Like all R packages,
groundhog is open source so you can see how everything works looking at the posted R Code, but this page explains intuitively how
groundhog achieves reproducibility.
groundhog to work, for R to load the version of a package based on the date in the
groundhog.library() command, it needs to
1) Identify the package version for that date.
2) Identify all dependencies of the package on that date, and their versions.
3) Obtain all those package-versions, and save them in the user’s computer.
4) Load the specified versions of packages into the R environment being used.
This document explains how each of these necessary steps are achieved.
1) Find the package version that matches the
groundhog relies on a database that contains virtually all package versions ever uploaded to CRAN, the date when they were published, and all dependencies. Here are a few rows of that file (updated daily, and available here: http://groundhogR.com/cran.toc.rds). When a user enters the date they want a package for, a local copy of this table is consulted finding the most recently published version of the package for that date.
Details on how this database was created The database was created in three steps. First, an R script read the DESCRIPTION file for every package in the CRAN archives, obtaining dependencies and Published dates for all of them. But, it turns out that hundreds of Published dates are incorrect in those DESCRIPTION files. For example the DESCRIPTION for
MASS_7.3-45 indicates it was published on 2016-04-21, but it was actually published six months earlier, in November of 2015. Therefore, the Published date was obtained by running the command
available.packages() on the daily MRAN copy of CRAN, and using the first date on which the package appears as available, as the publication date (for packages pre-MRAN, the DESCRIPTION date is used. After the database was first created, in early 2020, it is updated daily with an R script in the groundhogR.com server that runs
available.packages() on CRAN daily, adding any new packages to the database, with the Publish date for when they were first found.
The database was created in three steps. First, an R script read the DESCRIPTION file for every package in the CRAN archives, obtaining dependencies and Published dates for all of them. But, it turns out that hundreds of Published dates are incorrect in those DESCRIPTION files. For example the DESCRIPTION for
2) Find all the dependencies
Using the same
cran.toc.rds file, we see all dependencies for a given package version. The
groundhog.library() command includes the function
get.snowball() which runs a loop finding the dependencies for the dependencies and so on until no new dependencies are to be added, and they are then sorted into the ‘snowball’. First in the snowball are packages that depend on no other package (referred affectionately as ‘independencies’), and the very last package in the snowball list is the package called on by
3) Obtain all those package-versions, and save them in the user’s computer
Snowball in hand, a loop checks if each package-version is installed locally in the computer, if not they are looked for online. First looking for a binary on CRAN, if not found, a binary on MRAN, if not found, source from CRAN.
4) Load the specified versions of packages into the R environment being used
Base R uses by default a single library to store packages, consisting of a folder with package names as subfolders (without indicating package version). Those subfolders contain only the latest installed version of the corresponding package, and the files are deleted and replaced when a package gets updated.
For example, here is a print-screen for the library folder for my R 3.6
The folder “beeswarm” contains (some version of) the package with that name. If I run
library('beeswarm') I would load it without controlling or easily knowing which version it is. If I run
install.packages('beeswarm') I would replace it with whichever version is current, without documenting in any way that the package has been modified.
groundhog uses a similar storage approach, but it enables version control. Specifically, and simply, each version of each package gets its own folder:
groundhog.library("beeswarm","2016-01-02") the script identifies which version is needed, using
cran.toc.rds, and knows which folder would have such package. If that folder is not found, the package is downloaded.
groundhog.library() then loads and attaches the desired package itself, in this case
beeswarm_0.2.1, by running library() specifying as the ‘library’ path the sub-folder that’s needed (e.g.,
library('beewswarm', lib.loc="~/groundhogR/R-3.6.2/beewsarm_0.2.1"). That ‘library’ only has that one package.
groundhog thus makes R take into account package version by treating the folder for each package-version as a library that’s called on the spot. Dependencies are added to the namespace in a similar fashion, with commands that treat each subfolder as its own library.
groundhog.library() leaves the stored paths for packages in base R,
groundhog does not alter the normal functioning of based commands like
install.packages(). They behave after using
grounghog exactly as they behaved before
To discontinue using
grounghog all users do is stop running the
No uninstall. No changing settings.