Use pak when package installation is not found

[schloerke]

Fixes #234

This PR is to get the conversation going to hopefully remove maintenance requirements of shinyapps.io by offloading to pak which uses RSPM to query rstudio/r-system-requirements

Benefits:

• Unify the installation patterns
• Stop playing wack-a-mole on installations failures that are defined elsewhere
• From https://github.com/rstudio/r-system-requirements readme:

This metric indicates how good the rules are for the majority of packages R users are likely to install
Ubuntu 18
No rules 90.1%
With rules 99.2%".

Setup:

• If there is no install script, then pak is used.
  • This PR does not use the CRAN version of pak. Instead, it uses the hosted version provided by RStudio's r-lib team. This is done to update rapidly as bug fixes are found. I'd recommend moving to a CRAN installation once the dev version makes it to CRAN.
  • Disadvantage: This requires RSPM to work / function, whereas the static files are known at install time.
• If there is a package install script, the install script is used.
  • Using the existing install script will not install dependencies for the required packages. I do not know which packages are supplied at install time. Ex: rgl originally only wanted to install libgl1-mesa-dev and libgl-mesa-dev, where pak says it requires:

❯❯ pak::pkg_system_requirements("rgl", "ubuntu", "18.04")
 [1] "apt-get install -y imagemagick"      "apt-get install -y libmagick++-dev"  "apt-get install -y make"
 [4] "apt-get install -y libicu-dev"       "apt-get install -y pandoc"           "apt-get install -y libfreetype6-dev"
 [7] "apt-get install -y libglu1-mesa-dev" "apt-get install -y libpng-dev"       "apt-get install -y libgl1-mesa-dev"
[10] "apt-get install -y zlib1g-dev"

Alterations:

• I have removed simple installation files that immediately matched ubuntu 18.04. If there were more complicated ones, like sodium, I did not remove their install script.
• I am working on making a GitHub Action to test all known packages. (bionic && xenial)

Future:

Game plan moving forward. I'd recommend spamming the few handful of authors for packages like av which require system installations, but do not report them so that rstudio/r-system-requirements picks them up automatically. (Curious as to why av by Jeroen doesn't have any pak sys reqs when its SystemRequirements looks like: FFmpeg (>= 3.2); with at least libx264 and lame (mp3) drivers. Debian/Ubuntu:libavfilter-dev, Fedora/CentOS: ffmpeg-devel (via https://rpmfusion.org), MacOS Homebrew: ffmpeg.)

pak system requirements for existing packages

ubuntu 16.04 sys requirements

❯❯ pkgs %>% setNames(., .)%>% lapply(pak::pkg_system_requirements, "ubuntu", "16.04")
$animation
[1] "apt-get install -y imagemagick"          "apt-get install -y libmagick++-dev"
[3] "apt-get install -y texlive"              "apt-get install -y swftools"
[5] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"

$av
character(0)

$convertGraph
character(0)

$docxtractr
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libxml2-dev"

$gdalUtils
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:ubuntugis/ppa"
[3] "apt-get update"                                "apt-get install -y libgdal-dev"
[5] "apt-get install -y gdal-bin"                   "apt-get install -y libproj-dev"

$gert
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:cran/libgit2"
[3] "apt-get update"                                "apt-get install -y libcurl4-openssl-dev"
[5] "apt-get install -y libssl-dev"                 "apt-get install -y git"
[7] "apt-get install -y libgit2-dev"

$gmp
[1] "apt-get install -y libgmp3-dev"

$gridGraphics
character(0)

$gsl
[1] "apt-get install -y libgsl0-dev"

$hunspell
character(0)

$igraph
[1] "apt-get install -y libglpk-dev" "apt-get install -y libgmp3-dev" "apt-get install -y libxml2-dev"

$jqr
character(0)

$keyring
[1] "apt-get install -y libsodium-dev"   "apt-get install -y libsecret-1-dev" "apt-get install -y libssl-dev"

