configure, make and sudo make install steps)
./configure: configure everything before installation
make: connect libraries and the source before make install (doc)
make install: use to build (compile) source code to create binary files and install the application on our system as configured using ./configure, usually in /usr/local/bin.

Compiler

Apple can’t ship GNU Compiler Collection (GCC) with OpenMP enabled, similar story with Clang the other compiler used in macOS. Consequently, both need to be updateed manually if you want to run software that ues parallel computing (like stacks).

The command below fro both GCC and Clang will:

change directory to your downloads
download the compiler’s binaries
uncompress and move folders (bin, include, lib, libexec and share) of the compiler on your computer /usr/local directory.
remove the downloaded file
check the version of gcc

Update GCC

Choose the binary version number based on your OS and change the version accordingly link.

Sonoma gcc-14.1-m1-bin.tar.gz

#In Terminal
cd Downloads
sudo tar -zxvf gcc-14.1-m1-bin.tar.gz -C /usr/local --strip-components=2

sudo rm gcc-14.1-m1-bin.tar.gz
gcc -v

Update Clang

We want clang compiler with OpenMP enabled. The latest version is 19.1.3.

#In browser make sure you know if your mac as an Intel or Mac chips (M1, M2, etc)
https://github.com/llvm/llvm-project/releases/download/llvmorg-19.1.3/LLVM-19.1.3-macOS-X64.tar.xz
#In Terminal
cd Downloads
sudo tar -xzvf LLVM-19.1.3-macOS-X64.tar.xz -C/usr/local --strip-components=1

sudo rm LLVM-19.1.3-macOS-X64.tar.xz
clang -v

PATH

The shell start up script and PATH to programs**

To make things a little easier to talk to your computer, each time you open the Terminal a shell start up scripts tells your computer where to look for programs. The path for your programs can be modified in your shell start up script. When your computer is searching for programs, it looks into these path:

$PATH

The output should look like this: /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin. But sometimes, it will also say: No such file or directory (no worries, see below).

Use the pwd command to know exactly where you are!

The name of the shell startup file differs across platforms. Depending on OS it is called ~/.bash_profile and sometimes ~/.profile. Filename beginning with a dot “.” are reserved for the system and are invisible in the mac Finder.

Find your shell start up script with the following command:

ls -al ~ | grep profile

If this returns nothing (blank), you don’t have a shell start up script. Create one with this command

sudo touch $HOME/.bash_profile

To modify, you can use BBEdit to open or make and modify hidden items (using the option Show hidden items on the open file screen). Look for the free version. With Linux, use Vi!

Copy/paste the line below in your .bash_profile file:

PATH="$PATH:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"

After modifying your shell start up script always run the command source ~/.bash_profile to reload it.

Useful tools

Below are useful but not essential software you will like to have on your mac.

BBEdit

This is TextWrangler replacement and is a free text editor that will help you save time. Once installed, go in the Apple Menu bar -> BBEdit -> Install Command Line

pip

This is a Python installer tool that I highly recommend. To install or upgrade pip, securely download get-pip.py.

Run this from you Terminal:

cd ~/Downloads
sudo python get-pip.py

If you get command not found you might not have python installed.

pip install -U pip   # to upgrade

sudo rm -R ~/Downloads/get-pip.py # to remove the downloaded file

Linux

Make sure you have GCC and CLANG with OpenMP enabled. Several flavors available, check for the proper link

Install R

To install R v4.4.2 “Pile of Leaves” released on 2024-10-31 download the installer and follow the instructions

# for macOS
cd Downloads
curl -O https://cran.r-project.org/bin/macosx/R-4.4.2.pkg

To remove R completely from macOS

sudo rm -rf /Library/Frameworks/R.framework /Applications/R.app \
/usr/bin/R /usr/bin/Rscript

Rstudio

To download RStudio, check this link and download the installer for your OS.

