README

General tools for voice analysis. The voice package is being developed to be an easy-to-use set of tools to deal with audio analysis in R.
It is based on wrassp, tuneR, seewave, gm, as well as Parselmouth - a Python library for the Praat software - and pyannote-audio - an open-source toolkit written in Python for speaker diarization based on PyTorch machine learning framework.

Ubuntu Installation

The following steps were used to configure github.com/filipezabala/voice on Ubuntu 20.04 LTS (Focal Fossa). Note the software versions during installation, inconsistency reporting is welcome.
> Without the following Python items 3 and 10, you may run all the functions except poetry and extract_features_py, that run respectively pyannote-audio and Parselmouth.

1. Curl

Command line tool and library for transferring data with URLs. Find the latest version at https://curl.se/download.html. At terminal run:

# removing (if necessary) old curl installation
sudo apt remove curl
sudo apt purge curl
# removing (if necessary) the /cdrom folder
sudo sed -i '/cdrom/d' /etc/apt/sources.list
# installing dependencies
sudo apt-get update
sudo apt-get install -y libssl-dev autoconf libtool make
cd /usr/local/src
rm -rf curl*
# downloading latest version (check before install!)
sudo wget https://curl.se/download/curl-7.81.0.zip
sudo unzip curl-7.81.0.zip
cd curl-7.81.0
sudo apt-get install autoconf
sudo autoreconf -fi
sudo ./configure --with-ssl 
sudo make
sudo make install
# update the system’s binaries and symbol lookup
sudo cp /usr/local/bin/curl /usr/bin/curl
curl -V

You may take a look at this post if you have a message like WARNING: curl and libcurl versions do not match. Functionality may be affected.

2. Git

sudo apt-get update
sudo apt-get install git-all

3. pip

sudo apt-get update
sudo apt-get install python3-pip
pip3 --version

4. ffmpeg

ffmpeg is a cross-platform solution to record, convert and stream audio and video.

sudo apt-get update
sudo apt-get install ffmpeg

5. Audio drivers, extra packages and some cleaning

sudo apt-get update
sudo apt-get install portaudio19-dev libasound2-dev libfontconfig1-dev libmagick++-dev libxml2-dev libharfbuzz-dev libfribidi-dev libgdal-dev
sudo rm -Rf /usr/local/lib/R/site-library/00LOCK-digest

sudo apt-get update
sudo apt-get install cmake cmake-doc ninja-build

6. MuseScore

sudo add-apt-repository ppa:mscore-ubuntu/mscore-stable
sudo apt-get update
sudo apt-get install musescore

7. R

R is a free software environment for statistical computing and graphics. To find out your Ubuntu distribution use lsb_release -a at terminal.

sudo sh -c 'echo "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/" >> /etc/apt/sources.list.d/cran.list'
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 51716619E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -

sudo add-apt-repository ppa:c2d4u.team/c2d4u4.0+

sudo apt-get update && sudo apt-get upgrade
sudo apt-get install r-base
sudo apt-get install r-base-dev

8. RStudio Server

RStudio is an Integrated Development Environment (IDE) for R. Check for updates here.

sudo apt-get update
sudo apt-get install gdebi-core
wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2021.09.2-382-amd64.deb
sudo gdebi rstudio-server-2021.09.2-382-amd64.deb

9. R packages

“Packages are the fundamental units of reproducible R code.” Hadley Wickham and Jennifer Bryan. The installation may take several minutes. At terminal run:

sudo R

ini <- Sys.time()
packs <- c('audio','BART','devtools','e1071','ellipse','foreach','ggfortify','RColorBrewer','reticulate','R.utils','seewave','tidyverse','tuneR','VIM','wrassp')
install.packages(packs, dep = T); Sys.time()-ini
update.packages(ask = F); Sys.time()-ini
devtools::install_github('egenn/music'); Sys.time()-ini
devtools::install_github('filipezabala/voice'); Sys.time()-ini
devtools::install_github('flujoo/gm'); Sys.time()-ini
url <- 'http://www.rob-mcculloch.org/chm/nonlinvarsel_0.0.1.9001.tar.gz'
download.file(url, destfile = 'temp')
install.packages('temp', repos = NULL, type='source')

usethis::edit_r_environ()

Add the line MUSESCORE_PATH=/usr/bin/mscore to /root/.Renviron file. To exit use :wq at VI. Save and restart the R/RStudio session.

10. Miniconda

Miniconda is a free minimal installer for conda, an open source package, dependency and environment management system for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN and more, that runs on Windows, macOS and Linux.
Follow the instructions at https://docs.conda.io/en/latest/miniconda.html.

cd ~/Downloads/
wget -r -np -k https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
cd repo.anaconda.com/miniconda/
bash Miniconda3-latest-Linux-x86_64.sh

Miniconda3 will now be installed into this location: /home/user/miniconda3 [ENTER]

Do you wish the installer to initialize Miniconda3 by running conda init? yes.
Close and reopen terminal.

conda update -n base -c defaults conda

The following packages will be INSTALLED/REMOVED/UPDATED/DOWNGRADED:… Proceed ([y]/n)? y

conda create -n pyvoice38 python=3.8

The following (NEW) packages will be downloaded/INSTALLED:… Proceed ([y]/n)? y

conda activate pyvoice38
pip3 install -r https://raw.githubusercontent.com/filipezabala/voice/master/requirements.txt

MacOS Installation

The following steps were used to configure github.com/filipezabala/voice on MacOS Monterey. Note the software versions during installation, inconsistency reporting is welcome.
If the error “The package %@ is missing or invalid” appears during the upgrading from MacOS Catalina to Big Sur, press simultaneously command + option + p + r at restart. The processes may be accompanied using the keys command + space 'Activity Monitor'.
> Without the following Python items 3 and 11, you may run all the functions except poetry and extract_features_py, that run respectively pyannote-audio and Parselmouth.

