Refining system requirements

[michaelmayer2]

This is an early version of a PR that will enhance pak::pkg_system_requirements() so that it will check all R and Bioconductor type repositories on a given packagemanager (only URL of packagemanager needs to be specified) and extract system dependencies of a given set of packages.

Previously, pak::pkg_system_requirements() only worked for a single repository and the list of packages had to be split before making a function call.

In addition, the PR also automatically detects if a repository is of type Bioconductor and then appends bioc_version=x.y to the API call.

Example:

> pak::pkg_system_requirements(c("tidyverse","clustermq","flowcatchR"), os="ubuntu", os_release="20.04")
[1] "apt-get install -y  imagemagick  libmagick++-dev  gsfonts  libfreetype6-dev  libfribidi-dev  libharfbuzz-dev  libfontconfig1-dev  pandoc  libicu-dev  libjpeg-dev  libpng-dev  libtiff-dev  libzmq3-dev  zlib1g-dev  libssl-dev  make  libxml2-dev  libcurl4-openssl-dev"
> pak::pkg_system_requirements(c("tidyverse","clustermq","flowcatchR"), os="centos", os_release="7")
[1] "yum install -y epel-release"                                                                                                                                                                                                                                             
[2] "yum install -y  ImageMagick  ImageMagick-c++-devel  freetype-devel  fribidi-devel  harfbuzz-devel  fontconfig-devel  pandoc  libicu-devel  libjpeg-turbo-devel  libpng-devel  libtiff-devel  zeromq-devel  zlib-devel  openssl-devel  make  libxml2-devel  libcurl-devel"

Without the PR pak will report

> pak::pkg_system_requirements(c("tidyverse","clustermq","flowcatchR"), os="ubuntu", os_release="20.04")
Error: 
! error in pak subprocess
Caused by error in `asNamespace("pak")$system_requirements_internal(...)`:
! Could not locate package 'flowcatchR'
Type .Last.error to see the more details.

which is expected as flowcatchR is a Bioconductor package and as such not in the (default) CRAN repo.

Note:

• I deliberately left some verbose debug statements in. Also the code probably can be streamlined further by a more skilled R developers. Just wanted to make a start to get this functionality in in order to increase it's usability.
• the question around Bioconductor support probably needs to be discussed in more detail as the current PR has a hard dependency on the R package BiocManager.

[gaborcsardi]

Thanks! Unfortunately, this approach is not going to work, for a number of reasons. pak does not use the PPM API any more, to be able to match system requirements to individual R packages. Instead it matches SystemRequirements fields manually to the database at https://github.com/rstudio/r-system-requirements.

We could easily do the same for Bioc packages, but we would need another DB that lists the SystemRequirements fields of Bioc packages, as this is not part of the repository metadata.

[michaelmayer2]

Thanks for your feedback - does this mean the code https://github.com/r-lib/pak/blob/main/R/system-requirements.R#L72-L93 that still uses the RSPM API is no longer in use ?

[gaborcsardi]

Right. The sysreqs.R and sysreqs2.R files are used in the pkgdepends package.

[gaborcsardi]

With r-lib/pkgcache#96 and r-lib/pkgcache#97 (devel) pak now supports system requirements for Bioconductor packages:

> pak::pkg_sysreqs(c("r-lib/xml2", "CHRONOS"))
── Install scripts ──────────────────────────────────────────────────────────────── Ubuntu 22.04 ──
apt-get -y update
apt-get -y install libcurl4-openssl-dev libssl-dev libglpk-dev libgmp3-dev libxml2-dev \
  libpng-dev make default-jdk libicu-dev pandoc
R CMD javareconf
R CMD javareconf

── Packages and their system dependencies ─────────────────────────────────────────────────────────
CHRONOS – default-jdk, pandoc
curl    – libcurl4-openssl-dev, libssl-dev
igraph  – libglpk-dev, libgmp3-dev, libxml2-dev
openssl – libssl-dev
png     – libpng-dev
RCurl   – libcurl4-openssl-dev, make
rJava   – default-jdk, make
stringi – libicu-dev
XML     – libxml2-dev
xml2    – libxml2-dev

I hope this will solve your use cases.