Installing Libraries

Below is how I setup most of my computers after a clean macOS install. 1. Start with devtools and tidyverse

if (!require("devtools")) install.packages("devtools") # to install
install.packages("tidyverse")

The gsl package is required by numerous packages and can cause some headaches… Don’t install it from source.

install.packages("gsl")

If the console print this: Do you want to install from sources the package which needs compilation? (Yes/no/cancel). Always aswer no unless of course you know what you are doing.

Than, I install grur and assigner my packges with the higher number of dependencies, this way it’s installing automatically 90% of the packages I need (including radiator).

devtools::install_github("thierrygosselin/grur")
devtools::install_github("thierrygosselin/assigner")

Makevars file

For some packages you might have to compile from source and the use of different compiler is sometimes very useful. You need to tell R how to use the compilers. This might change from one package to another. Nothing is simple, you know this by now… All this is done through R’s Makevars file located in ~/.R/Makevars.

To modify or create the file, the fastest way is to use the package usethis (it’s installed automatically with devtools):

usethis::edit_r_makevars()

Makevars content required:

CC=/usr/local/bin/gcc
CXX=/usr/local/bin/g++
FC=/usr/local/bin/gfortran
F77=/usr/local/bin/gfortran
PKG_LIBS = -fopenmp -lgomp
PKG_CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp
PKG_CXXFLAGS=-fopenmp -std=c++11
CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp
SHLIB_OPENMP_CFLAGS = -fopenmp
SHLIB_OPENMP_CXXFLAGS = -fopenmp
SHLIB_OPENMP_FCFLAGS = -fopenmp
SHLIB_OPENMP_FFLAGS = -fopenmp
# change the nex line according to your computer compiler version (use gcc -v in terminal):
FLIBS=-L/usr/local/lib/gcc/x86_64-apple-darwin19/9.2.0/finclude 
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion

Errors and installation problems

Sometimes you’ll get warnings while installing dependencies required for x package.

#Warning: cannot remove prior installation of package ‘stringi’

To solve this problem, delete manually the problematic package in the installation folder (on mac: /Library/Frameworks/R.framework/Resources/library) or in the Terminal:

sudo rm -R /Library/Frameworks/R.framework/Resources/library/package_name
# Changing 'package_name' to the problematic package.
# Reinstall the package.

Using the latest version of R, RStudio and packages is recommended. If your heart start pounding just at the thought of having to install a new R version, you should have a look at packrat.
Look at the output in R console when you get an error message. If it’s related to one’s of the packages dependencies, try installing it separately before attempting to reinstall the problematic package.

Error: macOS Big Sur update

So far, I’ve only experience 1 problem after upgrading to Big Sur, and it’s linked to adegenet dependency on sf package (solution).

Error: checking whether the C++ compiler works… no

When rtying to compile a software if you get this error: checking whether the C++ compiler works... no or configure: error: C++ compiler cannot create executables

Try installing Xcode from the App Store.

Error: “https” not supported

If you get something like: https not supported or disabled in libcurl, install or re-install:

OpenSSL

Required if GCC compiler is used (TLS backend is then used). Not required if clang is used (securetransport backend is used).

#In browser
https://www.openssl.org/source/openssl-1.1.1.tar.gz

#In Terminal
cd ~/Downloads
curl -L https://www.openssl.org/source/openssl-1.1.1.tar.gz | tar xf -
cd openssl-1.1.1
./config
make -j12 #change with your number of CPU
make test #long
sudo make install
cd ..
sudo rm -R openssl*

curl

Check for the latest release of curl

#Copy/paste in your browser
https://curl.haxx.se/download/curl-7.85.0.tar.gz
# Terminal
cd ~/Downloads
tar -zxvf curl-7.85.0.tar.gz
cd curl-7.85.0

for more curl* option type curl -h*

The next step depends on the compiler used

With gcc:

./configure --with-ssl # to enable https via OpenSSL and using GCC

Note: with macOS 11.0.1 this give me an error configure: error: OpenSSL libs and/or directories were not found where specified!

