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Konrad Siek edited this page Oct 3, 2018
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I had to pin my repos in order to get some of the packages that are not in stretch from older distros:
/etc/apt/sources.list:
# deb http://ftp.debian.cz/debian stretch main
deb http://ftp.debian.cz/debian stretch main
deb-src http://ftp.debian.cz/debian stretch main
deb http://security.debian.org/debian-security stretch/updates main
deb-src http://security.debian.org/debian-security stretch/updates main
# stretch-updates, previously known as 'volatile'
deb http://ftp.debian.cz/debian stretch-updates main
deb-src http://ftp.debian.cz/debian stretch-updates main
# older release for older packages (pinned)
deb http://ftp.debian.cz/debian jessie main
deb-src http://ftp.debian.cz/debian jessie main
# even older release for even older packages (pinned)
deb http://ftp.debian.cz/debian wheezy main
deb-src http://ftp.debian.cz/debian wheezy main
/etc/apt/preferences:
Package: *
Pin: release o=Debian a=stretch
Pin-Priority: 700
Package: *
Pin: release o=Debian a=jessie
Pin-Priority: 300
Package: *
Pin: release o=Debian a=wheezy
Pin-Priority: 200
I used gdebi throughout, so install that. The alternative is to use dpkg -i instead.
sudo apt-get install gdebi
Missing packages:
-
install
texliveandinstall-info(needed formktexlsrintextmf)sudo apt-get install texlive install-info -
install missing packages from http://statmath.wu.ac.at/AASC/debian/archive-amd64/
wget http://statmath.wu.ac.at/AASC/debian/archive-amd64/aasc-base_0.5-4_all.deb \ http://statmath.wu.ac.at/AASC/debian/archive-amd64/aasc-texmf-site_20070427-1_all.deb \ http://statmath.wu.ac.at/AASC/debian/archive-amd64/openbugs_3.2.1-1_amd64.deb \ http://statmath.wu.ac.at/AASC/debian/archive-amd64/mosek_6.0.0.135-2_amd64.deb sudo gdebi aasc-base_0.5-4_all.deb sudo gdebi aasc-texmf-site_20070427-1_all.deb # see below in case of problems sudo gdebi openbugs_3.2.1-1_amd64.deb sudo gdebi mosek_6.0.0.135-2_amd64.deb -
If (or... when inadvertantly)
aasc-textmf-sitebreaks on install with the message:install-info: No such file or directory for texmf-lg.info.gz dpkg: error processing package aasc-texmf-site (--install): subprocess installed post-installation script returned error exit status 1 Errors were encountered while processing: aasc-texmf-siteEdit
/var/lib/dpkg/info/aasc-texmf-site.postinst, the path to/usr/local/share/info/texmf-lg.info.gzis wrong (give full path).Then:
sudo dpkg --configure -a -
mysql: install the deb containing the repo config: https://dev.mysql.com/doc/mysql-apt-repo-quick-guide/en/#apt-repo-fresh-installwget https://dev.mysql.com/get/mysql-apt-config_0.8.7-1_all.deb gdebi mysql-apt-config_0.8.7-1_all.deb sudo apt-get update
Install the debian rcheck metapackage for all OS dependencies: http://statmath.wu.ac.at/AASC/debian/
sudo apt-get update
wget http://statmath.wu.ac.at/AASC/debian/rcheckserver_2.15-54_amd64.deb
sudo gdebi rcheckserver_2.15-54_amd64.deb
