43 | ![]()
46 |
47 | License
44 | 45 |YEAR: 2020 48 | COPYRIGHT HOLDER: Iñaki Ucar 49 |50 | 51 |
${s.title}
`;
142 | } else if (s.previous_headings == "") {
143 | return `${s.dir} > ${s.title}
> ${s.what}`;
144 | } else {
145 | return `${s.dir} > ${s.title}
> ${s.previous_headings} > ${s.what}`;
146 | }
147 | },
148 | },
149 | },
150 | ]).on('autocomplete:selected', function(event, s) {
151 | window.location.href = s.path + "?q=" + q + "#" + s.id;
152 | });
153 | });
154 | })(window.jQuery || window.$)
155 |
156 |
157 |
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/docs/LICENSE-text.html:
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64 |
65 |
66 |
67 |
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70 |
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/docs/bootstrap-toc.js:
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1 | /*!
2 | * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
3 | * Copyright 2015 Aidan Feldman
4 | * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
5 | (function() {
6 | 'use strict';
7 |
8 | window.Toc = {
9 | helpers: {
10 | // return all matching elements in the set, or their descendants
11 | findOrFilter: function($el, selector) {
12 | // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/
13 | // http://stackoverflow.com/a/12731439/358804
14 | var $descendants = $el.find(selector);
15 | return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])');
16 | },
17 |
18 | generateUniqueIdBase: function(el) {
19 | var text = $(el).text();
20 | var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-');
21 | return anchor || el.tagName.toLowerCase();
22 | },
23 |
24 | generateUniqueId: function(el) {
25 | var anchorBase = this.generateUniqueIdBase(el);
26 | for (var i = 0; ; i++) {
27 | var anchor = anchorBase;
28 | if (i > 0) {
29 | // add suffix
30 | anchor += '-' + i;
31 | }
32 | // check if ID already exists
33 | if (!document.getElementById(anchor)) {
34 | return anchor;
35 | }
36 | }
37 | },
38 |
39 | generateAnchor: function(el) {
40 | if (el.id) {
41 | return el.id;
42 | } else {
43 | var anchor = this.generateUniqueId(el);
44 | el.id = anchor;
45 | return anchor;
46 | }
47 | },
48 |
49 | createNavList: function() {
50 | return $('');
51 | },
52 |
53 | createChildNavList: function($parent) {
54 | var $childList = this.createNavList();
55 | $parent.append($childList);
56 | return $childList;
57 | },
58 |
59 | generateNavEl: function(anchor, text) {
60 | var $a = $('');
61 | $a.attr('href', '#' + anchor);
62 | $a.text(text);
63 | var $li = $('');
64 | $li.append($a);
65 | return $li;
66 | },
67 |
68 | generateNavItem: function(headingEl) {
69 | var anchor = this.generateAnchor(headingEl);
70 | var $heading = $(headingEl);
71 | var text = $heading.data('toc-text') || $heading.text();
72 | return this.generateNavEl(anchor, text);
73 | },
74 |
75 | // Find the first heading level (`
42 |
52 |
53 |
54 | `, then ``, etc.) that has more than one element. Defaults to 1 (for ``).
76 | getTopLevel: function($scope) {
77 | for (var i = 1; i <= 6; i++) {
78 | var $headings = this.findOrFilter($scope, 'h' + i);
79 | if ($headings.length > 1) {
80 | return i;
81 | }
82 | }
83 |
84 | return 1;
85 | },
86 |
87 | // returns the elements for the top level, and the next below it
88 | getHeadings: function($scope, topLevel) {
89 | var topSelector = 'h' + topLevel;
90 |
91 | var secondaryLevel = topLevel + 1;
92 | var secondarySelector = 'h' + secondaryLevel;
93 |
94 | return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
95 | },
96 |
97 | getNavLevel: function(el) {
98 | return parseInt(el.tagName.charAt(1), 10);
99 | },
100 |
101 | populateNav: function($topContext, topLevel, $headings) {
102 | var $context = $topContext;
103 | var $prevNav;
104 |
105 | var helpers = this;
106 | $headings.each(function(i, el) {
107 | var $newNav = helpers.generateNavItem(el);
108 | var navLevel = helpers.getNavLevel(el);
109 |
110 | // determine the proper $context
111 | if (navLevel === topLevel) {
112 | // use top level
113 | $context = $topContext;
114 | } else if ($prevNav && $context === $topContext) {
115 | // create a new level of the tree and switch to it
116 | $context = helpers.createChildNavList($prevNav);
117 | } // else use the current $context
118 |
119 | $context.append($newNav);
120 |
121 | $prevNav = $newNav;
122 | });
123 | },
124 |
125 | parseOps: function(arg) {
126 | var opts;
127 | if (arg.jquery) {
128 | opts = {
129 | $nav: arg
130 | };
131 | } else {
132 | opts = arg;
133 | }
134 | opts.$scope = opts.$scope || $(document.body);
135 | return opts;
136 | }
137 | },
138 |
139 | // accepts a jQuery object, or an options object
140 | init: function(opts) {
141 | opts = this.helpers.parseOps(opts);
142 |
143 | // ensure that the data attribute is in place for styling
144 | opts.$nav.attr('data-toggle', 'toc');
145 |
146 | var $topContext = this.helpers.createChildNavList(opts.$nav);
147 | var topLevel = this.helpers.getTopLevel(opts.$scope);
148 | var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
149 | this.helpers.populateNav($topContext, topLevel, $headings);
150 | }
151 | };
152 |
153 | $(function() {
154 | $('nav[data-toggle="toc"]').each(function(i, el) {
155 | var $nav = $(el);
156 | Toc.init($nav);
157 | });
158 | });
159 | })();
160 |
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/docs/404.html:
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1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 | Page not found (404) • bspm
9 |
10 |
11 |
12 |
13 |
14 |
18 |
19 |
20 | Skip to contents
21 |
22 |
23 |
60 |
61 |
62 | ![]()
Page not found (404)
63 |
64 |
65 |
66 | Content not found. Please use links in the navbar.