If this is the case, use clang:

CC="/usr/local/bin/clang"
./configure --without-ssl #--with-darwinssl # to install via clang

make -j12 #change with your number of CPU
sudo make install
cd ..
sudo rm -R curl*

If you have an install problem, the problem might be very computer-specific. e.g. if the problem is related to strataG, copula and/or gsl, try installing libgsl0-dev in the Terminal (very easy now with the latest RStudio release!):

sudo apt-get install libgsl0-dev

Error: `vector memory exhausted`

For errors that highlight problems with vectors and memory similar to: vector memory exhausted (limit reached). In R, verify that you have a file called ~/.Renviron:

file.exists("~/.Renviron")

If you don’t have the file:

require(usethis)
usethis::edit_r_environ()

Add this to your .Renviron file located in ~/.Renviron:

R_MAX_VSIZE = 100Gb

You can also use a text editor that allows you to see hidden files (files starting with a . dot).

Error during package installation

Problem with string.h, math.h or any other .h
Problem with vroom
Problem with rmetasim

An example during vroom installation:

clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include" -I/usr/local/include  -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -fPIC  -Wall -g -O2 -c gen.cc -o gen.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include" -I/usr/local/include  -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -fPIC  -Wall -g -O2 -c index_collection.cc -o index_collection.o
/usr/local/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/progress/include" -I/usr/local/include   -fPIC  -I/usr/local/include -c localtime.c -o localtime.o
localtime.c:42:10: fatal error: 'string.h' file not found
#include <string.h>
^~~~~~~~~~

With macOS : your Makevars needs additional lines to make it work configuration.

Error `.setMaxGlobalSize`

Its a problem with a previous version of pbmcapply and it’s interaction with future.

Solution:

restart your computer
with a clean desk and session: open RStudio and update your packages
Restart R (RStudio > Session > Restart R)
Re-install my github package generating the error

Note: if your heart start pounding just at the thought of having to update everything on your computer you should definitely have a look at packrat: it’s very easy to use.

Error `.DynamicClusterCall`

If you have a PC and you’re getting this error or closely related error:

# Error in .DynamicClusterCall(cl, length(cl), .fun = function(.proc_idx,  :
# One of the nodes produced an error: Can not open file 'FILE PATH'. The process cannot access the file because it # is being used by another process.

Solution: Use parallel.core = 1 in the function generating the error.

Corrupt packages

The error below usually happens when several packages are updated:

# Error in get0(oNam, envir = ns) :
# lazy-load database '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/callr/R/callr.rdb' is corrupt
# In addition: Warning message:
# In get0(oNam, envir = ns) : internal error -3 in R_decompress1

Solution:

restart R
re-install the package that generated this error

Error: `dyn.load`

I see 2 problems and separate solutions. When the error is related to adegenet, strataG, assigner or packages that depends on sf package, see the solution below.

When the error is similar to:

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/rstudio/R/x86_64-pc-linux-gnu-library/3.6/units/libs/units.so':
  libudunits2.so.0: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted

Solution:

In R, check the output of this command that look for the environment variables:

Sys.getenv("LD_LIBRARY_PATH")
# [1]""

Note that if the output is not empty, like in the example above, write down the output.

Set the new environment variables by adding /usr/local/lib/ to the output above:

When it’s empty:

# in R:
Sys.setenv(LD_LIBRARY_PATH="/usr/local/lib/")
# For Linux you could use: /usr/local/lib/:/usr/lib64

When it’s not, add at the end, separated by :

Sys.setenv(LD_LIBRARY_PATH="/usr/local/lib64/R/lib:/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.amzn2.0.1.x86_64/jre/lib/amd64/server:/usr/local/lib/:/usr/lib64")

Long-term solution:

Instead of using Sys.setenv each time you have a similar problem, you could add the environment variables LD_LIBRARY_PATH to your .Renviron file. This is discussed in another problem above.

Error related to sf and `dyn.load`

Sometimes the problem related to dyn.load problems originates from specific packages. So far, for me, they are always linked to sf package. The problem for macOS is usually when updating os, e.g. from Catalina -> Big Sur. The solution is similar for Linux when you try to install adegenet.

