In thierrygosselin/assigner: Assignment Analysis with RADseq Data
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
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:
rmetasimXGBoostLightGBMrandomForestSRCrangermissRangerpcaMethods- 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.
```{bash eval=FALSE}
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](https://thoughtbot.com/blog/the-magic-behind-configure-make-make-install):
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](http://www.gnu.org/software/make/manual/make.html))
* `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](http://en.wikipedia.org/wiki/Compiler)
Collection (GCC) with OpenMP enabled,
similar story with [Clang](http://en.wikipedia.org/wiki/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](http://hpc.sourceforge.net).
**Sonoma** [gcc-14.1-m1-bin.tar.gz](http://prdownloads.sourceforge.net/hpc/gcc-14.1-m1-bin.tar.gz)
```{bash eval=FALSE}
#In Terminal
cd Downloads
sudo tar -zxvf gcc-14.1-m1-bin.tar.gz -C /usr/local --strip-components=2
```{bash eval=FALSE}
sudo rm gcc-14.1-m1-bin.tar.gz
gcc -v
### Update Clang
We want [clang](https://en.wikipedia.org/wiki/Clang) compiler with OpenMP enabled. The latest version is [19.1.3](https://github.com/llvm/llvm-project/releases/tag/llvmorg-19.1.3).
```{bash eval=FALSE}
#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
```{bash eval=FALSE}
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](http://en.wikipedia.org/wiki/Bash_(Unix_shell)) 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](http://en.wikipedia.org/wiki/PATH_(variable)):
```{bash eval=FALSE}
$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:
```{bash eval=FALSE}
ls -al ~ | grep profile
If this returns nothing (blank), you don't have a shell start up script. Create
one with this command
```{bash eval=FALSE}
sudo touch $HOME/.bash_profile
To modify, you can use BBEdit
to open or make and modify hidden items (using the option Show hidden items on the open file screen).
Look for the free version.
With Linux, use Vi!
Copy/paste the line below in your .bash_profile file:
```{bash eval=FALSE}
PATH="$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](http://www.barebones.com/products/bbedit/index.html)
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](https://pip.pypa.io/en/stable/)
This is a Python installer tool that I highly recommend.
To install or upgrade pip, securely download [get-pip.py](https://bootstrap.pypa.io/get-pip.py).
Run this from you Terminal:
```{bash eval=FALSE}
cd ~/Downloads
sudo python get-pip.py
If you get command not found you might not have python installed.
```{bash eval=FALSE}
pip install -U pip # to upgrade
```{bash eval=FALSE}
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
```{bash eval=FALSE}
for macOS
cd Downloads
curl -O https://cran.r-project.org/bin/macosx/R-4.4.2.pkg
**To remove R completely from macOS**
```{bash eval=FALSE}
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:
```{bash eval=FALSE}
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 {#Installation_problems}
Sometimes you'll get warnings while installing dependencies required for
*x* package.
```r
#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:
```{bash eval=FALSE}
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](https://www.rstudio.com/resources/webinars/managing-package-dependencies-in-r-with-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](https://r-spatial.github.io/sf/) package [(solution)](#sfprob).
## 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](https://www.openssl.org)
Required if GCC compiler is used (TLS backend is then used). Not required if clang is used (securetransport backend is used).
```{bash eval=FALSE}
#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*
Check for the latest release of curl
```{bash eval=FALSE}
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**:
```{bash eval=FALSE}
./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:
```{bash eval=FALSE}
CC="/usr/local/bin/clang"
./configure --without-ssl #--with-darwinssl # to install via clang
```{bash eval=FALSE}
make -j12 #change with your number of CPU
sudo make install
cd ..
sudo rm -R curl*
Linux related problem
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!):
```{bash eval=FALSE}
sudo apt-get install libgsl0-dev
## Error: `vector memory exhausted` {#Renviron}
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`:
```r
file.exists("~/.Renviron")
If you don't have the file:
```{bash eval=FALSE}
require(usethis)
usethis::edit_r_environ()
Add this to your `.Renviron` file located in `~/.Renviron`:
```{bash eval=FALSE}
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:
```{bash vroom problem, eval=FALSE}
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
^~~~~~~~~~
**With macOS** : your `Makevars` needs additional lines to make it work [configuration](#Makevars_config).
## 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](https://www.rstudio.com/resources/webinars/managing-package-dependencies-in-r-with-packrat/): it's very easy to use.