67 |
68 |
69 |
70 |
71 |
72 |
83 |
84 |
85 |
86 |
87 |
88 |
89 |
90 |
91 |
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/inst/service/bspm.py:
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1 | #!/usr/bin/python3
2 |
3 | from os import path
4 | WDIR = path.dirname(path.realpath(__file__))
5 | exec(open(WDIR + "/dbus-paths").read())
6 |
7 | def read_conf(force_discover=False):
8 | global PREF, EXCL
9 | pref = WDIR + "/bspm.pref"
10 | excl = WDIR + "/bspm.excl"
11 |
12 | force_discover = force_discover and not path.exists(WDIR + "/nodiscover")
13 | if force_discover or not path.exists(pref) or not path.exists(excl):
14 | import backend
15 | conf = backend.discover()
16 | with open(pref, "w") as fpref, open(excl, "w") as fexcl:
17 | for i in conf["prefixes"]:
18 | print(i, file=fpref)
19 | for i in conf["exclusions"]:
20 | print(i, file=fexcl)
21 | with open(pref) as fpref, open(excl) as fexcl:
22 | PREF = [line.rstrip() for line in fpref]
23 | EXCL = [line.rstrip() for line in fexcl]
24 |
25 | def call_backend(cmd, pkgs=None, root=False):
26 | import backend
27 | msg = cmd.capitalize() + " system packages"
28 | if root:
29 | msg = msg + " as root"
30 | msg = msg + "..."
31 | print(msg, flush=True)
32 | if pkgs:
33 | return getattr(backend, cmd)(PREF, pkgs, EXCL)
34 | return getattr(backend, cmd)(PREF, EXCL)
35 |
36 | def run_as_service():
37 | from gi.repository import GLib
38 |
39 | import dbus
40 | import dbus.service
41 | import dbus.mainloop.glib
42 |
43 | from functools import wraps
44 | from contextlib import redirect_stdout
45 | import signal
46 |
47 | class PackageManagerException(dbus.DBusException):
48 | _dbus_error_name = IFACE + ".PackageManagerException"
49 |
50 | def stderr(pid):
51 | return open("/proc/" + str(pid) + "/fd/2", "w")
52 |
53 | def redirect_output(fn):
54 | @wraps(fn)
55 | def wrapper(self, pid, *args, **kw):
56 | with stderr(pid) as f, redirect_stdout(f):
57 | return fn(self, pid, *args, **kw)
58 | return wrapper
59 |
60 | def handle_exceptions(timeout):
61 | def _handle_exceptions(fn):
62 | @wraps(fn)
63 | def wrapper(*args, **kw):
64 | signal.alarm(0)
65 | try:
66 | out = fn(*args, **kw)
67 | except Exception as err:
68 | raise PackageManagerException(str(err))
69 | finally:
70 | signal.alarm(timeout)
71 | return out
72 | return wrapper
73 | return _handle_exceptions
74 |
75 | class PackageManager(dbus.service.Object):
76 |
77 | @dbus.service.method(IFACE, in_signature="i", out_signature="")
78 | @handle_exceptions(10)
79 | @redirect_output
80 | def discover(self, pid):
81 | read_conf(True)
82 | return
83 |
84 | @dbus.service.method(IFACE, in_signature="i", out_signature="as")
85 | @handle_exceptions(10)
86 | @redirect_output
87 | def available(self, pid):
88 | return call_backend("available")
89 |
90 | @dbus.service.method(IFACE, in_signature="ias", out_signature="as")
91 | @handle_exceptions(10)
92 | @redirect_output
93 | def install(self, pid, pkgs):
94 | return call_backend("install", pkgs)
95 |
96 | @dbus.service.method(IFACE, in_signature="ias", out_signature="as")
97 | @handle_exceptions(10)
98 | @redirect_output
99 | def remove(self, pid, pkgs):
100 | return call_backend("remove", pkgs)
101 |
102 | def sigterm_handler(_signo, _stack_frame):
103 | mainloop.quit()
104 |
105 | dbus.mainloop.glib.DBusGMainLoop(set_as_default=True)
106 | signal.signal(signal.SIGINT, sigterm_handler)
107 | signal.signal(signal.SIGTERM, sigterm_handler)
108 | signal.signal(signal.SIGALRM, sigterm_handler)
109 |
110 | bus = dbus.SystemBus()
111 | bus.request_name(BUS_NAME)
112 | pm = PackageManager(bus, OPATH)
113 |
114 | mainloop = GLib.MainLoop()
115 | mainloop.run()
116 |
117 | def run_as_root(args):
118 | try:
119 | if args.cmd == "discover":
120 | read_conf(True)
121 | return
122 | read_conf()
123 | pkgs = None
124 | if hasattr(args, "pkg"):
125 | pkgs = args.pkg
126 | pkgs = call_backend(args.cmd, pkgs, root=True)
127 | if args.o is not None:
128 | with open(args.o, "a") as f:
129 | for pkg in pkgs:
130 | print(pkg, file=f)
131 | else:
132 | print("Result:", pkgs)
133 | except Exception as err:
134 | if args.o is not None:
135 | with open(args.o, "a") as f:
136 | print(str(err), file=f)
137 | raise err
138 |
139 | if __name__ == "__main__":
140 | import argparse
141 |
142 | parser = argparse.ArgumentParser()
143 | subparser = parser.add_subparsers(dest="cmd")
144 | parser_discover = subparser.add_parser("discover", aliases=["available"])
145 | parser_discover.add_argument("-o", metavar="file", type=str, help="output file")
146 | parser_install = subparser.add_parser("install", aliases=["remove"])
147 | parser_install.add_argument("pkg", type=str, nargs="+")
148 | parser_install.add_argument("-o", metavar="file", type=str, help="output file")
149 |
150 | args = parser.parse_args()
151 | if args.cmd is None:
152 | read_conf()
153 | run_as_service()
154 | else:
155 | run_as_root(args)
156 |
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/R/utils.R:
--------------------------------------------------------------------------------
1 | #' Find Shadowed Packages
2 | #'
3 | #' Find packages that are \emph{shadowed} by others in library locations
4 | #' with a higher priority.