$lwgeom
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:ubuntugis/ppa"
[3] "apt-get update"                                "apt-get install -y libgeos-dev"
[5] "apt-get install -y libproj-dev"                "apt-get install -y libgdal-dev"
[7] "apt-get install -y gdal-bin"                   "apt-get install -y libudunits2-dev"

$magick
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y imagemagick"          "apt-get install -y libmagick++-dev"

$ncdf4
[1] "apt-get install -y libnetcdf-dev"

$openbabel
character(0)

$pagedown
[1] "apt-get install -y libicu-dev" "apt-get install -y pandoc"     "apt-get install -y make"
[4] "apt-get install -y libssl-dev"

$pdftools
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libpoppler-cpp-dev"

$pensieve
character(0)

$ragg
[1] "apt-get install -y libfontconfig1-dev" "apt-get install -y libfreetype6-dev"
[3] "apt-get install -y libjpeg-dev"        "apt-get install -y libpng-dev"
[5] "apt-get install -y libtiff-dev"        "apt-get install -y libfribidi-dev"
[7] "apt-get install -y libharfbuzz-dev"

$RAmazonS3
character(0)

$rcbc
character(0)

$rcdd
[1] "apt-get install -y libgmp3-dev"

$rDEA
[1] "apt-get install -y libglpk-dev"

$redland
[1] "apt-get install -y libxml2-dev" "apt-get install -y libicu-dev"  "apt-get install -y librdf0-dev"
[4] "apt-get install -y pandoc"

$rgdal
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:ubuntugis/ppa"
[3] "apt-get update"                                "apt-get install -y libgdal-dev"
[5] "apt-get install -y gdal-bin"                   "apt-get install -y libproj-dev"

$rgeos
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:ubuntugis/ppa"
[3] "apt-get update"                                "apt-get install -y libgeos-dev"

$rgl
 [1] "apt-get install -y imagemagick"      "apt-get install -y libmagick++-dev"  "apt-get install -y make"
 [4] "apt-get install -y libicu-dev"       "apt-get install -y pandoc"           "apt-get install -y libfreetype6-dev"
 [7] "apt-get install -y libglu1-mesa-dev" "apt-get install -y libpng-dev"       "apt-get install -y libgl1-mesa-dev"
[10] "apt-get install -y zlib1g-dev"

$Rglpk
[1] "apt-get install -y libglpk-dev"

$rJava
[1] "apt-get install -y make"        "apt-get install -y default-jdk"

$Rmpfr
[1] "apt-get install -y libgmp3-dev" "apt-get install -y libmpfr-dev"

$Rpoppler
[1] "apt-get install -y libglib2.0-dev"     "apt-get install -y libpoppler-cpp-dev"

$rPython
character(0)

$RSelenium
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libxml2-dev"

$rsvg
[1] "apt-get install -y librsvg2-dev"

$Rsymphony
character(0)

$seewave
[1] "apt-get install -y libsndfile1-dev"

$sf
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:ubuntugis/ppa"
[3] "apt-get update"                                "apt-get install -y libgdal-dev"
[5] "apt-get install -y gdal-bin"                   "apt-get install -y libgeos-dev"
[7] "apt-get install -y libproj-dev"                "apt-get install -y libudunits2-dev"

$sodium
[1] "apt-get install -y libsodium-dev"

$ssh
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y git"                  "apt-get install -y libssh2-1-dev"

$staplr
[1] "apt-get install -y make"        "apt-get install -y default-jdk" "apt-get install -y libxml2-dev"
[4] "apt-get install -y libicu-dev"

$tensorflow
[1] "apt-get install -y python"

$tesseract
[1] "apt-get install -y libleptonica-dev"     "apt-get install -y libtesseract-dev"
[3] "apt-get install -y tesseract-ocr-eng"    "apt-get install -y libcurl4-openssl-dev"
[5] "apt-get install -y libssl-dev"           "apt-get install -y libpoppler-cpp-dev"

$tiff
[1] "apt-get install -y libjpeg-dev" "apt-get install -y libtiff-dev"

