diff --git a/integration-scripts/install_codeface_R.sh b/integration-scripts/install_codeface_R.sh index 9d153b34..2937212f 100755 --- a/integration-scripts/install_codeface_R.sh +++ b/integration-scripts/install_codeface_R.sh @@ -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" diff --git a/integration-scripts/install_codeface_node.sh b/integration-scripts/install_codeface_node.sh index 6611865c..322312ea 100755 --- a/integration-scripts/install_codeface_node.sh +++ b/integration-scripts/install_codeface_node.sh @@ -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 .. diff --git a/integration-scripts/install_codeface_python.sh b/integration-scripts/install_codeface_python.sh index 72c0034b..7624335f 100755 --- a/integration-scripts/install_codeface_python.sh +++ b/integration-scripts/install_codeface_python.sh @@ -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! diff --git a/integration-scripts/install_common.sh b/integration-scripts/install_common.sh index 182a10ad..f67032f7 100755 --- a/integration-scripts/install_common.sh +++ b/integration-scripts/install_common.sh @@ -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. diff --git a/integration-scripts/install_cppstats.sh b/integration-scripts/install_cppstats.sh index 8b8ef710..aaf487be 100755 --- a/integration-scripts/install_cppstats.sh +++ b/integration-scripts/install_cppstats.sh @@ -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" diff --git a/integration-scripts/install_repositories.sh b/integration-scripts/install_repositories.sh index d87c7779..7a8a2f34 100755 --- a/integration-scripts/install_repositories.sh +++ b/integration-scripts/install_repositories.sh @@ -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 - diff --git a/packages.r b/packages.r index b43cf6c9..2681d864 100644 --- a/packages.r +++ b/packages.r @@ -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") +# gitdevtools::install_url("https://cloud.r-project.org/CRAN/src/contrib/Archive/tm/tm_0.7-1.tar.gz") +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")) diff --git a/setup.py b/setup.py index 5ae58935..00c8aaf3 100644 --- a/setup.py +++ b/setup.py @@ -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'] )