Hardware
. MacBook Air (13-inch, 2017)
. Processor 1.8 GHz Dual-Core Intel Core i5
. Memory 8GB 1600 MHz DDR3
. Graphics Intel HD Graphics 6000 1536 MB

1. Homebrew

Install Homebrew, ‘The Missing Package Manager for macOS (or Linux)’ and remember to brew doctor eventually. At terminal (command + space 'terminal') run:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
sudo chown -R $(whoami) /usr/local/lib/pkgconfig /usr/local/share/info /usr/local/share/man/man3 /usr/local/share/man/man5
chmod u+w /usr/local/lib/pkgconfig /usr/local/share/info /usr/local/share/man/man3 /usr/local/share/man/man5

2. wget

GNU Wget is a free software package for retrieving files using HTTP, HTTPS, FTP and FTPS, the most widely used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.

brew install wget

3. Python

Python is a programming language that integrate systems. According to this post, it is recommended to install Python 3.8 and 3.9 and make it consistent.

brew install python@3.8
brew install python@3.9
brew unlink python@3.9
brew unlink python@3.8
brew link python@3.8
echo 'export PATH="/usr/local/opt/python@3.8/bin:$PATH"' >> ~/.zshrc
python3 --version 
pip3 --version

4. ffmpeg

ffmpeg is a cross-platform solution to record, convert and stream audio and video. The installation may take several minutes.

brew install ffmpeg

5. XQuartz

The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on macOS.

. Download and run https://github.com/XQuartz/XQuartz/releases/download/XQuartz-2.8.1/XQuartz-2.8.1.dmg
. Will take 319.2 MB of disk space
. Send XQuartz-2.8.1.dmg to Trash

6. MacPorts

wget https://github.com/macports/macports-base/releases/download/v2.7.2/MacPorts-2.7.2.tar.bz2
tar xjvf MacPorts-2.7.2.tar.bz2
cd MacPorts-2.7.2
cd ../; rm -rf MacPorts-2.7.2*
sudo nano /etc/paths

/opt/local/bin
/opt/local/sbin

Use Ctrl+O and return to save the file and Ctrl+X to cloe nano editor. Reboot your terminal.

7. tcllib

sudo port selfupdate && sudo port upgrade tcllib
sudo port install tcllib

7. MuseScore

MuseScore is an open source notation software.
. Download and run https://musescore.org/en/download/musescore.dmg
. Drag MuseScore 3 to Applications folder
. Will take 314 MB of disk space
. Unmount MuseScore-3.6.2 virtual disk and send MuseScore-3.6.2.548020600.dmg to Trash

8. R

R is a free software environment for statistical computing and graphics.
. Download and run https://cloud.r-project.org/bin/macosx/base/R-4.2.0.pkg
. Will take around 180 MB of disk space
. Send R-4.2.0.pkg to Trash

9. RStudio

RStudio is an Integrated Development Environment (IDE) for R.
. Download and run https://download1.rstudio.org/desktop/macos/RStudio-2022.02.3-492.dmg
. Drag RStudio to Applications folder
. Will take around 770 MB of disk space
. Unmount RStudio virtual disk and send RStudio-2022.02.3-492.dmg to Trash
. Type command + space 'rstudio'
. Tools > Global Options… > Appearance > Merbivore (Restart required)

10. R packages

“Packages are the fundamental units of reproducible R code.” Hadley Wickham and Jennifer Bryan. Type command + space 'terminal'

sudo R

ini <- Sys.time()
packs <- c('audio','BART','devtools','e1071','ellipse','foreach','ggfortify','RColorBrewer','reticulate','R.utils','seewave','tidyverse','tuneR','VIM','wrassp')
install.packages(packs, dep = T); Sys.time()-ini
update.packages(ask = F); Sys.time()-ini
devtools::install_github('egenn/music'); Sys.time()-ini
devtools::install_github('filipezabala/voice'); Sys.time()-ini
devtools::install_github('flujoo/gm'); Sys.time()-ini
url <- 'http://www.rob-mcculloch.org/chm/nonlinvarsel_0.0.1.9001.tar.gz'
download.file(url, destfile = 'temp')
install.packages('temp', repos = NULL, type='source')

11. Miniconda

cd ~/Downloads
wget -r -np -k https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
cd repo.anaconda.com/miniconda/
bash Miniconda3-latest-MacOSX-x86_64.sh

Miniconda3 will now be installed into this location: /Users/[your_user]/miniconda3 [ENTER]

Do you wish the installer to initialize Miniconda3 by running conda init? yes.

export PATH="~/miniconda3/bin:$PATH"
conda update -n base -c defaults conda

The following packages will be INSTALLED/REMOVED/UPDATED/DOWNGRADED:… Proceed ([y]/n)? y

conda create -n pyvoice38 python=3.8

The following (NEW) packages will be downloaded/INSTALLED:… Proceed ([y]/n)? y

conda activate pyvoice38
pip3 install -r https://raw.githubusercontent.com/filipezabala/voice/master/requirements.txt