There are solutions using Homebrew, but I’m not a fan for the shortcuts.

brewless version to execute in the terminal:

udunits

cd ~/Downloads
curl -L https://artifacts.unidata.ucar.edu/repository/downloads-udunits/current/udunits-2.2.28.tar.gz | tar xf -
cd udunits*
./configure && make -j56 && sudo make install
cd ..
sudo rm -R udunits*

sqlite

cd ~/Downloads
curl -L https://www.sqlite.org/2022/sqlite-autoconf-3390400.tar.gz | tar xf -
cd sqlite-autoconf*
./configure && make -j56 && sudo make install
cd ..
sudo rm -R sqlite-autoconf*

libtiff

cd ~/Downloads
curl -L https://download.osgeo.org/libtiff/tiff-4.4.0.tar.gz | tar xf -
cd tiff*
./configure && make -j56 && sudo make install
cd ..
sudo rm -R tiff*

proj

cd ~/Downloads
curl -L  https://download.osgeo.org/proj/proj-9.1.0.tar.gz | tar xf -
cd proj*
mkdir build
cd build
cmake ..
cmake --build .
sudo cmake --build . --target install
cd ~/Downloads
sudo rm -R proj*
# with prior releases, when configure was necessary
# ./configure --libdir=/usr/local/lib && make -j56 && sudo make install

GDAL

export LDFLAGS="-L/usr/local/lib"
export CPPFLAGS="-I/usr/local/include"

cd ~/Downloads
curl -L https://github.com/OSGeo/gdal/releases/download/v3.5.3/gdal-3.5.3.tar.gz | tar xf -
cd gdal*
mkdir build
cd build
cmake ..
cmake --build .
sudo cmake --build . --target install
cd ~/Downloads
sudo rm -R gdal*
# previous install command required
#./configure --prefix=/usr/local --libdir=/usr/local/lib --with-proj=/usr/local && make -j56 && sudo make install #time for coffee...

GEOS

cd ~/Downloads
git clone https://git.osgeo.org/gitea/geos/geos.git
cd geos*
mkdir build
cd build
cmake ..
cmake --build .
sudo cmake --build . --target install
cd ~/Downloads
sudo rm -R geos*
# previous install command required
#./autogen.sh
#./configure --libdir=/usr/local/lib && make -j56 && sudo make install

Back in R/RStudio

install.packages("rgeos", repos="http://R-Forge.R-project.org", type="source")
install.packages("rgdal", repos="http://R-Forge.R-project.org", type="source")
devtools::install_github("r-spatial/sf", configure.args = "--with-proj-lib=/usr/local")
install.packages("adegenet")

Error: `HTTP status was 404 Not Found`

This error is sometimes poping after a new R upgrade. Try installing the problematic package differently.

Instead of:

BiocManager::install("SeqArray")

Try:

remotes::install_local(path = "SeqArray_latest.tar.gz")

Error: `C stacks usage`

Error: C stack usage  7971092 is too close to the limit

So far, I haven’t found the cure to this computer-specific problem.

Potential solutions:

Make sure you have enough RAM on your computer for the dataset you want to analyze (16GB is the bare minimum these days for small-medium RADseq dataset).
Closing all windows/app running in the background somtimes help.
Updating to the latest version of R, RStudio and libraries.
Not a fan of upgrading to latest version, use Packrat.
Follow the guidelines to prepare your computer in this vignette, from the start…

Google is your next best friend…

Specific librairies installation

`fst` & `fstcore` & `data.table`

Better to install and compile them from source to enable OpenMP. Install in the terminal zstd and lz4:

cd ~/Downloads
curl -L https://github.com/lz4/lz4/archive/refs/tags/v1.10.0.tar.gz | tar xf -
cd lz4*
make 
sudo make install
cd .. 
sudo rm -R lz4*

cd ~/Downloads
curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.6.tar.gz | tar xf -
cd zstd*
make 
sudo make install
cd .. 
sudo rm -R zstd*

fstcore, fst and data.table requires these R Makevars specifications. If you have other lines, comment (#) before saving and installing from source:

usethis::edit_r_makevars()