## Error `.DynamicClusterCall`
If you have a PC and you're getting this error or closely related error:
```{bash, eval=FALSE}
# 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:
```{bash, eval=FALSE}
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:**
1. restart R
2. re-install the package that generated this error
## Error: `dyn.load` {#Dynload}
I see 2 problems and separate solutions. When the error is related to
*adegenet*, *strataG*, *assigner* or packages that depends on
[sf](https://r-spatial.github.io/sf/) package, [see the solution below](#sfprob).
When the error is similar to:
```{bash, eval=FALSE}
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 {#sfprob}
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:
```{bash eval=FALSE}
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](https://www.sqlite.org)
```{bash eval=FALSE}
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*
```{bash eval=FALSE}
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](https://proj.org/about.html)
```{bash eval=FALSE}
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
```{bash eval=FALSE}
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](https://trac.osgeo.org/geos)
```{bash eval=FALSE}
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:
```{bash eval=FALSE}
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
```{bash eval=FALSE}
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
```{bash eval=FALSE}
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:
```{bash eval=FALSE}
sed -i -e 's/#define MAXLOCI 10001/#define MAXLOCI 20000/g' rmetasim-master/src/const.h
Makevars configuration {#Makevars_config}
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:
```{bash eval=FALSE}
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
```{bash eval=FALSE}
R CMD INSTALL "rmetasim-master" # Terminal command
sudo rm -R rmetasim* # to remove the folders no longer required
XGBoost
Download the github version
```{bash eval=FALSE}
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](#Installation_problems) 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:
```{bash eval=FALSE}
# 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()
```{bash eval=FALSE}
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
```{bash eval=FALSE}
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
```{bash eval=FALSE}
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:
```{bash eval=FALSE}
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
```{bash eval=FALSE}
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](http://web.ccs.miami.edu/~hishwaran/ishwaran.html) 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:
```r
usethis::edit_r_makevars()
```{bash eval=FALSE}
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:
```{bash eval=FALSE}
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:
```{bash eval=FALSE}
in Terminal
cd ~/Downloads
autoconf
Should output: `autoconf: error: no input file`,
if not, install following the [steps here](#useful).
```{bash eval=FALSE}
# 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
```{bash Linux, eval=FALSE}
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
```{bash macOS, eval=FALSE}
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:
```{bash chunk common to both OS, eval=FALSE}
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`:
```{bash, eval=FALSE}
which fsc26
# in macOS:
# /usr/local/bin/fsc26
If that doesn't work, do:
```{bash, eval=FALSE}
source ~/.bash_profile
Remove the files in the folder:
```{bash, eval=FALSE}
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.
```{bash macOS openmpi-1.6.5, eval=FALSE}
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](https://www.zsl.org/science/software/colony). The file you need to
uncompress is named: `colony2.mac_.20180730.zip`.
### Linux
To download COLONY, follow instructions on Jinliang Wang [ZSL website](https://www.zsl.org/science/software/colony). The file you need to
uncompress is named: `colony2.linux_.20180730.zip`.
Several options are available depending on the compiler you have installed.
# Useful {#useful}
## Update [Github](http://en.wikipedia.org/wiki/Github)
macOS comes with [Github](https://github.com), 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:
1. Install [GNU Autoconf](http://www.gnu.org/software/autoconf/)
```{bash eval=FALSE}
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
```{bash eval=FALSE}
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!
```r
knitr::include_graphics("terminal_folder_shortcut.png")
Shortcut to folder path
With macOS, open the Automator application.
