V3: Package versions and dependencies

Introduction

RWsearch stands for « Search in R packages, task views, CRAN and in the Web ».

This vignette introduces the following features cited in the README file:

.7. Plot the graph of the package dependencies in an html page in your browser.

.8. List the parent and children dependencies of one or several packages, either the first level or the full list (termed recursive).

.9. Use this information to reinstall or install packages and their dependencies in the right order, from the lowest number to the largest number of dependencies, and avoid mic-mac (very useful).

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)

{ width=67% }

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:

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    16

Packages 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     6

p_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))


Try the RWsearch package in your browser

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RWsearch documentation built on June 5, 2021, 5:06 p.m.