5 | #'
6 | #' @param lib.loc character vector describing the location of the \R library
7 | #' trees to search through, or \code{NULL} for all known trees
8 | #' (see \code{\link{.libPaths}}).
9 | #' @return A \code{data.frame} with one row per package, row names the package
10 | #' names and column names (currently) "Package", "LibPath", "Version",
11 | #' "Shadow.LibPath", "Shadow.Version", "Shadow.Newer".
12 | #'
13 | #' @details \R supports setting several locations for library trees. This is a
14 | #' powerful feature, but many times packages end up installed in multiple
15 | #' locations, and in such cases \R silently uses the one in the path with the
16 | #' highest priority (appearing first in \code{\link{.libPaths}}), thus
17 | #' \emph{shadowing} packages in locations with a lower priority.
18 | #'
19 | #' For \pkg{bspm} installations, this means that outdated user packages may
20 | #' break system libraries. This utility reports packages that are shadowed
21 | #' (one per row) with information on which location ("Shadow.LibPath")
22 | #' and version ("Shadow.Version") has priority over it.
23 | #' The \code{\link{moveto_sys}} method is a great complement to move such
24 | #' outdated versions to the system libraries.
25 | #'
26 | #' @seealso \code{\link{moveto_sys}}
27 | #' @export
28 | shadowed_packages <- function(lib.loc=NULL) {
29 | if (is.null(lib.loc)) lib.loc <- .libPaths()
30 |
31 | fields <- c("Package", "LibPath", "Version")
32 | sfields <- paste("Shadow", fields, sep=".")
33 | shadow <- data.frame(matrix(nrow=0, ncol=5))
34 | colnames(shadow) <- c(fields, sfields[-1])
35 |
36 | pkgs <- data.frame(utils::installed.packages(lib.loc)[, fields])
37 | pkgs <- split(pkgs, factor(pkgs$LibPath, levels=lib.loc))
38 |
39 | idx <- seq_along(pkgs)
40 | for (i in idx) {
41 | colnames(pkgs[[i]]) <- sfields
42 | for (j in idx[-seq_len(i)]) {
43 | hidden <- merge(pkgs[[j]], pkgs[[i]], by.x=fields[1], by.y=sfields[1])
44 | shadow <- rbind(shadow, hidden)
45 | }
46 | }
47 |
48 | row.names(shadow) <- shadow[, "Package"]
49 | shadow$Version <- as.package_version(shadow$Version)
50 | shadow$Shadow.Version <- as.package_version(shadow$Shadow.Version)
51 | newer <- shadow[, "Version"] < shadow[, "Shadow.Version"]
52 | shadow <- cbind(shadow, Shadow.Newer = newer)
53 | shadow
54 | }
55 |
56 | list_inst <- function() {
57 | libs <- unique(c(.Library.site, .Library))
58 | inst <- unique(row.names(utils::installed.packages(libs)))
59 | inst
60 | }
61 |
62 | list_deps <- function(packages, db, which, recursive) {
63 | deps <- tools::package_dependencies(packages, db, which, recursive)
64 | deps <- unique(unlist(deps, use.names=FALSE))
65 | deps
66 | }
67 |
68 | # get package dependencies
69 | pkg_deps <- function(pkgs, dependencies, db, all=TRUE) {
70 | pkgs <- unique(pkgs)
71 | deps <- list_deps(pkgs, db, c("Depends", "Imports"), recursive=TRUE)
72 | if (!all)
73 | deps <- c(deps, list_deps(pkgs, db, "LinkingTo", recursive=FALSE))
74 | if (isTRUE(dependencies) || "Suggests" %in% dependencies)
75 | deps <- c(deps, list_deps(pkgs, db, "Suggests", recursive=FALSE))
76 | if ("Enhances" %in% dependencies)
77 | deps <- c(deps, list_deps(pkgs, db, "Enhances", recursive=FALSE))
78 | deps <- unique(c(setdiff(deps, list_inst()), if (all) pkgs))
79 | deps
80 | }
81 |
82 | # get LinkingTo-only dependencies for src packages
83 | hard_deps <- function(pkgs, db, mask) {
84 | srcs <- c(pkgs$bins[mask], pkgs$srcs)
85 | deps <- list_deps(srcs, db, "LinkingTo", recursive=FALSE)
86 | deps <- setdiff(deps, c(list_inst(), pkgs$bins, pkgs$srcs))
87 | deps
88 | }
89 |
90 | # adapted from install.packages
91 | # get available binaries and pkgs with later versions available
92 | check_versions <- function(pkgs, db) {
93 | dbb <- available_sys()
94 | row.names(dbb) <- tolower(row.names(dbb))
95 |
96 | bins <- pkgs[tolower(pkgs) %in% row.names(dbb)]