```{bash eval=FALSE}
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:
```r
knitr::include_graphics("copy_path.png")
{bash eval=FALSE}
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.
thierrygosselin/assigner documentation built on Nov. 9, 2024, 3:38 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
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
grurand it's dependencies or simulations withstrataG. - specific installation instructions for:
rmetasimXGBoostLightGBMrandomForestSRCrangermissRangerpcaMethods- 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.
```{bash eval=FALSE} 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](https://thoughtbot.com/blog/the-magic-behind-configure-make-make-install):
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](http://www.gnu.org/software/make/manual/make.html))
* `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](http://en.wikipedia.org/wiki/Compiler)
Collection (GCC) with OpenMP enabled,
similar story with [Clang](http://en.wikipedia.org/wiki/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](http://hpc.sourceforge.net).
**Sonoma** [gcc-14.1-m1-bin.tar.gz](http://prdownloads.sourceforge.net/hpc/gcc-14.1-m1-bin.tar.gz)
```{bash eval=FALSE}
#In Terminal
cd Downloads
sudo tar -zxvf gcc-14.1-m1-bin.tar.gz -C /usr/local --strip-components=2
```{bash eval=FALSE} sudo rm gcc-14.1-m1-bin.tar.gz gcc -v
### Update Clang
We want [clang](https://en.wikipedia.org/wiki/Clang) compiler with OpenMP enabled. The latest version is [19.1.3](https://github.com/llvm/llvm-project/releases/tag/llvmorg-19.1.3).
```{bash eval=FALSE}
#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
```{bash eval=FALSE} 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](http://en.wikipedia.org/wiki/Bash_(Unix_shell)) 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](http://en.wikipedia.org/wiki/PATH_(variable)):
```{bash eval=FALSE}
$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:
```{bash eval=FALSE} ls -al ~ | grep profile
If this returns nothing (blank), you don't have a shell start up script. Create
one with this command
```{bash eval=FALSE}
sudo touch $HOME/.bash_profile
To modify, you can use BBEdit to open or make and modify hidden items (using the option Show hidden items on the open file screen). Look for the free version. With Linux, use Vi!
Copy/paste the line below in your .bash_profile file:
```{bash eval=FALSE}
PATH="$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](http://www.barebones.com/products/bbedit/index.html)
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](https://pip.pypa.io/en/stable/)
This is a Python installer tool that I highly recommend.
To install or upgrade pip, securely download [get-pip.py](https://bootstrap.pypa.io/get-pip.py).
Run this from you Terminal:
```{bash eval=FALSE}
cd ~/Downloads
sudo python get-pip.py
If you get command not found you might not have python installed.
```{bash eval=FALSE} pip install -U pip # to upgrade
```{bash eval=FALSE}
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 ```{bash eval=FALSE}
for macOS
cd Downloads curl -O https://cran.r-project.org/bin/macosx/R-4.4.2.pkg
**To remove R completely from macOS**
```{bash eval=FALSE}
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: ```{bash eval=FALSE} 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 {#Installation_problems}
Sometimes you'll get warnings while installing dependencies required for
*x* package.
```r
#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:
```{bash eval=FALSE} 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](https://www.rstudio.com/resources/webinars/managing-package-dependencies-in-r-with-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](https://r-spatial.github.io/sf/) package [(solution)](#sfprob).
## 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](https://www.openssl.org)
Required if GCC compiler is used (TLS backend is then used). Not required if clang is used (securetransport backend is used).
```{bash eval=FALSE}
#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*
Check for the latest release of curl ```{bash eval=FALSE}
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**:
```{bash eval=FALSE}
./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: ```{bash eval=FALSE} CC="/usr/local/bin/clang" ./configure --without-ssl #--with-darwinssl # to install via clang
```{bash eval=FALSE}
make -j12 #change with your number of CPU
sudo make install
cd ..
sudo rm -R curl*
Linux related problem
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!):
```{bash eval=FALSE} sudo apt-get install libgsl0-dev
## Error: `vector memory exhausted` {#Renviron}
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`:
```r
file.exists("~/.Renviron")
If you don't have the file:
```{bash eval=FALSE} require(usethis) usethis::edit_r_environ()
Add this to your `.Renviron` file located in `~/.Renviron`:
```{bash eval=FALSE}
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.hor any other.h - Problem with
vroom - Problem with
rmetasim
An example during vroom installation:
```{bash vroom problem, eval=FALSE} 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
^~~~~~~~~~
**With macOS** : your `Makevars` needs additional lines to make it work [configuration](#Makevars_config).
## 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](https://www.rstudio.com/resources/webinars/managing-package-dependencies-in-r-with-packrat/): it's very easy to use.
