1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
|
#!/usr/bin/env r
#
# A simple example to install one or more packages from GitHub
#
# Copyright (C) 2014 - 2026 Carl Boettiger and Dirk Eddelbuettel
#
# Released under GPL (>= 2)
## load docopt and remotes (or devtools) from CRAN
suppressMessages({
library(docopt) # we need docopt (>= 0.3) as on CRAN
library(remotes) # or can use devtools as a fallback
})
## configuration for docopt
doc <- "Usage: installGithub.r [-h] [-x] [-d DEPS] [-u UPDATE] [-r REPOS...] [-t TYPE] [GHREPOS...]
-d --deps DEPS install suggested dependencies as well? [default: NA]
-u --update UPDATE update dependencies? [default: TRUE]
-r --repos REPOS repositor(y|ies) to use if deps required [default: getOption]
-t --type TYPE installation type as used by `install.packages` [default: source]
-h --help show this help text
-x --usage show help and short example usage
Note that if `bspm` is seen and option `bspm.version.check` is `FALSE` the `type` option is
switched to `both` to permit `bspm` to install e.g. build-dependencies as r2u binaries."
opt <- docopt(doc) # docopt parsing
if (opt$usage) {
cat(doc, "\n\n")
cat("where GHREPOS... is one or more GitHub repositories.
Basic usage:
installGithub.r RcppCore/RcppEigen
Install multiple R packages from GitHub:
installGithub.r RcppCore/Rcpp RcppCore/RcppEigen
Install multiple R packages from GitHub listing the packages on separate lines with some comments:
installGithub.r \\
RcppCore/Rcpp \\
RcppCore/RcppEigen
Installing a specific branch, tag or commit:
installGithub.r RcppCore/Rcpp@1.0.0
Installing from a repo subdirectory:
installGithub.r chanzuckerberg/cellxgene-census/api/r/cellxgene.census
Setting multiple R package repositories to install dependencies of the R package:
installGithub.r -r https://cloud.r-project.org -r https://eddelbuettel.github.io/drat RcppCore/RcppEigen
installGithub.r is part of littler which brings 'r' to the command-line.
See http://dirk.eddelbuettel.com/code/littler.html for more information.\n")
q("no")
}
## ensure installation is stripped
Sys.setenv("_R_SHLIB_STRIP_"="true")
if (opt$deps == "TRUE" || opt$deps == "FALSE") {
opt$deps <- as.logical(opt$deps)
} else if (opt$deps == "NA") {
opt$deps <- NA
}
if (length(opt$repos) == 1 && opt$repos == "getOption") {
## as littler can now read ~/.littler.r and/or /etc/littler.r we can preset elsewhere
opt$repos <- getOption("repos")
}
if (requireNamespace("bspm", quietly=TRUE) & isFALSE(getOption("bspm.version.check", TRUE))) {
## when bspm is installed and set to prefer binaries, select type both
opt$type <- "both"
}
opt$update <- as.logical(opt$update)
invisible(sapply(opt$GHREPOS, function(r) install_github(r, dependencies = opt$deps, upgrade = opt$update, repos = opt$repos, type = opt$type)))
|
