inst/markdowns/Installation_questions.md

In beauchamplab/rave: R Analysis and Visualization of 'ECOG/iEEG' Data

Installation Q&A - Linux Version

Author: Zhengjia Wang

Date: Oct 28,2018

We need to nail down some terms:

• Terminal: system terminal. In MacOS, you can find it via spotlight. In Ubuntu, find it by searching apps. In windows, it's cmd.exe, search it in your startup menu.
• RStudio console: Open RStudio, in one of four panels (usually bottom-left one), there is a tab called Console. By saying "typing in the R console", I mean entering something here. (NOT system terminal)

Topics:

• Recommended system packages *Recommended settings to avoid most of errors
• How to install brew (optional) *If you miss some system packages but don't know where to find
• Installation Errors and Solutions
• Cannot install devtools *To install RAVE from github
• No package fftw3 found *Wavelet, Hilbert, Fourier transforms
• Config error for V8 *Web Service
• Config error for xml2 *Dependencies
• hdf5 not found *A commonly used data format
• hdf5 version is too low
• httpuv compiler failure *Web Service

Recommended Settings

I tested under Ubuntu 16.04 and CentOS 7.

• For debian-based systems (like ubuntu), open system terminal, copy this line and run

sudo apt-get install libssl-dev libcurl4-openssl-dev libssh2-1-dev libfftw3-dev libv8-3.14-dev libxml2-dev libhdf5-dev libtiff5-dev

• For rpm-based systems (like centos), open system terminal, copy this line and run

sudo yum install -y libcurl-devel openssl-devel libssh2-devel fftw-devel v8-devel libxml2-devel hdf5-devel

• In case of failure or you have other linux systems, you might want to install brew first. Then, use Linux-brew to install part of the packages

brew install openssl@1.1 fftw v8@3.15 libxml2 hdf5 libssh2

Brew might not install libcurl, fftw3, V8 and libssh2 correctly, so you might want to search online or try the following lines to see if you can install them. (you are more than welcome to post any issues to this github repository)

Try:

sudo apt-get install libcurl4 libfftw3-dev libv8-3.14-dev
sudo yum install -y libcurl-devel fftw-devel v8-314-devel

How to install brew

For linux, we recommend installing brew, which helps you save time for 3rd-party softwares. Here is the official document of linux-brew.

Open system terminal, enter:

For Debian or Ubuntu:

sudo apt-get install build-essential curl file git

For Fedora

sudo dnf groupinstall 'Development Tools' && sudo dnf install curl file git

For CentOS or Red Hat,

sudo yum groupinstall 'Development Tools' && sudo yum install curl file git

Then, run

sh -c "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install.sh)"

to download brew.

To enable command, copy and paste:

test -d ~/.linuxbrew && PATH="$HOME/.linuxbrew/bin:$HOME/.linuxbrew/sbin:$PATH"
test -d /home/linuxbrew/.linuxbrew && PATH="/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:$PATH"
test -r ~/.bash_profile && echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >>~/.bash_profile
echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >>~/.profile
echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >>~/.bash_profile
echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >>~/.bashrc
brew install hello

devtools

- ERROR: dependencies ‘git2r’, ‘httr’, ‘usethis’ are not available for package ‘devtools’

Reason

This is because libcurl and openssl are not installed to your system.

Solution:

Open system terminal,

• (Debian, Ubuntu, etc) sudo apt-get install libssl-dev libcurl4-openssl-dev
• (Fedora, CentOS, RHEL) sudo yum install -y libcurl-devel openssl-devel
• (MacOS) brew install openssl@1.1

Restart RStudio and try

install.packages('devtools')

If passed, continue installing RAVE

Notes:

Detailed errors are provided to you. Instructions has been already included in the error code

ERROR: dependencies ‘git2r’, ‘httr’, ‘usethis’ are not available for package ‘devtools’

# Relative informations:

# 1. libssh
 * libssh2-1-dev (package on e.g. Debian and Ubuntu)
 * libssh2-devel (package on e.g. Fedora, CentOS and RHEL)
 * libssh2 (Homebrew package on OS X)

# 2. libcurl
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
 * csw: libcurl_dev (Solaris)

# 3. openssl
 * deb: libssl-dev (Debian, Ubuntu, etc)
 * rpm: openssl-devel (Fedora, CentOS, RHEL)
 * csw: libssl_dev (Solaris)
 * brew: openssl@1.1 (Mac OSX)

# 4. libgit2
 * libgit2-dev   (package on e.g. Debian and Ubuntu)
 * libgit2-devel (package on e.g. Fedora, CentOS and RHEL)
 * libgit2       (Homebrew package on OS X)

fftw

- Error: No package `fftw3` found

Reason

RAVE requires fftw package for faster wavelet transforms. Some systems might not have the library.