## Error `.DynamicClusterCall`
If you have a PC and you're getting this error or closely related error:
```{bash, eval=FALSE}
# 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:
```{bash, eval=FALSE}
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:**
1. restart R
2. re-install the package that generated this error
## Error: `dyn.load` {#Dynload}
I see 2 problems and separate solutions. When the error is related to
*adegenet*, *strataG*, *assigner* or packages that depends on
[sf](https://r-spatial.github.io/sf/) package, [see the solution below](#sfprob).
When the error is similar to:
```{bash, eval=FALSE}
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 {#sfprob}
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:
```{bash eval=FALSE} 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](https://www.sqlite.org)
```{bash eval=FALSE}
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*
```{bash eval=FALSE} 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](https://proj.org/about.html)
```{bash eval=FALSE}
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
```{bash eval=FALSE} 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](https://trac.osgeo.org/geos)
```{bash eval=FALSE}
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:
```{bash eval=FALSE} 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
```{bash eval=FALSE}
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 ```{bash eval=FALSE} 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: ```{bash eval=FALSE} sed -i -e 's/#define MAXLOCI 10001/#define MAXLOCI 20000/g' rmetasim-master/src/const.h
Makevars configuration {#Makevars_config}
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: ```{bash eval=FALSE} 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
```{bash eval=FALSE}
R CMD INSTALL "rmetasim-master" # Terminal command
sudo rm -R rmetasim* # to remove the folders no longer required
XGBoost
Download the github version
```{bash eval=FALSE}
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](#Installation_problems) 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:
```{bash eval=FALSE}
# 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()
```{bash eval=FALSE} 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
```{bash eval=FALSE}
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
```{bash eval=FALSE}
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:
```{bash eval=FALSE}
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
```{bash eval=FALSE} 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](http://web.ccs.miami.edu/~hishwaran/ishwaran.html) 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: ```r usethis::edit_r_makevars()
```{bash eval=FALSE} 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:
```{bash eval=FALSE}
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: ```{bash eval=FALSE}
in Terminal
cd ~/Downloads autoconf
Should output: `autoconf: error: no input file`, if not, install following the [steps here](#useful). ```{bash eval=FALSE} # 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
```{bash Linux, eval=FALSE} 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
```{bash macOS, eval=FALSE}
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:
```{bash chunk common to both OS, eval=FALSE} 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`:
```{bash, eval=FALSE}
which fsc26
# in macOS:
# /usr/local/bin/fsc26
If that doesn't work, do: ```{bash, eval=FALSE} source ~/.bash_profile
Remove the files in the folder:
```{bash, eval=FALSE}
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.
```{bash macOS openmpi-1.6.5, eval=FALSE} 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](https://www.zsl.org/science/software/colony). The file you need to uncompress is named: `colony2.mac_.20180730.zip`. ### Linux To download COLONY, follow instructions on Jinliang Wang [ZSL website](https://www.zsl.org/science/software/colony). The file you need to uncompress is named: `colony2.linux_.20180730.zip`. Several options are available depending on the compiler you have installed. # Useful {#useful} ## Update [Github](http://en.wikipedia.org/wiki/Github) macOS comes with [Github](https://github.com), 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: 1. Install [GNU Autoconf](http://www.gnu.org/software/autoconf/) ```{bash eval=FALSE} 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
```{bash eval=FALSE} 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!
```r
knitr::include_graphics("terminal_folder_shortcut.png")
Shortcut to folder path
With macOS, open the Automator application.
```{bash eval=FALSE} 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:
```r
knitr::include_graphics("copy_path.png")
{bash eval=FALSE}
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.
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