97 | srcs <- pkgs[! pkgs %in% bins]
98 |
99 | binvers <- dbb[tolower(bins), "Version"]
100 | srcvers <- sapply(bins, function(bin) # may not be in db
101 | if (bin %in% row.names(db)) db[bin, "Version"] else "0")
102 |
103 | later <- as.numeric_version(binvers) < srcvers
104 |
105 | list(bins=bins, srcs=srcs, binvers=binvers, srcvers=srcvers, later=later)
106 | }
107 |
108 | # consider as "later" packages with the same version installed from remotes
109 | remotes_as_newer <- function(pkgs, lib) {
110 | for (i in which(as.numeric_version(pkgs$binvers) == pkgs$srcvers))
111 | if (!is.na(utils::packageDescription(pkgs$bins[i], lib, "RemoteSha")))
112 | pkgs$later[i] <- TRUE
113 | pkgs
114 | }
115 |
116 | # adapted from install.packages
117 | # determine whether later versions should be preferred
118 | ask_user <- function(later, bins, binvers, srcvers) {
119 | if (!any(later)) return(later)
120 |
121 | msg <- ngettext(
122 | sum(later),
123 | "There is a binary version available but the source version is later",
124 | "There are binary versions available but the source versions are later")
125 | cat("\n", paste(strwrap(msg, indent = 2, exdent = 2), collapse = "\n"),
126 | ":\n", sep = "")
127 | print(data.frame(`binary` = binvers, `source` = srcvers,
128 | row.names = bins, check.names = FALSE)[later, ])
129 | cat("\n")
130 | action <- getOption("install.packages.compile.from.source", "interactive")
131 | if (action == "interactive" && interactive()) {
132 | msg <- gettext("Do you prefer later versions from sources?")
133 | res <- utils::askYesNo(msg)
134 | if (is.na(res)) stop("Cancelled by user")
135 | if (!isTRUE(res)) later <- FALSE
136 | } else if (action == "never") {
137 | cat(" Binaries will be preferred\n")
138 | later <- FALSE
139 | }
140 |
141 | later
142 | }
143 |
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/NEWS.md:
--------------------------------------------------------------------------------
1 | # bspm devel
2 |
3 | - Fix "invalid escape sequence" SyntaxWarning (@pekkarr in #84).
4 | - Catch and show early errors (e.g. no backend found) in root mode.
5 |
6 | # bspm 0.5.7
7 |
8 | - Restrict D-Bus service configuration to installations in Linux machines
9 | with admininistrative privileges.
10 |
11 | # bspm 0.5.6
12 |
13 | - Move to cran4linux org on GitHub, update URLs.
14 | - Try binary installation of build-only dependencies for source packages
15 | (#82 addressing #81).
16 |
17 | # bspm 0.5.5
18 |
19 | - Fix test to feed character input to `numeric_version`.
20 |
21 | # bspm 0.5.4
22 |
23 | - Fix DNF backend to ensure that the system configuration is used (228407a).
24 | - Minor documentation improvements.
25 |
26 | # bspm 0.5.3
27 |
28 | - Add workaround for underscores in Arch package versions (#71).
29 | - Fix BioArchLinux instructions in README.
30 | - Fix discovery of installed system packages in Arch (#73).
31 |
32 | # bspm 0.5.2
33 |
34 | - Fix package deduplication in dependency getter (#68 addressing #67).
35 | - Rename scripts manual page to `bspm-scripts`.
36 |
37 | # bspm 0.5.1
38 |
39 | - Add support for littler in scripts (@eddelbuettel in #64).
40 | - Refactor + fixes + improve testing (#66 addressing #63).
41 |
42 | # bspm 0.5.0
43 |
44 | - New function `moveto_sys()` moves existing user packages to the system
45 | library to avoid _package shadowing_; the associated script `mass_move`
46 | enables mass-calling this function for several users and/or libraries to
47 | facilitate `bspm` deployment in multitenant servers (#60 addressing #59).
48 | - New function `shadowed_packages()` analyzes the library tree and reports
49 | which packages, one per row, are shadowed by others (#62 addressing #58).
50 | - Add new `options(bspm.version.check=FALSE)` (true by default) to globally
51 | enable `binary-source` installation type (#61).
52 | - Add a specific manual page `bspm-options` documenting all supported options.
