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
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
|
snapshotPackratDependencies <- function(bundleDir,
implicit_dependencies = character(),
verbose = FALSE) {
addPackratSnapshot(bundleDir, implicit_dependencies, verbose = verbose)
lockFilePath <- packratLockFile(bundleDir)
df <- as.data.frame(read.dcf(lockFilePath), stringsAsFactors = FALSE)
unlink(dirname(lockFilePath), recursive = TRUE)
# get repos defined in the lockfile
repos <- gsub("[\r\n]", " ", df[1, "Repos"])
repos <- strsplit(unlist(strsplit(repos, "\\s*,\\s*", perl = TRUE)), "=", fixed = TRUE)
repos <- setNames(
sapply(repos, "[[", 2),
sapply(repos, "[[", 1)
)
# get packages records defined in the lockfile
records <- utils::tail(df, -1)
if (nrow(records) == 0) {
return(data.frame())
}
rownames(records) <- NULL
records <- records[manifestPackageColumns(records)]
records[c("Source", "Repository")] <- standardizeRecords(records, repos)
records$description <- lapply(records$Package, package_record)
records
}
standardizeRecords <- function(records, repos) {
availablePackages <- availablePackages(repos)
repos <- standardizeRepos(repos)
rows <- lapply(seq_len(nrow(records)), function(i) {
standardizePackratPackage(records[i, ], availablePackages, repos = repos)
})
rows <- lapply(rows, as.data.frame, stringsAsFactors = FALSE)
rbind_fill(rows, c("Source", "Repository"))
}
standardizeRepos <- function(repos) {
# Ensure that each repository has a unique name
names(repos) <- ifelse(
names2(repos) == "",
paste0("repo_", seq_along(repos)),
names2(repos)
)
# And strip trailing /
repos <- gsub("/$", "", repos)
repos
}
standardizePackratPackage <- function(record, availablePackages, repos = character()) {
pkg <- record$Package
source <- record$Source
# source types are defined by packrat:
# https://github.com/rstudio/packrat/blob/v0.9.0/R/pkg.R#L328
if (source %in% c("github", "gitlab", "bitbucket")) {
# SCM information is recorded elsewhere
repository <- NA_character_
} else if (source == "source") {
# can't install source packages elsewhere
repository <- NA_character_
source <- NA_character_
} else if (source == "CustomCRANLikeRepository" && isDevVersion(record, availablePackages)) {
# Package was installed from source, but packrat guessed it was installed
# from a known repo.
repository <- NA_character_
source <- NA_character_
} else if (source %in% c("CRAN", "Bioconductor")) {
# shinyapps & posit.cloud will ignore, but connect will use (unless admin
# has set up an override)
repository <- findRepoUrl(pkg, availablePackages)
} else {
# Installed from custom repository. Find URL from available.packages()
# and then name from repos.
repository <- findRepoUrl(pkg, availablePackages)
source <- findRepoName(repository, repos)
}
list(Source = source, Repository = repository)
}
findRepoName <- function(repository, repos) {
idx <- match(repository, repos)
names(repos)[idx]
}
findRepoUrl <- function(pkg, availablePackages) {
idx <- match(pkg, availablePackages[, "Package"])
if (!is.na(idx)) {
repo <- availablePackages[[idx, "Repository"]]
# Strip `/src/contrib/*` from package repository: `contrib.url()`
# adds /src/contrib, and RSPM adds additional directories
gsub("/src/contrib.*$", "", repo)
} else {
NA_character_
}
}
isDevVersion <- function(record, availablePackages) {
idx <- match(record$Package, availablePackages[, "Package"])
if (is.na(idx)) {
return(FALSE)
}
local_version <- record$Version
repo_version <- availablePackages[idx, "Version"]
package_version(local_version) > package_version(repo_version)
}
addPackratSnapshot <- function(bundleDir,
implicit_dependencies = character(),
verbose = FALSE) {
# if we discovered any extra dependencies, write them to a file for packrat to
# discover when it creates the snapshot
recordExtraDependencies(bundleDir, implicit_dependencies)
withCallingHandlers(
performPackratSnapshot(bundleDir, verbose = verbose),
error = function(err) {
abort("Failed to snapshot dependencies", parent = err)
},
warning = function(cnd) {
invokeRestart("muffleWarning")
}
)
invisible()
}
recordExtraDependencies <- function(bundleDir, pkgs, env = caller_env()) {
if (length(pkgs) == 0) {
return()
}
depPath <- file.path(bundleDir, "__rsconnect_deps.R")
writeLines(paste0("library(", pkgs, ")\n"), depPath)
# Automatically delete when the _caller_ finishes
defer(unlink(depPath), env = env)
invisible()
}
performPackratSnapshot <- function(bundleDir, verbose = FALSE) {
# ensure we snapshot recommended packages
srp <- packrat::opts$snapshot.recommended.packages()
packrat::opts$snapshot.recommended.packages(TRUE, persist = FALSE)
defer(packrat::opts$snapshot.recommended.packages(srp, persist = FALSE))
# Force renv dependency scanning within packrat unless the option has been
# explicitly configured. This is a no-op for older versions of packrat.
renvDiscovery <- getOption("packrat.dependency.discovery.renv")
if (is.null(renvDiscovery)) {
old <- options("packrat.dependency.discovery.renv" = TRUE)
defer(options(old))
}
# attempt to eagerly load the BiocInstaller or BiocManaager package if
# installed, to work around an issue where attempts to load the package could
# fail within a 'suppressMessages()' context
packages <- c("BiocManager", "BiocInstaller")
for (package in packages) {
if (is_installed(package)) {
requireNamespace(package, quietly = TRUE)
break
}
}
suppressMessages(
packrat::.snapshotImpl(
project = bundleDir,
snapshot.sources = FALSE,
fallback.ok = TRUE,
verbose = verbose,
implicit.packrat.dependency = FALSE
)
)
invisible()
}
packratLockFile <- function(bundleDir) {
file.path(bundleDir, "packrat", "packrat.lock")
}
|