#fstcore fst data.table
CC=/usr/local/bin/gcc -fopenmp
CXX=/usr/local/bin/g++ -fopenmp
CXX11=/usr/local/bin/g++ -fopenmp
CXX14=/usr/local/bin/g++ -fopenmp
CXX17=/usr/local/bin/g++ -fopenmp
CXX1X=/usr/local/bin/g++ -fopenmp
CXX98=/usr/local/bin/g++ -fopenmp

install.packages("fstcore", type = "source")
install.packages("fst", type = "source")
install.packages("data.table", type = "source")

`rmetasim`

Download

Download the latest github release of Allan Strand’s rmetasim

cd ~/Downloads
curl -L -O https://github.com/stranda/rmetasim/archive/master.zip
unzip master.zip

Modify the number of loci: MAXLOCI

If you want to use more loci during your simulations (default is 10001), you need to modify rmetasim before compiling. With a text editor, modify the const.h file in the src folder: rmetasim-master/src/const.h. Navigate to lane 33 and change the integer to the desired maximum number of loci. Or do this in the Terminal:

sed -i -e 's/#define MAXLOCI               10001/#define MAXLOCI               20000/g' rmetasim-master/src/const.h

Makevars configuration

rmetasim requires these Makevars (~/.R/Makevars file) specifications. If you have other lines, comment (#) before compiling rmetasim:

usethis::edit_r_makevars()

macOS

This latest os requires extra lines:

CC=/usr/local/bin/clang
CXX=/usr/local/bin/clang++
CXX1X=/usr/local/bin/clang++
FLIBS=-L/usr/local/lib
LDFLAGS=-L/usr/local/lib
SHLIB_OPENMP_CFLAGS= -fopenmp
SHLIB_OPENMP_FCFLAGS= -fopenmp
SHLIB_OPENMP_FFLAGS= -fopenmp
SHLIB_OPENMP_CXXFLAGS= -fopenmp
CFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CCFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXXFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CPPFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

Compile

R CMD INSTALL "rmetasim-master" # Terminal command
sudo rm -R rmetasim* # to remove the folders no longer required

`XGBoost`

Download the github version

# terminal
cd Downloads
git clone --recursive https://github.com/dmlc/xgboost
cd xgboost

Error?

If you’re getting this error: "https" not supported or disabled in libcurl, extra steps are required, check the installation problems section to install OpenSSL and curl and enabling https with --with-ssl option.

Modification

Modify in a text editor the configure file inside the xgboost/R-package folder:

# Go to line 1676
# change
ac_pkg_openmp=no
# to
ac_pkg_openmp=yes
#save the file under the same name

Makevars configuration

XGBoost requires these Makevars specifications. If you have other lines, comment (#) before compiling:

usethis::edit_r_makevars()

CC=/usr/local/bin/gcc
CXX=/usr/local/bin/g++
CXX11=/usr/local/bin/g++
CXX14=/usr/local/bin/g++
CXX17=/usr/local/bin/g++
SHLIB_OPENMP_CFLAGS= -fopenmp
SHLIB_OPENMP_FCFLAGS= -fopenmp
SHLIB_OPENMP_FFLAGS= -fopenmp
SHLIB_OPENMP_CXXFLAGS= -fopenmp
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L/usr/local/lib -Wl,-rpath,/usr/local/lib
CPPFLAGS=-I/usr/local/include -I/usr/local/include

Compile

sudo R CMD INSTALL R-package

Test R-package

You should see a time difference between both runs

require(xgboost)
x <-  matrix(rnorm(100*10000), 10000, 100)
y <-  x %*% rnorm(100) + rnorm(1000)

system.time({bst = xgboost(data = x, label = y, nthread = 1, nround = 100, verbose = FALSE)})
system.time({bst = xgboost(data = x, label = y, nthread = 4, nround = 100, verbose = FALSE)})

`LightGBM`

LightGBM requires an OpenMP-enabled compiler. Currently, it doesn’t work well with clang, so make sure you have updated your GCC compiler (instructions above). Additionally, LightGBM requires CMake