53 | - Add support for the installation of binary Suggests and Enhances if they are
54 | supplied to the `dependencies` argument of `install.packages`.
55 | `LinkingTo` now is omitted for binary packages as documented (#32).
56 |
57 | # bspm 0.4.2
58 |
59 | - Fix error forwarding in root mode (#54).
60 | - Fix installation error when `type="binary-source"` is set and
61 | a package without binary version available is requested (#56).
62 | - Fix installation error in `options(pkgType="both")` mode (default) when an
63 | available binary is not available as source (#57).
64 |
65 | # bspm 0.4.1
66 |
67 | - New `type="binary-source"` option (or _fast mode_) tries to install as many
68 | binaries as possible (requested packages and dependencies), and then falls
69 | back to source installation (per @eddelbuettel's wish).
70 | - Fix the call to `available.packages()` when the `repos` argument is specified
71 | (#52 addressing #51).
72 |
73 | # bspm 0.4.0
74 |
75 | - New function `available_sys()` returns a matrix of available packages with
76 | `"Package"`, `"Version"`, and `"Repository"` (#47 addressing #41).
77 | - Honor `type` option, set by default to `"both"`, which means 'use binary
78 | if available and current, otherwise try source' (#48 addressing #46).
79 | As a consequence, the option `bspm.always.install.deps` has been removed.
80 |
81 | # bspm 0.3.10
82 |
83 | - Check backend availability on `enable()`, and trigger a warning if the
84 | service is required but not found. This check can be disabled by setting
85 | `options(bspm.backend.check=FALSE)` (#40).
86 |
87 | # bspm 0.3.9
88 |
89 | - Force `sudo` unconditionally also with autodetection (#27, #28).
90 | - Call `update_cache` in DNF install transactions (#29).
91 | - Add ALPM backend (#35 addressing #34).
92 | - Fix repeated installation issue in APT backend (#36).
93 |
94 | # bspm 0.3.8
95 |
96 | - Fix spurious error with `options(bspm.always.install.deps=TRUE)` (#25).
97 | - Ensure that `options(bspm.sudo=TRUE)` forces `sudo` unconditionally (#28).
98 | - Add new `options(bspm.sudo.autodetect=TRUE)` (not set by default) to enable
99 | passwordless `sudo` autodetection on every call (#27).
100 |
101 | # bspm 0.3.7
102 |
103 | - Fix spurious error with `options(bspm.always.install.deps=TRUE)` (#24).
104 |
105 | # bspm 0.3.6
106 |
107 | - Make APT call fail if there are unmet dependencies (#20).
108 | - Add new `options(bspm.always.install.deps=TRUE)` (not set by default) to
109 | always try to install recursive hard dependencies of packages from system
110 | repositories even if the requested package is not available (#14, #23).
111 | - Add a note about SELinux (#19).
112 |
113 | # bspm 0.3.5
114 |
115 | - Fix noise when `busctl` is installed but there's no system bus (docker) (#12).
116 | - Workaround issue with file permissions under `/tmp` (#13).
117 | - Fix compatibility with Python 3.6 (#16 addressing #15).
118 | - Workaround PATH for old versions of APT/dpkg (#17 addressing #15).
119 | - Prioritize `options(bspm.sudo=TRUE)` over DBus calls (as part of #16), so that
120 | any DBus error or incompatibility can be at least bypassed with `sudo`.
121 |
122 | # bspm 0.3.4
123 |
124 | - Fix installation issue reported by CRAN on Solaris.
125 |
126 | # bspm 0.3.3
127 |
128 | - Cosmetic changes suggested by CRAN.
129 | - Small configure fix.
130 |
131 | # bspm 0.3.2
132 |
133 | - Implement functions to discover new prefixes dynamically (#3).
134 | - Fall back to `sudo` if no root permissions nor D-Bus service are available.
135 | - More documentation, some examples, and testing.
136 |
137 | # bspm 0.3.1
138 |
139 | - Simplified installation, because D-Bus files are always in the same place.
140 | - Support for multiple prefixes and exclusions (#1).
141 | - Improve APT cache management (#4).
142 | - Fix newlines in APT output (#5).
143 | - Load D-Bus variables locally instead of in the global environment (#6).
144 |
145 | # bspm 0.3.0
146 |
147 | - New package name, as suggested by @eddelbuettel; improved title & description.
148 | - Allow root user to talk directly to the system package manager, without D-Bus.
149 |
150 | # PackageManager 0.2.1
151 |
152 | - Add APT backend.
153 |
154 | # PackageManager 0.2.0
155 |
156 | - Initial fork from cran2copr project, reworked to make it extensible.
157 | - Currently, only DNF backend supported.
158 |
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1 |
2 | Call Internal Scripts — bspm-scripts • bspm
6 | Skip to contents
7 |
8 |
9 |
41 |
42 |
47 |
48 |
49 | Internal scripts can be called via Rscript (see examples).
50 |
51 |
52 |
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1 |
2 | Authors and Citation • bspm
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41 |
42 |
43 | ![]()
Authors and Citation
44 |
45 |
46 |
54 |
55 |
56 | Citation
57 | Source: DESCRIPTION
58 |
59 | Ucar I (2024).
60 | bspm: Bridge to System Package Manager.
61 | R package version 0.5.7, https://cran4linux.github.io/bspm/.
