RSQLite install

# when attempting to install RSQLite in a pristine Vagrant VM, I get a strange error (see lower)
# plus, logging in on the VM confirms that the RSQLite package /IS/ installed: `require('RSQLite')` is OK.
# if I comment the first line and uncomment the second line, installation completes fine.

# this error seems to randomly appear with other packages too...

(for the full script, see end of this file) 

#####################################################################
#####################################################################

apt-get install -q -y \
        sqlite3 libsqlite3-dev \
        \

    
    #devtools::install_github("rstats-db/RSQLite")

    R --no-save --quiet << HERE
    require('RSQLite') || install.packages("RSQLite", repos='http://cran.rstudio.com/')  # <-- FIXME: reports an error
    #install.packages("RSQLite", repos='http://cran.rstudio.com/') # seems to work
HERE


#####################################################################
#####################################################################


result:

==> dev: installing to /usr/local/lib/R/site-library/RSQLite/libs
==> dev: ** R
==> dev: ** inst
==> dev: ** preparing package for lazy loading
==> dev: ** help
==> dev: *** installing help indices
==> dev: ** building package indices
==> dev: ** installing vignettes
==> dev: ** testing if installed package can be loaded
==> dev: * DONE (RSQLite)
==> dev: The downloaded source packages are in
==> dev:        ‘/tmp/RtmpDEGcbT/downloaded_packages’
==> dev: Error in require("RSQLite") || install.packages("RSQLite", repos = "http://cran.rstudio.com/") :
==> dev:   invalid 'y' type in 'x || y'
==> dev: In addition:
==> dev: Warning message:
==> dev: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
==> dev:
==> dev:
==> dev:  there is no package called ‘RSQLite’
==> dev: Execution halted


#####################################################################
#####################################################################

full script:

#!/usr/bin/env bash

cd /tmp

set -x
set -e

THIS=`basename $0`

locale-gen en_IE.UTF-8
locale-gen nl_BE.UTF-8

#source my.config

function apt_update(){

# The Debian backports archives on CRAN are signed with the key of "Johannes Ranke (CRAN Debian archive) " with key ID 381BA480. You can fetch this with
#gpg --keyserver subkeys.pgp.net --recv-key 381BA480
#gpg -a --export 381BA480 > jranke_cran.asc
#apt-key add jranke_cran.asc

apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
# or
#gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E084DAB9
#gpg -a --export E084DAB9 | apt-key add -

#MIRROR=http://lib.ugent.be/CRAN
MIRROR=http://www.freestatistics.org/cran/

cat > /etc/apt/sources.list << EOF
deb http://ftp.belnet.be/ubuntu.com/ubuntu trusty main restricted universe multiverse
deb http://ftp.belnet.be/ubuntu.com/ubuntu trusty-updates main restricted universe multiverse
deb http://security.ubuntu.com/ubuntu trusty-security main restricted universe multiverse
deb $MIRROR/bin/linux/ubuntu trusty/
#deb $MIRROR trusty-backports main restricted universe
EOF

apt-get update

}

function install_R(){

    apt-get install -y \
        r-base \
        \

    #apt-get install -y \
        #    r-base-dev texlive-full \
    #    \
        #
        #apt-get build-dep r-base-core

    R --version

}

function install_RStudio_server(){

    set -x

    rstudio-server version && return || echo "installing rstudio-server"

    apt-get install -y \
        gdebi-core \
        \

    FILE=rstudio-server-1.0.136-amd64.deb
    DEB=https://download2.rstudio.org/$FILE
    wget --no-verbose $DEB
    gdebi --non-interactive $FILE
    rm $FILE

    #rstudio-server verify-installation
    rstudio-server version

}

function install_R_Shiny(){

    set -x

    R --no-save --quiet << HERE
    require('shiny') || install.packages('shiny', repos='https://cran.rstudio.com/')
HERE

    FILE=shiny-server-1.5.3.838-amd64.deb

    if [ ! -f $FILE ]; then
        DEB=https://download3.rstudio.org/ubuntu-12.04/x86_64/$FILE
        wget --no-verbose $DEB
        gdebi --non-interactive $FILE || rm $FILE 'fail' # trigger `exit 1` after removing the file
     else
         echo "shiny-server should be OK"
         return
     fi

    R --no-save --quiet << HERE
    require('shinyjs') || install.packages("shinyjs", repos='http://cran.rstudio.com/')
    require('DT') || install.packages("DT", repos='http://cran.rstudio.com/')
    # devtools::install_github('daattali/shinyjs')
HERE

}

function install_R_packages(){

    R --no-save --quiet << HERE

    require('rmarkdown') || install.packages("rmarkdown", repos='http://cran.rstudio.com/')
    require('caTools') || install.packages("caTools", repos='http://cran.rstudio.com/')

HERE

}

function install_sqlite(){

    apt-get install -q -y \
        sqlite3 libsqlite3-dev \
        \

    
    #devtools::install_github("rstats-db/RSQLite")

    R --no-save --quiet << HERE
    require('RSQLite') || install.packages("RSQLite", repos='http://cran.rstudio.com/')
    #install.packages("RSQLite", repos='http://cran.rstudio.com/') # for some reason, install.packages("RSQLite", repos='http://cran.rstudio.com/') returns an error
HERE

}

function install_MySQL(){

    apt-get install -y -q \
        debconf-utils \
        \

    MYSQL_DBA_PASSWORD="root"

    export DEBIAN_FRONTEND=noninteractive
    debconf-set-selections <<< "mysql-server-5.5 mysql-server/root_password password "$MYSQL_DBA_PASSWORD
    debconf-set-selections <<< "mysql-server-5.5 mysql-server/root_password_again password "$MYSQL_DBA_PASSWORD
    apt-get install -q -y \
        mysql-server-5.5 \
        \

# Run the MySQL Secure Installation wizard
#mysql_secure_installation
#
#sed -i 's/127\.0\.0\.1/0\.0\.0\.0/g' /etc/mysql/my.cnf
#mysql -uroot -p -e 'USE mysql; UPDATE `user` SET `Host`="%" WHERE `User`="root" AND `Host`="localhost"; DELETE FROM `user` WHERE `Host` != "%" AND `User`="root"; FLUSH PRIVILEGES;'


}

function install_varia(){

    apt-get install -q -y \
        git \
        tree \
        htop \
        \

}

function install_devtools() {

    apt-get install -q -y \
        libcurl4-gnutls-dev \
        libxml2-dev \
        libssl-dev \
        \

    R --no-save --quiet << HERE
    require('devtools') || install.packages('devtools', repos='http://cran.rstudio.com/')
HERE
}

# create users
#useradd --shell /bin/bash --create-home --home /home/user user

# create directories
# ...

#./install.sh

apt_update

install_varia

install_R
#install_devtools

# database

install_sqlite
#install_MySQL

install_RStudio_server
install_R_Shiny

echo "$THIS: done!"