Download and install CMake

#In browser or using curl in Terminal
https://cmake.org/files/v3.12/cmake-3.12.2-Darwin-x86_64.dmg
# double-click on the disk image and follow instructions

To add CMake to the PATH:

PATH="/Applications/CMake.app/Contents/bin":"$PATH"
# Or, to install symlinks to '/usr/local/bin', run:
sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install
# Or, to install symlinks to another directory, run:
sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install=/path/to/bin
#Then, run the following commands to install LightGBM:

Download and Install LightGBM

cd Downloads
git clone --recursive https://github.com/Microsoft/LightGBM
cd LightGBM
Rscript build_r.R
# previous version required running these lines instead
#cd LightGBM/R-package
#export CC=/usr/local/bin/gcc CXX=/usr/local/bin/g++
#R CMD INSTALL --build . --no-multiarch

`randomForestSRC`

randomForestSRC requires the GCC OpenMP-enabled compiler to run in parallel. See instructions above if not already done.

Makevars configuration

Check that the lines below are not commented in your ~/.R/Makevars file:

usethis::edit_r_makevars()

CC=/usr/local/bin/gcc
CXX=/usr/local/bin/g++
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
PKG_CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp
PKG_CXXFLAGS=-fopenmp -std=c++11
FC=/usr/local/bin/gfortran
F77=/usr/local/bin/gfortran
LDFLAGS=-L/usr/local/lib
PKG_LIBS = "-liconv"

Download and install

From the Terminal run these steps to download and compile randomForestSRC:

cd ~/Downloads
curl -L https://cran.r-project.org/src/contrib/randomForestSRC_2.9.3.tar.gz | tar xf -
cd randomForestSRC

Make sure you have autoconf installed:

# in Terminal
cd ~/Downloads
autoconf

Should output: autoconf: error: no input file, if not, install following the steps here.

# in Terminal
cd ~/Downloads/randomForestSRC
autoconf
cd ~/Downloads
R CMD INSTALL --preclean --clean randomForestSRC

You want to make sure that this line is printed during execution of the previous command: checking whether OpenMP will work in a package... yes or checking for /usr/local/bin/gcc option to support OpenMP... -fopenmp

`ranger`

ranger is easy to install.

install.packages("ranger")

`missRanger`

missRanger is also very easy to install.

install.packages("missRanger")

`miceRanger`

miceRanger easy to install.

install.packages("miceRanger")

`pcaMethods`

To install pcaMethods, from bioconductor:

BiocManager::install("pcaMethods")

`fastsimcoal2`

To install fastsimcoal2 v.2.6.0.3, to use in grur::simulate_rad:

LINUX

curl -O http://cmpg.unibe.ch/software/fastsimcoal2/downloads/fsc26_linux64.zip
unzip fsc26_linux64.zip
sudo mv fsc26_linux64/fsc26 /usr/local/bin/fsc26 # will ask for your computer password

MacOS

cd ~/Downloads
curl -O http://cmpg.unibe.ch/software/fastsimcoal2/downloads/fsc26_mac64.zip
unzip fsc26_mac64.zip
sudo mv fsc26_mac64/fsc26 /usr/local/bin/fsc26 # will ask for your computer password

Common to both OS:

sudo chmod 777 /usr/local/bin/fsc26
fsc26

Re-start R and the software fastsimcoal2 will automatically be in your PATH…

PATH

To see the path of the installation, in the Terminal:

which fsc26
# in macOS:
# /usr/local/bin/fsc26

If that doesn’t work, do:

source ~/.bash_profile

Remove the files in the folder:

sudo rm -R ~/Downloads/fsc26_mac64*

`COLONY`

To install COLONY 30/07/2018, V2.0.6.5:

MacOS

The old openmpi version (openmpi-1.6.5) is required, saddly.

cd ~/Downloads
curl -L https://download.open-mpi.org/release/open-mpi/v1.6/openmpi-1.6.5.tar.gz | tar xf -
cd openmpi-1.6.5
export TMPDIR=/tmp
./configure F77=gfortran #--prefix=/usr/local -openmp # no longer work for some reason
make -j 12
sudo make install
sudo rm -R ~/Downloads/openmpi*

To download COLONY, follow instructions on Jinliang Wang ZSL website. The file you need to uncompress is named: colony2.mac_.20180730.zip.