62 |
63 | @Manual{,
64 | title = {bspm: Bridge to System Package Manager},
65 | author = {Iñaki Ucar},
66 | year = {2024},
67 | note = {R package version 0.5.7},
68 | url = {https://cran4linux.github.io/bspm/},
69 | }
70 |
71 |
73 |
74 |
75 |
84 |
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86 |
87 |
88 |
89 |
90 |
91 |
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1 |
2 | Function reference • bspm
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7 |
8 |
9 |
41 |
42 |
43 | ![]()
Function reference
44 |
45 |
46 |
53 |
54 |
55 |
56 |
57 | -
58 |
59 |
bspm-options
60 |
61 | - Package Options
62 |
-
63 |
64 |
bspm-package
65 |
66 | - bspm: Bridge to System Package Manager
67 |
-
68 |
69 |
bspm-scripts
70 |
71 | - Call Internal Scripts
72 |
-
78 |
79 |
install_sys() remove_sys() moveto_sys() available_sys() discover()
80 |
81 | - Manage Packages from System Repositories
82 |
-
83 |
84 |
shadowed_packages()
85 |
86 | - Find Shadowed Packages
87 |
88 |
89 |
90 |
91 |
100 |
101 |
102 |
103 |
104 |
105 |
106 |
107 |
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/docs/reference/bspm-options.html:
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1 |
2 | Package Options — bspm-options • bspm
8 | Skip to contents
9 |
10 |
11 |
43 |
44 |
49 |
50 |
51 | List of options() supported to configure bspm's behavior.
52 | In general, these should be set before calling any package function.
53 |
54 |
55 |
56 |
57 | Options specific to bspm
58 |
59 |
60 | bspm.backend.check:logical, default TRUE. If false,
62 | the initial check on enable() is not performed.
bspm.version.check:logical, default TRUE. If false,
66 | as many binaries are installed as possible without any version check,
67 | and then installation from source is used as a fallback.
bspm.sudo.autodetect:logical, default FALSE. If true,
71 | enables autodetection and selection of password-less sudo.
bspm.sudo:logical, default FALSE. If true, forces
75 | sudo unconditionally as the preferred mechanism.
79 |
80 | Options from base R
81 |
82 |
83 | These are used in the same way as in base R. See options for
84 | a detailed description.
askYesNo
install.packages.compile.from.source
87 |
88 |
90 |
91 |
92 |
101 |
102 |
103 |
104 |
105 |
106 |
107 |
108 |
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/docs/reference/bspm-package.html:
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1 |
2 | bspm: Bridge to System Package Manager — bspm-package • bspm
18 | Skip to contents
19 |
20 |
21 |
53 |
54 |
59 |
60 |
61 | Enables binary package installations on Linux distributions.
62 | Provides functions to manage packages via the distribution's package
63 | manager. Also provides transparent integration with R's install.packages
64 | and a fallback mechanism. When installed as a system package, interacts
65 | with the system's package manager without requiring administrative
66 | privileges via an integrated D-Bus service; otherwise, uses sudo.
67 | Currently, the following backends are supported: DNF, APT, ALPM.
68 |
69 |
70 |
71 |
75 |
76 | See also
77 | manager, integration,
78 | bspm-scripts, bspm-options
79 |
80 |
84 |
85 |
87 |
88 |
89 |
98 |
99 |
100 |
101 |
102 |
103 |
104 |
105 |
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1 |
2 | Find Shadowed Packages — shadowed_packages • bspm
8 | Skip to contents
9 |
10 |
11 |
43 |
44 |
49 |
50 |
51 | Find packages that are shadowed by others in library locations
52 | with a higher priority.
53 |
54 |
55 |
59 |
60 |
61 | Arguments
62 | - lib.loc
63 | character vector describing the location of the R library
64 | trees to search through, or NULL for all known trees
65 | (see .libPaths).
68 |
69 | Value
70 |
71 |
72 | A data.frame with one row per package, row names the package
73 | names and column names (currently) "Package", "LibPath", "Version",
74 | "Shadow.LibPath", "Shadow.Version", "Shadow.Newer".
75 |
76 |
77 | Details
78 | R supports setting several locations for library trees. This is a
79 | powerful feature, but many times packages end up installed in multiple
80 | locations, and in such cases R silently uses the one in the path with the
81 | highest priority (appearing first in .libPaths), thus
82 | shadowing packages in locations with a lower priority.
83 | For bspm installations, this means that outdated user packages may
84 | break system libraries. This utility reports packages that are shadowed
85 | (one per row) with information on which location ("Shadow.LibPath")
86 | and version ("Shadow.Version") has priority over it.
87 | The moveto_sys method is a great complement to move such
88 | outdated versions to the system libraries.
89 |
90 |
94 |
95 |
97 |
98 |
99 |
108 |
109 |
110 |
111 |
112 |
113 |
114 |
115 |
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`).