sudo apt-get update
sudo apt-get install subversion calibre rsync anacron xvfb xkb-data build-essential gfortran \
libreadline-dev time libglu1-mesa-dev xorg-dev bwidget fftw-dev graphviz-dev \
lam-runtime lam4-dev libboost-dev libgdal-dev libgmp3-dev libgsl-dev libperl-dev \
portaudio19-dev libquantlib0-dev pvm-dev libgtk2.0-dev libxml2-dev libhdf5-serial-dev \
imagemagick ttf-sjfonts ggobi libsprng2-dev libproj-dev dieharder libdieharder-dev \
libgd2-xpm-dev wordnet-dev poppler-utils locate libglade2-dev texlive-full ess auctex \
r-base r-recommended aasc-texmf-site jags libicu-dev libspreadsheet-parseexcel-perl \
libtext-csv-xs-perl libqt4-dev libxslt1-dev ant kdelibs5-dev xclip libmpfr-dev \
libtiff5-dev libitpp-dev xserver-xorg iwidgets4 libdb-dev noweb libfftw3-dev \
libprotobuf-dev libprotoc-dev protobuf-compiler libarmadillo-dev libmagickwand-dev \
libmpich-dev libopenmpi-dev openmpi-bin libudunits2-dev coinor-libsymphony-dev \
libscalapack-mpi-dev pari-gp qpdf libgeos-dev lua5.1 liblua5.2-dev libnetcdf-dev \
netcdf-bin libmpc-dev coinor-libclp-dev libjpeg-dev libboost-program-options-dev \
highlight libraptor2-dev default-jdk libglpk-dev openbugs libc6-dev-i386 libev-dev \
cmake mosek tk-table heirloom-mailx liboctave-dev libsndfile-dev libapparmor-dev \
coinor-libcgl-dev coinor-libosi-dev python-dev libpoppler-glib-dev python-pygments \
rst2pdf python-mechanize mongodb gdal-bin biber tcl-dev tk-dev python-numpy \
libhiredis-dev libnlopt-dev pandoc libv8-dev libzmq3-dev curl libapt-pkg-dev \
libsasl2-dev pandoc-citeproc librdf-dev ipython libsbml-dev saga libboost-regex-dev \
libboost-system-dev libsodium-dev libboost-iostreams-dev libpoppler-cpp-dev \
libhunspell-dev libimage-exiftool-perl libmagick++-dev libmagic-dev
sudo apt-get install ttf-kochi-gothic
sudo apt-get install libmysqlclient-dev libmariadb-client-lgpl-dev-compat libmariadb-dev
# these were not listed in the metapackage, but are required
sudo apt-get install libssl-dev libssh2-1-dev gdal-bin libgdal-dev
# this conflicts...
sudo apt-get install libmariadb-client-lgpl-dev
OpenBUGS requires manual installation, AFAIK:
PPWD="$PWD"
mkdir /tmp/OpenBUGS
cd /tmp/OpenBUGS
wget 'http://www.openbugs.net/w/OpenBUGS_3_2_3?action=AttachFile&do=get&target=OpenBUGS-3.2.3.tar.gz' -O OpenBUGS-3.2.3.tar.gz
tar zxvf OpenBUGS-3.2.3.tar.gz
cd OpenBUGS-3.2.3
./configure
make
sudo make install
cd "$PPWD"
NVCC/CUDA (on ubuntu):
wget https://developer.nvidia.com/compute/cuda/9.0/Prod/local_installers/cuda-repo-ubuntu1604-9-0-local_9.0.176-1_amd64-deb
sudo dpkg -i cuda-repo-ubuntu1604-9-0-local_9.0.176-1_amd64-deb
sudo apt-key add /var/cuda-repo-9-0-local/7fa2af80.pub
sudo apt-get update
sudo apt-get install cuda
BOOST (on Ubuntu):
sudo apt-get install libboost-all-dev
List of ubuntu packages (rcheck.sels): https://github.com/PRL-PRG/R-dyntrace/wiki/Ubuntu-Package-List
sudo dpkg --set-selections < rcheck.sels
sudo aptitude install
sudo apt-get dselect-upgrade
Blind leading the blind?