Solution:

Open system terminal,

• (Debian, Ubuntu, etc) sudo apt-get install libfftw3-dev
• (Fedora, CentOS, RHEL) sudo yum install -y fftw-devel

In RStudio console, enter

install.packages('fftw')

If passed, continue installing RAVE

Notes:

Alternative might be installing brew first (see instructions), or if you have brew installed,

brew install fftw

V8

- ERROR: configuration failed for package ‘V8’

Solution:

Open system terminal,

• (Debian, Ubuntu, etc) sudo apt-get install libv8-3.14-dev
• (Fedora, CentOS, RHEL) sudo yum install -y v8-devel
• (MacOS) brew install v8@3.15

In RStudio console,

install.packages('V8')

If passed, continue installing RAVE

Notes:

Here's detailed error code when I first install this package

ERROR: configuration failed for package ‘V8’

------------------------- ANTICONF ERROR ---------------------------
Configuration failed because  was not found. Try installing:
 * deb: libv8-3.14-dev (formerly: libv8-dev) (Debian, Ubuntu)
 * rpm: v8-314-devel (formerly: v8-devel) (Fedora, EPEL)
 * brew: v8@3.15 (OSX) -- NOT regular v8! Tap from homebrew/versions
 * csw: libv8_dev (Solaris)
To use a custom libv8, set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
------------------------- ANTICONF ERROR ---------------------------

xml2

- ERROR: configuration failed for package ‘xml2’

Solution:

Open system terminal,

• (Debian, Ubuntu, etc) sudo apt-get install libxml2-dev
• (Fedora, CentOS, RHEL) sudo yum install -y libxml2-devel

In RStudio console,

install.packages('xml2')

If passed, continue installing RAVE

Notes:

Here's detailed error code when I first install this package

------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
 * deb: libxml2-dev (Debian, Ubuntu, etc)
 * rpm: libxml2-devel (Fedora, CentOS, RHEL)
 * csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘xml2’

hdf5r

There might be two errors for this dependency

No hdf5 detected

- Error: hdf5 does not seem to be installed on your platform. Please install the hdf5 library.

Reason

hdf5 is a data file format that shares across platform and can be loaded via R, Python, Matlab, C, Julia and Java. RAVE uses hdf5 to store data, which requires hdf5 library to be installed.

Solution:

Open system terminal,

• (Debian, Ubuntu, etc) sudo apt-get install libhdf5-dev
• (Fedora, RHEL) sudo yum install -y hdf5-devel
• (MacOS) brew install hdf5

In RStudio console

install.packages('hdf5r')

If passed, continue installing RAVE

Notes:

Original error message has some misleading information:

1. Using brew install hdf5 instead of instructed
2. On CentOS simply yum install won't help because rpm only has old hdf5-1.8.12 for this system.

configure: error: hdf5 does not seem to be installed on your platform.
  Please install the hdf5 library.
  The required HDF5 library files can be installed as follows:
      - Debian-based (e.g. Debian >= 8.0, Ubuntu >= 15.04): 'sudo apt-get install libhdf5-dev'
        - Old Debian-based (e.g Debian < 8.0, Ubuntu < 15.04): Install from source (see INSTALL)
        - OS X using Homebrew: 'brew install homebrew/science/hdf5'
        - RPM-based (e.g Fedora): 'sudo yum install hdf5-devel'
ERROR: configuration failed for package ‘hdf5r’

hdf5 requires at least version XX.XX.XX

- configure: error: The version of hdf5 installed on your system is not sufficient. Please ensure that at least version 1.8.13 is installed

Reason

Your system hdf5 version is too old. To fix it, you need to install brew. You might also have gcc version that is too low.

Solution:

Install brew first (see here, or reference official docs).

Open your system terminal, check gcc version

gcc --version

If the version is below 5, install gcc@5 first

brew install gcc@5

Next, install hdf5

brew install hdf5

Restart RStudio and try

install.packages('hdf5r')

If passed, continue installing RAVE.

If fails, you might need to specify hdf5 library path.

Find hdf5 path by typing in system terminal:

which h5cc

or

which h5pcc

I got result on my computer: home/linuxbrew/.linuxbrew/Cellar/hdf5/1.10.4/bin/h5cc

Replace configure.vars below with your results.

# One of the following two works
install.packages(
  'hdf5r',
  configure.args = '--with-hdf5 [YOUR h5cc PATH]',
  type = 'source'
)

install.packages(
  'hdf5r',
  configure.args = 'with-hdf5',
  configure.vars = '[YOUR h5cc PATH]'
)

httpuv

- g++: internal compiler error: Killed (program cc1plus).
- compilation failed for package ‘httpuv’

Reason

Usually this is because memory (RAM) is too low and you might want to increase your RAM to at least 4GB.

Solution:

Increase RAM to at lease 4GB.

If still fail, check this.

beauchamplab/rave documentation built on Feb. 23, 2024, 7:20 a.m.