76 | getTopLevel: function($scope) {
77 | for (var i = 1; i <= 6; i++) {
78 | var $headings = this.findOrFilter($scope, 'h' + i);
79 | if ($headings.length > 1) {
80 | return i;
81 | }
82 | }
83 |
84 | return 1;
85 | },
86 |
87 | // returns the elements for the top level, and the next below it
88 | getHeadings: function($scope, topLevel) {
89 | var topSelector = 'h' + topLevel;
90 |
91 | var secondaryLevel = topLevel + 1;
92 | var secondarySelector = 'h' + secondaryLevel;
93 |
94 | return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
95 | },
96 |
97 | getNavLevel: function(el) {
98 | return parseInt(el.tagName.charAt(1), 10);
99 | },
100 |
101 | populateNav: function($topContext, topLevel, $headings) {
102 | var $context = $topContext;
103 | var $prevNav;
104 |
105 | var helpers = this;
106 | $headings.each(function(i, el) {
107 | var $newNav = helpers.generateNavItem(el);
108 | var navLevel = helpers.getNavLevel(el);
109 |
110 | // determine the proper $context
111 | if (navLevel === topLevel) {
112 | // use top level
113 | $context = $topContext;
114 | } else if ($prevNav && $context === $topContext) {
115 | // create a new level of the tree and switch to it
116 | $context = helpers.createChildNavList($prevNav);
117 | } // else use the current $context
118 |
119 | $context.append($newNav);
120 |
121 | $prevNav = $newNav;
122 | });
123 | },
124 |
125 | parseOps: function(arg) {
126 | var opts;
127 | if (arg.jquery) {
128 | opts = {
129 | $nav: arg
130 | };
131 | } else {
132 | opts = arg;
133 | }
134 | opts.$scope = opts.$scope || $(document.body);
135 | return opts;
136 | }
137 | },
138 |
139 | // accepts a jQuery object, or an options object
140 | init: function(opts) {
141 | opts = this.helpers.parseOps(opts);
142 |
143 | // ensure that the data attribute is in place for styling
144 | opts.$nav.attr('data-toggle', 'toc');
145 |
146 | var $topContext = this.helpers.createChildNavList(opts.$nav);
147 | var topLevel = this.helpers.getTopLevel(opts.$scope);
148 | var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
149 | this.helpers.populateNav($topContext, topLevel, $headings);
150 | }
151 | };
152 |
153 | $(function() {
154 | $('nav[data-toggle="toc"]').each(function(i, el) {
155 | var $nav = $(el);
156 | Toc.init($nav);
157 | });
158 | });
159 | })();
160 |
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8 | Page not found (404) • bspm
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20 | Skip to contents
21 |
22 |
23 |
60 |
61 |
62 | ![]()
Page not found (404)
63 |
64 |
65 |
66 | Content not found. Please use links in the navbar.
67 |
68 |
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70 |
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83 |
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91 |
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/inst/service/bspm.py:
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1 | #!/usr/bin/python3
2 |
3 | from os import path
4 | WDIR = path.dirname(path.realpath(__file__))
5 | exec(open(WDIR + "/dbus-paths").read())
6 |
7 | def read_conf(force_discover=False):
8 | global PREF, EXCL
9 | pref = WDIR + "/bspm.pref"
10 | excl = WDIR + "/bspm.excl"
11 |
12 | force_discover = force_discover and not path.exists(WDIR + "/nodiscover")
13 | if force_discover or not path.exists(pref) or not path.exists(excl):
14 | import backend
15 | conf = backend.discover()
16 | with open(pref, "w") as fpref, open(excl, "w") as fexcl:
17 | for i in conf["prefixes"]:
18 | print(i, file=fpref)
19 | for i in conf["exclusions"]:
20 | print(i, file=fexcl)
21 | with open(pref) as fpref, open(excl) as fexcl:
22 | PREF = [line.rstrip() for line in fpref]
23 | EXCL = [line.rstrip() for line in fexcl]
24 |
25 | def call_backend(cmd, pkgs=None, root=False):
26 | import backend
27 | msg = cmd.capitalize() + " system packages"
28 | if root:
29 | msg = msg + " as root"
30 | msg = msg + "..."
31 | print(msg, flush=True)
32 | if pkgs:
33 | return getattr(backend, cmd)(PREF, pkgs, EXCL)
34 | return getattr(backend, cmd)(PREF, EXCL)
35 |
36 | def run_as_service():
37 | from gi.repository import GLib
38 |
39 | import dbus
40 | import dbus.service
41 | import dbus.mainloop.glib
42 |
43 | from functools import wraps
44 | from contextlib import redirect_stdout
45 | import signal
46 |
47 | class PackageManagerException(dbus.DBusException):
48 | _dbus_error_name = IFACE + ".PackageManagerException"
49 |
50 | def stderr(pid):
51 | return open("/proc/" + str(pid) + "/fd/2", "w")
52 |
53 | def redirect_output(fn):
54 | @wraps(fn)
55 | def wrapper(self, pid, *args, **kw):
56 | with stderr(pid) as f, redirect_stdout(f):
57 | return fn(self, pid, *args, **kw)
58 | return wrapper
59 |
60 | def handle_exceptions(timeout):
61 | def _handle_exceptions(fn):
62 | @wraps(fn)
63 | def wrapper(*args, **kw):
64 | signal.alarm(0)
65 | try:
66 | out = fn(*args, **kw)
67 | except Exception as err:
68 | raise PackageManagerException(str(err))
