ccb-hms / nhanes-database

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More Ubuntu package install candidates #101

Closed deepayan closed 9 months ago

deepayan commented 11 months ago

This is a tentative list of new packages that users may prefer to have installed in the Docker. Caveat: this list is based on Debian, so may need to be adjusted for Ubuntu.

The following list gives the additional packages installed by the rocker R-devel container, excluding the ones currently installed (explicitly) by the NHANES docker:

bash-completion bison debhelper default-jdk gdb groff-base libblas-dev libcurl4-openssl-dev 
libjpeg-dev liblapack-dev libncurses-dev libpango1.0-dev libtiff5-dev libxt-dev mpack tcl-dev 
texlive-base texlive-extra-utils texlive-fonts-extra texlive-fonts-recommended 
texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-plain-generic tk-dev 
x11proto-core-dev xdg-utils xfonts-base xvfb zlib1g-dev

These are basic packages that a user locally building R packages will expect to be available, I think.

CRAN sysadmins maintain a Debian metapackage called rcheckserver that pulls in additional packages that should then allow building all CRAN packages. This may be overkill for us, but for the record, this currently installs the following packages, again excluding all packages already accounted for above (current NHANES + rocker/R-devel).

4ti2 anacron ant aspell aspell-en auctex biber bindfs bsd-mailx build-essential bwidget calibre 
cargo coinor-libcgl-dev coinor-libclp-dev coinor-libosi-dev coinor-libsymphony-dev 
default-libmysqlclient-dev devscripts dieharder dvisvgm ffmpeg fftw-dev flex fonts-sjfonts 
gdal-bin ggobi golang gretl highlight hunspell hunspell-en-gb hunspell-en-us imagemagick 
ipython3 iwidgets4 jags jupyter-client jupyter-core jupyter-nbconvert lam-runtime lam4-dev 
libapparmor-dev libapt-pkg-dev libarchive-dev libarmadillo-dev libavfilter-dev libboost-dev 
libboost-iostreams-dev libboost-locale-dev libboost-program-options-dev libboost-regex-dev 
libboost-system-dev libbsd-dev libc6-dev-i386 libcgal-dev libdb-dev libdeflate-dev 
libdieharder-dev libev-dev libfftw3-dev libgd-dev libgdal-dev libgeos-dev libgeos++-dev 
libglade2-dev libglpk-dev libglu1-mesa-dev libgmp3-dev libgpgme-dev libgraphviz-dev libgsl-dev 
libgtk2.0-dev libhdf5-serial-dev libhiredis-dev libhunspell-dev libidn-dev 
libimage-exiftool-perl libitpp-dev libjq-dev liblapacke-dev libleptonica-dev liblua5.2-dev 
libmagic-dev libmagick++-dev libmagickwand-dev libmecab-dev libmpc-dev libmpfr-dev libmpich-dev 
libnetcdf-dev libopencv-dev libopenmpi-dev libperl-dev libpoppler-cpp-dev libpoppler-glib-dev 
libproj-dev libprotobuf-dev libprotoc-dev libquantlib0-dev librabbitmq-dev libraptor2-dev 
librdf-dev librrd-dev libsasl2-dev libsbml-dev libscalapack-mpi-dev libsecret-1-dev 
libsndfile-dev libsodium-dev libspreadsheet-parseexcel-perl libsprng2-dev libssh-dev 
libtesseract-dev libtext-csv-xs-perl libudunits2-dev libv8-dev libxslt1-dev libzmq3-dev locate 
lua5.1 netcdf-bin noweb octave-dev openbugs openmpi-bin pandoc pari-gp poppler-utils 
portaudio19-dev protobuf-compiler pvm-dev python3-mechanize python3-numpy python3-pkg-resources 
python3-pygments qpdf rrdtool rsync s-nail saga scala subversion 
tesseract-ocr-eng texlive-full tidy time tk-table wordnet-dev xclip xkb-data xorg-dev 
xserver-xorg
nathan-palmer commented 9 months ago

fixed with version-0.2.0