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Update of installation scripts to run on Ubuntu 22.04 #10

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Update of installation scripts to run on Ubuntu 22.04 #10

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31b076f
Uptade of intgration-scripts to install codeface in a local virtual m…
alcemirsantos Jun 10, 2023
689a9c6
Changed the base urls for automatic redirection to servers worldwide.
alcemirsantos Jun 10, 2023
2c90c36
Comment out line requesting the installation of a package knwon as a …
alcemirsantos Jun 12, 2023
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30 changes: 20 additions & 10 deletions integration-scripts/install_codeface_R.sh
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Expand Up @@ -4,21 +4,31 @@

echo "Providing R libraries"

sudo DEBIAN_FRONTEND=noninteractive apt-get -qqy install r-base r-base-dev

sudo apt install r-base-core=4.1.2-1ubuntu2
sudo apt install r-base-dev=4.1.2-1ubuntu2
sudo apt-mark hold r-base-core r-base-dev
sudo R CMD javareconf

sudo DEBIAN_FRONTEND=noninteractive apt-get -qqy install \
r-cran-zoo r-cran-xts \
r-cran-xtable r-cran-reshape r-cran-stringr r-cran-scales \
r-cran-scales r-cran-rmysql r-cran-rcurl r-cran-mgcv \
r-cran-rjson r-cran-testthat libx11-dev libssl-dev libssh2-1-dev \
libudunits2-dev
sudo apt install r-cran-littler=0.3.15-1
sudo apt install r-cran-lattice=0.20-45-1
sudo apt install r-cran-zoo
sudo apt install r-cran-xts
sudo apt install r-cran-xtable
sudo apt install r-cran-reshape
sudo apt install r-cran-stringr
sudo apt install r-cran-scales
sudo apt install r-cran-rmysql
sudo apt install r-cran-rcurl
sudo apt install r-cran-nlme=3.1.155-1
sudo apt install r-cran-matrix=1.4-0-1
sudo apt install r-cran-mgcv=1.8-39-1
sudo apt install r-cran-rjson
sudo apt install r-cran-testthat
sudo apt install libx11-dev libssl-dev libssh2-1-dev libudunits2-dev

# install newer version of GDAL for compatibility with automatically selected packages
sudo add-apt-repository -y ppa:ubuntugis/ppa
sudo apt-get update -qq
sudo DEBIAN_FRONTEND=noninteractive apt-get -y install libgdal-dev libgdal20
sudo DEBIAN_FRONTEND=noninteractive apt-get -y install libgdal-dev libgdal30

echo "Providing R libraries - packages.r"

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3 changes: 1 addition & 2 deletions integration-scripts/install_codeface_node.sh
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Expand Up @@ -6,8 +6,7 @@ echo "Providing id_service"

sudo DEBIAN_FRONTEND=noninteractive apt-get -qqy install npm
cd id_service
sudo mkdir node_modules
sudo chown vagrant.vagrant node_modules
mkdir node_modules
npm set ca null
npm install --no-bin-links
cd ..
6 changes: 3 additions & 3 deletions integration-scripts/install_codeface_python.sh
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Expand Up @@ -4,9 +4,9 @@

echo "Providing codeface python"

sudo pip install --upgrade setuptools
sudo pip install --upgrade mock
sudo pip install --upgrade subprocess32
sudo pip2 install --upgrade setuptools
sudo pip2 install --upgrade mock
sudo pip2 install --upgrade subprocess32

# Only development mode works
# install fails due to R scripts accessing unbundled resources!
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8 changes: 4 additions & 4 deletions integration-scripts/install_common.sh
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Expand Up @@ -9,13 +9,13 @@ echo "mysql-server mysql-server/root_password_again password" | sudo debconf-set

sudo DEBIAN_FRONTEND=noninteractive apt-get -qqy install sinntp texlive default-jdk \
mysql-common mysql-client libgraphviz-dev libarchive13 libhunspell-dev \
mysql-server python-dev universal-ctags nodejs git subversion libxslt1-dev \
mysql-server python3-dev universal-ctags nodejs git subversion libxslt1-dev \
sloccount graphviz doxygen libxml2-dev libcurl4-openssl-dev \
libmysqlclient-dev libcairo2-dev libxt-dev libcairo2-dev libmysqlclient-dev \
astyle xsltproc libxml2 libxml2-dev python build-essential libyaml-dev \
astyle xsltproc libxml2 libxml2-dev python3 build-essential libyaml-dev \
libxml2-dev libcurl4-openssl-dev xorg-dev libx11-dev libgles2-mesa-dev \
gfortran libglu1-mesa-dev libxt-dev libpoppler-dev libpoppler-glib-dev python-mock \
libapparmor-dev libpoppler-cpp-dev
gfortran libglu1-mesa-dev libxt-dev libpoppler-dev libpoppler-glib-dev python3-mock \
libapparmor-dev libpoppler-cpp-dev cmake libmagick++-dev python2-dev python-pip libharfbuzz-dev libfribidi-dev

