Package dependencies
Let’s assume we wish to update or install the packages RWsearch, tfestimators and their respective dependencies depicted in the image below. In which order should we install them ?
A simple strategy is to apply install.packages(c(“RWsearch”, “tfestimators”)) and let the function manage the dependency order. A better strategy is to list all packages from the ones with no parent to the ones with many parents, then install these packages according to the list order. (Parallel) Installation is much faster and more secure as there is no recursive call and no branching. The list and the package order is provided with no pain by the instruction p_vers_deps().
crandb_load(system.file("data", "zcrandb.rda", package = "RWsearch"))
# or
# crandb_down()p_graphF() generates the graph of the package dependencies
p_graphF() generates a graph of the package dependencies and send it to the browser. See the image.
p_graphF(RWsearch, tfestimators)
p_vers_deps() lists the package dependencies in a proper order
dfr <- p_vers_deps(tfestimators, RWsearch) ; dfr
# nsloaded version crandb compare tdeps ndeps
# forge FALSE <NA> <NA> 3 0 0
# tfruns FALSE <NA> <NA> 3 0 0
# reticulate FALSE 1.20 <NA> 2 0 0
# config FALSE 0.3.1 <NA> 2 0 0
# yaml FALSE 2.2.1 <NA> 2 0 0
# pkgconfig TRUE 2.0.3 <NA> 2 0 0
# digest TRUE 0.6.25 <NA> 2 0 0
# base64enc FALSE 0.1-3 <NA> 2 0 0
# progress FALSE 1.2.2 <NA> 2 0 0
# tidyselect FALSE 1.1.1 <NA> 2 0 0
# purrr FALSE 0.3.4 <NA> 2 0 0
# tibble FALSE 3.1.2 <NA> 2 0 0
# tidyr FALSE 1.1.3 <NA> 2 0 0
# processx FALSE 3.4.2 <NA> 2 0 0
# rstudioapi FALSE 0.13 <NA> 2 0 0
# rlang TRUE 0.4.10 0.4.11 -1 0 0
# brew TRUE 1.0-6 1.0-6 0 0 0
# latexpdf TRUE 0.1.6 0.1.6 0 0 0
# sig TRUE 0.0-5 0.0-5 0 0 0
# magrittr TRUE 2.0.1 2.0.1 0 0 0
# jsonlite FALSE 1.7.1 1.7.2 -1 1 0
# XML TRUE 3.99-0.3 3.99-0.6 -1 2 0
# sos TRUE 2.0-2 2.0-2 0 1 1
# igraph TRUE 1.2.5 1.2.6 -1 10 2
# htmltools TRUE 0.4.0 0.5.1.1 -1 5 3
# htmlwidgets TRUE 1.5.1 1.5.3 -1 9 6
# tensorflow FALSE <NA> 2.4.0 -2 9 7
# networkD3 TRUE 0.4 0.4 0 18 10
# tfestimators FALSE <NA> 1.9.1 -2 18 16
# RWsearch TRUE 4.9.1 4.8.0 1 24 16 The colnames are the following:
- nsloaded: is the package loaded in the namespace or not? Here, RWsearch and its dependencies are looded and locked. A (ns)loaded package cannot be updated on the spot (especially if it has a dll/shared library, or S4 classes) but requires a fresh version of R with no external package loaded. Use preferably install.packages() or in some extreme cases R CMD INSTALL.
- version is the current version installed in your computer or NA if the package is not installed.
- crandb is the tar.gz version recorded in the crandb data.frame (here, a minimalist crandb with 110 packages was saved on 2021-06-02) and in your CRAN repository.
- compare compares the two version numbers:
- -2 is for a package not installed on the computer but available on CRAN.
- -1 is for a package installed on the computer but with an older version than the one on CRAN.
- 0 are for installed packages up to date.
- +1 is for a fresh package that is more recent than the one on CRAN, typically the packages under development or downloaded from another repository.
- +2 is for a package installed on the computer but not available on CRAN. It can be either a package that comes from another repository (github, gitlab, Bioconductor, R-forge, etc) or a pckage that has been removed from CRAN and archived.
- +3 is for a package that is not installed on the computer and not available. It can ba for a instance a package available on another repository (github, gitlab, Bioconductor, R-forge, etc).
- tdeps is the total number of recursive parent dependencies, including the generic packages (stats, utils, tools, parallel, etc).
- ndeps is the total number of recursive parent dependencies excluding the generic packages, since they are provided with every R version and are not stored on CRAN.
Note: In this current version of RWsearch, the comparison is done with the tar.gz version stored on the repository (CRAN, miniCRAN, local, etc), not with the binary versions (macOS, Windows) that are published a few days later. The installation of mixed source/binary version is therefore recommended for Windows and mcOS users (but requires Rtools to be installed).
Packages with comparison number -2 and -1 can be installed according to the list order, which is from low values to high values of ndeps.
Subset the data.frame of the package dependencies
Packages that can be installed on the spot are:
dfr1 <- subset(dfr, compare < 0 & nsloaded == FALSE) ; dfr1
# nsloaded version crandb compare tdeps ndeps
# jsonlite FALSE 1.7.1 1.7.2 -1 1 0
# tensorflow FALSE <NA> 2.4.0 -2 9 7
# tfestimators FALSE <NA> 1.9.1 -2 18 16Packages to be installed later are:
subset(dfr, compare < 0 & nsloaded == TRUE)
# nsloaded version crandb compare tdeps ndeps
# rlang TRUE 0.4.10 0.4.11 -1 0 0
# XML TRUE 3.99-0.3 3.99-0.6 -1 2 0
# igraph TRUE 1.2.5 1.2.6 -1 10 2
# htmltools TRUE 0.4.0 0.5.1.1 -1 5 3
# htmlwidgets TRUE 1.5.1 1.5.3 -1 9 6p_inst() installs the packages
p_inst() is a simple wrapper around install.packages() with non-standard evaluation permitted. For all non-standard cases, use more sophisticated functions like install.packages() or remotes::remotes().
p_inst(rownames(dfr1))