Linux

To download COLONY, follow instructions on Jinliang Wang ZSL website. The file you need to uncompress is named: colony2.linux_.20180730.zip.

Several options are available depending on the compiler you have installed.

Useful

Update Github

macOS comes with Github, a Version Control System (VCS), pre-installed. However, the install is in /usr/bin/git which can make it difficult for beginners to update. To change this, run these commands:

Install GNU Autoconf

cd ~/Downloads
curl -L http://ftp.gnu.org/gnu/autoconf/autoconf-latest.tar.gz | tar xf -
cd autoconf-2.69
./configure
make
sudo make install
cd .. 
sudo rm -R ~/Downloads/autoconf-*

Install Github

git --version                   # show current git version installed
which git                       # returns where is git on your computer
cd ~/Downloads
git clone https://github.com/git/git # install the latest Git
cd git
make configure
./configure
make -j12
sudo make install
cd .. 
sudo rm -R ~/Downloads/git/     # remove git folder
source ~/.bash_profile          # reload startup script
git --version                   # confirmed the version you just installed
which git                       # returns /usr/local/bin

macOS Terminal from specific folder

In System Preferences choose Keyboard -> Shortcuts. From the left panel, choose Services. In the right panel, under Files and Folders, choose New Terminal at Folder and/or New Terminal Tab at Folder. Now you can right-click your track pad or mouse on a folder and choose Services -> New Terminal at Folder!

Shortcut to folder path

With macOS, open the Automator application.

File -> New (cmd-N)
Choose: Services
Left panel, choose: Library -> Utilities
Middle, choose: Copy to Clipboard and drag it to the right panel
Now you want to have: Service receives selected FILES OR FOLDERS in FINDER>
You should have something similar to the image below:

Save (cmd-S) or File -> Save service as: copy path to clipboard

Go in the Finder, select a folder and right click on it you should see ‘copy path to clipboard’ at the bottom or in Services.

computer setup

2024-11-06

macOS

Update your OS

Get administrator and root user access

Apple’s Command Line Tools

Compiler

Update GCC

Update Clang

PATH

Useful tools

BBEdit

pip

Linux

Install R

Rstudio

Installing Libraries

Makevars file

Errors and installation problems

Error: macOS Big Sur update

Error: checking whether the C++ compiler works… no

Error: “https” not supported

Linux related problem

Error: vector memory exhausted

Error during package installation

Error .setMaxGlobalSize

Error .DynamicClusterCall

Corrupt packages

Error: dyn.load

Error related to sf and dyn.load

Error: HTTP status was 404 Not Found

Error: C stacks usage

Google is your next best friend…

Specific librairies installation

fst & fstcore & data.table

rmetasim

Download

Modify the number of loci: MAXLOCI

Makevars configuration

Compile

XGBoost

Download the github version

Error?

Modification

Makevars configuration

Compile

Test R-package

LightGBM

Download and install CMake

Download and Install LightGBM

randomForestSRC

Makevars configuration

Download and install

ranger

missRanger

miceRanger

pcaMethods

fastsimcoal2

LINUX

MacOS

Common to both OS:

PATH

COLONY

MacOS

Linux

Useful

Update Github

macOS Terminal from specific folder

Shortcut to folder path

Error: `vector memory exhausted`

Error `.setMaxGlobalSize`

Error `.DynamicClusterCall`

Error: `dyn.load`

Error related to sf and `dyn.load`

Error: `HTTP status was 404 Not Found`

Error: `C stacks usage`

`fst` & `fstcore` & `data.table`

`rmetasim`

`XGBoost`

`LightGBM`

`randomForestSRC`

`ranger`

`missRanger`

`miceRanger`

`pcaMethods`

`fastsimcoal2`

`COLONY`