$tkrplot
character(0)

$tm
[1] "apt-get install -y libxml2-dev"

$topicmodels
[1] "apt-get install -y libxml2-dev" "apt-get install -y libgsl0-dev"

$udunits2
[1] "apt-get install -y libudunits2-dev"

$units
[1] "apt-get install -y libudunits2-dev"

$V8
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libv8-dev"

$websocket
[1] "apt-get install -y make"       "apt-get install -y libssl-dev"

$xslt
[1] "apt-get install -y libxml2-dev" "apt-get install -y libxslt-dev"

ubuntu 18.04 sys requirements

$animation
[1] "apt-get install -y imagemagick"          "apt-get install -y libmagick++-dev"
[3] "apt-get install -y texlive"              "apt-get install -y swftools"
[5] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"

$av
character(0)

$convertGraph
character(0)

$docxtractr
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libxml2-dev"

$gdalUtils
[1] "apt-get install -y libgdal-dev" "apt-get install -y gdal-bin"    "apt-get install -y libproj-dev"

$gert
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:cran/libgit2"
[3] "apt-get update"                                "apt-get install -y libcurl4-openssl-dev"
[5] "apt-get install -y libssl-dev"                 "apt-get install -y git"
[7] "apt-get install -y libgit2-dev"

$gmp
[1] "apt-get install -y libgmp3-dev"

$gridGraphics
character(0)

$gsl
[1] "apt-get install -y libgsl0-dev"

$hunspell
character(0)

$igraph
[1] "apt-get install -y libglpk-dev" "apt-get install -y libgmp3-dev" "apt-get install -y libxml2-dev"

$jqr
[1] "apt-get install -y libjq-dev"

$keyring
[1] "apt-get install -y libsodium-dev"   "apt-get install -y libsecret-1-dev" "apt-get install -y libssl-dev"

$lwgeom
[1] "apt-get install -y libgeos-dev"     "apt-get install -y libproj-dev"     "apt-get install -y libgdal-dev"
[4] "apt-get install -y gdal-bin"        "apt-get install -y libudunits2-dev"

$magick
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y imagemagick"          "apt-get install -y libmagick++-dev"

$ncdf4
[1] "apt-get install -y libnetcdf-dev"

$openbabel
character(0)

$pagedown
[1] "apt-get install -y libicu-dev" "apt-get install -y pandoc"     "apt-get install -y make"
[4] "apt-get install -y libssl-dev"

$pdftools
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libpoppler-cpp-dev"

$pensieve
character(0)

$ragg
[1] "apt-get install -y libfontconfig1-dev" "apt-get install -y libfreetype6-dev"
[3] "apt-get install -y libjpeg-dev"        "apt-get install -y libpng-dev"
[5] "apt-get install -y libtiff-dev"        "apt-get install -y libfribidi-dev"
[7] "apt-get install -y libharfbuzz-dev"

$RAmazonS3
character(0)

$rcbc
character(0)

$rcdd
[1] "apt-get install -y libgmp3-dev"

$rDEA
[1] "apt-get install -y libglpk-dev"

$redland
[1] "apt-get install -y libxml2-dev" "apt-get install -y libicu-dev"  "apt-get install -y librdf0-dev"
[4] "apt-get install -y pandoc"

$rgdal
[1] "apt-get install -y libgdal-dev" "apt-get install -y gdal-bin"    "apt-get install -y libproj-dev"

$rgeos
[1] "apt-get install -y libgeos-dev"

$rgl
 [1] "apt-get install -y imagemagick"      "apt-get install -y libmagick++-dev"  "apt-get install -y make"
 [4] "apt-get install -y libicu-dev"       "apt-get install -y pandoc"           "apt-get install -y libfreetype6-dev"
 [7] "apt-get install -y libglu1-mesa-dev" "apt-get install -y libpng-dev"       "apt-get install -y libgl1-mesa-dev"
[10] "apt-get install -y zlib1g-dev"