The directory where we want to download CRAN is $CRAN_DIR. This is not the directory where it is going to be installed, just where our local repository will be located.
export CRAN_SOURCES="/data/kondziu/R/CRAN"
mkdir -p "$CRAN_SOURCES"
rsync -rtlzv --delete cran.r-project.org::CRAN/src/contrib "$CRAN_SOURCES"Before running R, make sure you have DISPLAY set for an available X server, some packages need it; so if you are running on a remote server, you can do:
nohup Xvfb :6 -screen 0 1280x1024x24 >/dev/null 2>&1 &
export DISPLAY=:6Create a fresh directory where packages should be installed, eg. /data/R/libs/.
Set your R_LIBS to point to that directory:
export R_LIBS=/data/kondziu/R/installed
mkdir -p $R_LIBS(TODO: set this variable in run_vignettes.sh etc. and add it to metadata)
Set all relevant environmental variables:
export R_COMPILE_PKGS=1
export R_DISABLE_BYTECODE=0
export R_ENABLE_JIT=0
export R_KEEP_PKG_SOURCE=yes
Then open up R and:
dir.create("/tmp/install_R_pkg")
setwd("/tmp/install_R_pkg")
contrib.url <- paste("file://", "/home/kondziu/R/sources/CRAN" ,"/contrib/", sep="")
install_all_of_these <- function(packages) {
already.installed <- installed.packages()
installed_packages <- setdiff(packages, already.installed[,"Package"])
install.packages(
pkgs=installed_packages, # which packages to install
contriburl=contrib.url, # where to install packages from
# lib=R_LIBS, # where to install packages to
Ncpus=8, # run in parallel using N cores
#keep_outputs=T, # keeps outputs in ".out" files in current directory
INSTALL_opts=c(
"--byte-compile", # byte-compile packages
"--example", # extract and keep examples
"--install-tests", # copy and retain test directory for the package
"--with-keep.source", # keep line numbers
"--no-multiarch"),
dependencies = c("Depends") # also install packages this package requires
# "Imports",
# "LinkingTo",
# "Suggests",
# "Enhances"))
)
}
source("https://bioconductor.org/biocLite.R")
library(BiocInstaller)
install_all_of_these_bioc <- function(packages) {
already.installed <- installed.packages()
installed_packages <- setdiff(packages, already.installed[,"Package"])
biocLite(
installed_packages, # which packages to install
Ncpus=8, # run in parallel using N cores
INSTALL_opts=c(
"--byte-compile", # byte-compile packages
"--example", # extract and keep examples
"--install-tests", # copy and retain test directory for the package
"--with-keep.source", # keep line numbers
"--no-multiarch"),
dependencies = c("Depends") # also install packages this package requires
)
}
packages_status <- function() {
already_installed_packages <- installed.packages()[, "Package"]
all_cran_packages <- available.packages(contriburl=contrib.url)[, "Package"]
already_installed_cran_packages <- intersect(all_cran_packages, already_installed_packages)
all_bioc_packages <- available.packages(repos = biocinstallRepos()[1])[, "Package"]
already_installed_bioc_packages <- intersect(all_bioc_packages, already_installed_packages)
all_packages <- union(all_cran_packages, all_bioc_packages)
data.frame(
all_packages=length(all_packages),
all_already_installed_packages=length(already_installed_packages),
cran_packages=length(all_cran_packages),
cran_already_installed_packages=length(already_installed_cran_packages),
bioc_packages=length(all_bioc_packages),
bioc_already_installed_packages=length(already_installed_bioc_packages)
)
}
get_packages_to_install_cran <- function () {
all.packages <- available.packages(contriburl=contrib.url)
already.installed <- installed.packages()
setdiff(all.packages[,"Package"], already.installed[,"Package"])
}
get_packages_to_install_bioc <- function () {
all.packages <- available.packages(repos = biocinstallRepos()[1])
already.installed <- installed.packages()
setdiff(all.packages[,"Package"], already.installed[,"Package"])
}
install_all_of_these(get_packages_to_install_cran())
install_all_of_these_bioc(get_packages_to_install_cran())
install_all_of_these_bioc(get_packages_to_install_bioc())