# Make sure that the mysql socket file is available as /var/run/mysqld/mysqld.sock
# and /tmp/mysql.sock.
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2 changes: 1 addition & 1 deletion integration-scripts/install_cppstats.sh
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Expand Up @@ -23,7 +23,7 @@ fi
(cd ${TMPDIR} &&
tar -xvf ${TMPDIR}/cppstats.tar.gz &&
cd cppstats-${CPPSTATS_VERSION} &&
sudo python setup.py install)
sudo python2 setup.py install)

echo "Providing srcML"
SRCML_URL="http://131.123.42.38/lmcrs/beta/srcML-Ubuntu14.04-64.deb"
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12 changes: 2 additions & 10 deletions integration-scripts/install_repositories.sh
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Expand Up @@ -6,16 +6,8 @@ sudo DEBIAN_FRONTEND=noninteractive apt-get -qqy install software-properties-com
echo "Adding R cran repositories"
version=`lsb_release -r | awk '{ print $2;}'`

case ${version} in
"14.04")
echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" | sudo tee -a /etc/apt/sources.list
;;
"16.04")
echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" | sudo tee -a /etc/apt/sources.list
;;
*) echo "Unsupported version of Ubuntu detected, aborting"
exit 1;;
esac
deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -
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19 changes: 10 additions & 9 deletions packages.r
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Expand Up @@ -61,15 +61,16 @@ if (is.na(num.cores)) {
## install potentially unresolvable dependencies
install.packages("devtools")
library(devtools)
devtools::install_url("https://cran.r-project.org/src/contrib/Archive/BH/BH_1.75.0-0.tar.gz")
devtools::install_url("https://cran.r-project.org/src/contrib/Archive/slam/slam_0.1-40.tar.gz")
devtools::install_url("https://cran.r-project.org/src/contrib/Archive/arules/arules_1.5-0.tar.gz")
devtools::install_url("https://cran.r-project.org/src/contrib/Archive/proxy/proxy_0.4-16.tar.gz")
#devtools::install_url("https://cran.r-project.org/src/contrib/Archive/tm/tm_0.7-1.tar.gz")
devtools::install_url("https://cran.r-project.org/src/contrib/Archive/logging/logging_0.8-104.tar.gz")
#devtools::install_url("https://cran.r-project.org/src/contrib/Archive/markovchain/markovchain_0.6.9.11.tar.gz")
devtools::install_url("https://cran.r-project.org/src/contrib/Archive/rjson/rjson_0.2.20.tar.gz")
devtools::install_github("nathan-russell/hashmap")
devtools::install_url("https://cloud.r-project.org/CRAN/src/contrib/Archive/BH/BH_1.75.0-0.tar.gz")
devtools::install_url("https://cloud.r-project.org/CRAN/src/contrib/Archive/slam/slam_0.1-40.tar.gz")
devtools::install_url("https://cloud.r-project.org/CRAN/src/contrib/Archive/arules/arules_1.5-0.tar.gz")
devtools::install_url("https://cloud.r-project.org/CRAN/src/contrib/Archive/proxy/proxy_0.4-16.tar.gz")
devtools::install_url("https://cloud.r-project.org/CRAN/src/contrib/Archive/tm/tm_0.7-1.tar.gz")
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This line regarding package "tm" was commented out on purpose, as other packages were not compatible with tm_0.7-1 any more. I remember that I had encountered some errors with this version of tm last year, and therefore, I had commented out this line --- when this line is commented out and no other version of tm is already installed, the most recent version of this package is installed further below in this script, which was version 0.7-8 in my case. So, I would recommend to use version tm_0.7-8 instead of tm_0.7-1 to prevent errors here.

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I commented the line out again.

devtools::install_url("https://cloud.r-project.org/CRAN/src/contrib/Archive/logging/logging_0.8-104.tar.gz")
devtools::install_url("https://cloud.r-project.org/CRAN/src/contrib/Archive/markovchain/markovchain_0.8.6.tar.gz")
devtools::install_url("https://cloud.r-project.org/CRAN/src/contrib/Archive/rjson/rjson_0.2.20.tar.gz")
devtools::install_url("https://cloud.r-project.org/CRAN/src/contrib/Archive/hashmap/hashmap_0.2.2.tar.gz")
# devtools::install_github("nathan-russell/hashmap")

## install from BioConductor
p <- filter.installed.packages(c("BiRewire", "BiocGenerics", "graph"))
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5 changes: 3 additions & 2 deletions setup.py
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Expand Up @@ -27,6 +27,7 @@
packages=find_packages(exclude=['experiments']),
package_data={'codeface': ['R/*.r', 'R/cluster/*.r', 'perl/*.pl']},
entry_points={'console_scripts': ['codeface = codeface.cli:main']},
install_requires=['progressbar', 'VCS', 'python-ctags3','PyYAML',
'mysqlclient', 'jira', 'ftfy<5']
install_requires=['progressbar', 'VCS', 'python-ctags3','PyYAML==3.12',
'mysqlclient<2', 'jira==1.0.14', 'ftfy<5', 'requests==2.18.4', 'Pygments==2.1.3',
'certifi==2018.1.18']
)