$Rglpk
[1] "apt-get install -y libglpk-dev"

$rJava
[1] "apt-get install -y make"        "apt-get install -y default-jdk"

$Rmpfr
[1] "apt-get install -y libgmp3-dev" "apt-get install -y libmpfr-dev"

$Rpoppler
[1] "apt-get install -y libglib2.0-dev"     "apt-get install -y libpoppler-cpp-dev"

$rPython
character(0)

$RSelenium
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libxml2-dev"

$rsvg
[1] "apt-get install -y librsvg2-dev"

$Rsymphony
character(0)

$seewave
[1] "apt-get install -y libsndfile1-dev"

$sf
[1] "apt-get install -y libgdal-dev"     "apt-get install -y gdal-bin"        "apt-get install -y libgeos-dev"
[4] "apt-get install -y libproj-dev"     "apt-get install -y libudunits2-dev"

$sodium
[1] "apt-get install -y libsodium-dev"

$ssh
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y git"                  "apt-get install -y libssh2-1-dev"

$staplr
[1] "apt-get install -y make"        "apt-get install -y default-jdk" "apt-get install -y libxml2-dev"
[4] "apt-get install -y libicu-dev"

$tensorflow
[1] "apt-get install -y python"

$tesseract
[1] "apt-get install -y libleptonica-dev"     "apt-get install -y libtesseract-dev"
[3] "apt-get install -y tesseract-ocr-eng"    "apt-get install -y libcurl4-openssl-dev"
[5] "apt-get install -y libssl-dev"           "apt-get install -y libpoppler-cpp-dev"

$tiff
[1] "apt-get install -y libjpeg-dev" "apt-get install -y libtiff-dev"

$tkrplot
character(0)

$tm
[1] "apt-get install -y libxml2-dev"

$topicmodels
[1] "apt-get install -y libxml2-dev" "apt-get install -y libgsl0-dev"

$udunits2
[1] "apt-get install -y libudunits2-dev"

$units
[1] "apt-get install -y libudunits2-dev"

$V8
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libv8-dev"

$websocket
[1] "apt-get install -y make"       "apt-get install -y libssl-dev"

$xslt
[1] "apt-get install -y libxml2-dev" "apt-get install -y libxslt-dev"

ubuntu 20.04 sys requirements

$animation
[1] "apt-get install -y imagemagick"          "apt-get install -y libmagick++-dev"
[3] "apt-get install -y texlive"              "apt-get install -y libcurl4-openssl-dev"
[5] "apt-get install -y libssl-dev"

$av
character(0)

$convertGraph
character(0)

$docxtractr
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libxml2-dev"

$gdalUtils
[1] "apt-get install -y libgdal-dev" "apt-get install -y gdal-bin"    "apt-get install -y libproj-dev"

$gert
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y git"                  "apt-get install -y libgit2-dev"

$gmp
[1] "apt-get install -y libgmp3-dev"

$gridGraphics
character(0)

$gsl
[1] "apt-get install -y libgsl0-dev"

$hunspell
character(0)

$igraph
[1] "apt-get install -y libglpk-dev" "apt-get install -y libgmp3-dev" "apt-get install -y libxml2-dev"

$jqr
[1] "apt-get install -y libjq-dev"

$keyring
[1] "apt-get install -y libsodium-dev"   "apt-get install -y libsecret-1-dev" "apt-get install -y libssl-dev"

$lwgeom
[1] "apt-get install -y libgeos-dev"     "apt-get install -y libproj-dev"     "apt-get install -y libgdal-dev"
[4] "apt-get install -y gdal-bin"        "apt-get install -y libudunits2-dev"

$magick
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y imagemagick"          "apt-get install -y libmagick++-dev"

$ncdf4
[1] "apt-get install -y libnetcdf-dev"

$openbabel
character(0)

$pagedown
[1] "apt-get install -y libicu-dev" "apt-get install -y pandoc"     "apt-get install -y make"
[4] "apt-get install -y libssl-dev"

$pdftools
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libpoppler-cpp-dev"

$pensieve
character(0)

$ragg
[1] "apt-get install -y libfontconfig1-dev" "apt-get install -y libfreetype6-dev"
[3] "apt-get install -y libjpeg-dev"        "apt-get install -y libpng-dev"
[5] "apt-get install -y libtiff-dev"        "apt-get install -y libfribidi-dev"
[7] "apt-get install -y libharfbuzz-dev"

$RAmazonS3
character(0)

$rcbc
character(0)

$rcdd
[1] "apt-get install -y libgmp3-dev"

$rDEA
[1] "apt-get install -y libglpk-dev"

$redland
[1] "apt-get install -y libxml2-dev" "apt-get install -y libicu-dev"  "apt-get install -y librdf0-dev"
[4] "apt-get install -y pandoc"

$rgdal
[1] "apt-get install -y libgdal-dev" "apt-get install -y gdal-bin"    "apt-get install -y libproj-dev"

$rgeos
[1] "apt-get install -y libgeos-dev"

$rgl
 [1] "apt-get install -y imagemagick"      "apt-get install -y libmagick++-dev"  "apt-get install -y make"
 [4] "apt-get install -y libicu-dev"       "apt-get install -y pandoc"           "apt-get install -y libfreetype6-dev"
 [7] "apt-get install -y libglu1-mesa-dev" "apt-get install -y libpng-dev"       "apt-get install -y libgl1-mesa-dev"
[10] "apt-get install -y zlib1g-dev"

$Rglpk
[1] "apt-get install -y libglpk-dev"

$rJava
[1] "apt-get install -y make"        "apt-get install -y default-jdk"

$Rmpfr
[1] "apt-get install -y libgmp3-dev" "apt-get install -y libmpfr-dev"

$Rpoppler
[1] "apt-get install -y libglib2.0-dev"     "apt-get install -y libpoppler-cpp-dev"

$rPython
character(0)

$RSelenium
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libxml2-dev"

$rsvg
[1] "apt-get install -y librsvg2-dev"

$Rsymphony
character(0)

$seewave
[1] "apt-get install -y libsndfile1-dev"

$sf
[1] "apt-get install -y libgdal-dev"     "apt-get install -y gdal-bin"        "apt-get install -y libgeos-dev"
[4] "apt-get install -y libproj-dev"     "apt-get install -y libudunits2-dev"

$sodium
[1] "apt-get install -y libsodium-dev"

$ssh
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y git"                  "apt-get install -y libssh2-1-dev"

$staplr
[1] "apt-get install -y make"        "apt-get install -y default-jdk" "apt-get install -y libxml2-dev"
[4] "apt-get install -y libicu-dev"

$tensorflow
[1] "apt-get install -y python"

$tesseract
[1] "apt-get install -y libleptonica-dev"     "apt-get install -y libtesseract-dev"
[3] "apt-get install -y tesseract-ocr-eng"    "apt-get install -y libcurl4-openssl-dev"
[5] "apt-get install -y libssl-dev"           "apt-get install -y libpoppler-cpp-dev"

$tiff
[1] "apt-get install -y libjpeg-dev" "apt-get install -y libtiff-dev"

$tkrplot
character(0)

$tm
[1] "apt-get install -y libxml2-dev"

$topicmodels
[1] "apt-get install -y libxml2-dev" "apt-get install -y libgsl0-dev"

$udunits2
[1] "apt-get install -y libudunits2-dev"

$units
[1] "apt-get install -y libudunits2-dev"

$V8
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libv8-dev"

$websocket
[1] "apt-get install -y make"       "apt-get install -y libssl-dev"

$xslt
[1] "apt-get install -y libxml2-dev" "apt-get install -y libxslt-dev"

GitHub Actions Testing

Testing all packages on focal and xenial. Packages that have an install file will use it, otherwise pak will be used.

https://github.com/schloerke/shinyapps-package-dependencies/runs/2143004651?check_suite_focus=true

---

cc @samperman