69 | finally:
70 | signal.alarm(timeout)
71 | return out
72 | return wrapper
73 | return _handle_exceptions
74 |
75 | class PackageManager(dbus.service.Object):
76 |
77 | @dbus.service.method(IFACE, in_signature="i", out_signature="")
78 | @handle_exceptions(10)
79 | @redirect_output
80 | def discover(self, pid):
81 | read_conf(True)
82 | return
83 |
84 | @dbus.service.method(IFACE, in_signature="i", out_signature="as")
85 | @handle_exceptions(10)
86 | @redirect_output
87 | def available(self, pid):
88 | return call_backend("available")
89 |
90 | @dbus.service.method(IFACE, in_signature="ias", out_signature="as")
91 | @handle_exceptions(10)
92 | @redirect_output
93 | def install(self, pid, pkgs):
94 | return call_backend("install", pkgs)
95 |
96 | @dbus.service.method(IFACE, in_signature="ias", out_signature="as")
97 | @handle_exceptions(10)
98 | @redirect_output
99 | def remove(self, pid, pkgs):
100 | return call_backend("remove", pkgs)
101 |
102 | def sigterm_handler(_signo, _stack_frame):
103 | mainloop.quit()
104 |
105 | dbus.mainloop.glib.DBusGMainLoop(set_as_default=True)
106 | signal.signal(signal.SIGINT, sigterm_handler)
107 | signal.signal(signal.SIGTERM, sigterm_handler)
108 | signal.signal(signal.SIGALRM, sigterm_handler)
109 |
110 | bus = dbus.SystemBus()
111 | bus.request_name(BUS_NAME)
112 | pm = PackageManager(bus, OPATH)
113 |
114 | mainloop = GLib.MainLoop()
115 | mainloop.run()
116 |
117 | def run_as_root(args):
118 | try:
119 | if args.cmd == "discover":
120 | read_conf(True)
121 | return
122 | read_conf()
123 | pkgs = None
124 | if hasattr(args, "pkg"):
125 | pkgs = args.pkg
126 | pkgs = call_backend(args.cmd, pkgs, root=True)
127 | if args.o is not None:
128 | with open(args.o, "a") as f:
129 | for pkg in pkgs:
130 | print(pkg, file=f)
131 | else:
132 | print("Result:", pkgs)
133 | except Exception as err:
134 | if args.o is not None:
135 | with open(args.o, "a") as f:
136 | print(str(err), file=f)
137 | raise err
138 |
139 | if __name__ == "__main__":
140 | import argparse
141 |
142 | parser = argparse.ArgumentParser()
143 | subparser = parser.add_subparsers(dest="cmd")
144 | parser_discover = subparser.add_parser("discover", aliases=["available"])
145 | parser_discover.add_argument("-o", metavar="file", type=str, help="output file")
146 | parser_install = subparser.add_parser("install", aliases=["remove"])
147 | parser_install.add_argument("pkg", type=str, nargs="+")
148 | parser_install.add_argument("-o", metavar="file", type=str, help="output file")
149 |
150 | args = parser.parse_args()
151 | if args.cmd is None:
152 | read_conf()
153 | run_as_service()
154 | else:
155 | run_as_root(args)
156 |
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/R/utils.R:
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1 | #' Find Shadowed Packages
2 | #'
3 | #' Find packages that are \emph{shadowed} by others in library locations
4 | #' with a higher priority.
5 | #'
6 | #' @param lib.loc character vector describing the location of the \R library
7 | #' trees to search through, or \code{NULL} for all known trees
8 | #' (see \code{\link{.libPaths}}).
9 | #' @return A \code{data.frame} with one row per package, row names the package
10 | #' names and column names (currently) "Package", "LibPath", "Version",
11 | #' "Shadow.LibPath", "Shadow.Version", "Shadow.Newer".
12 | #'
13 | #' @details \R supports setting several locations for library trees. This is a
14 | #' powerful feature, but many times packages end up installed in multiple
15 | #' locations, and in such cases \R silently uses the one in the path with the
16 | #' highest priority (appearing first in \code{\link{.libPaths}}), thus
17 | #' \emph{shadowing} packages in locations with a lower priority.
18 | #'
19 | #' For \pkg{bspm} installations, this means that outdated user packages may
20 | #' break system libraries. This utility reports packages that are shadowed
21 | #' (one per row) with information on which location ("Shadow.LibPath")
22 | #' and version ("Shadow.Version") has priority over it.
23 | #' The \code{\link{moveto_sys}} method is a great complement to move such
24 | #' outdated versions to the system libraries.
25 | #'
26 | #' @seealso \code{\link{moveto_sys}}
27 | #' @export
28 | shadowed_packages <- function(lib.loc=NULL) {
29 | if (is.null(lib.loc)) lib.loc <- .libPaths()
30 |
31 | fields <- c("Package", "LibPath", "Version")
32 | sfields <- paste("Shadow", fields, sep=".")
33 | shadow <- data.frame(matrix(nrow=0, ncol=5))
34 | colnames(shadow) <- c(fields, sfields[-1])
35 |
36 | pkgs <- data.frame(utils::installed.packages(lib.loc)[, fields])
37 | pkgs <- split(pkgs, factor(pkgs$LibPath, levels=lib.loc))
38 |
39 | idx <- seq_along(pkgs)
40 | for (i in idx) {
41 | colnames(pkgs[[i]]) <- sfields
42 | for (j in idx[-seq_len(i)]) {
43 | hidden <- merge(pkgs[[j]], pkgs[[i]], by.x=fields[1], by.y=sfields[1])
44 | shadow <- rbind(shadow, hidden)
45 | }
46 | }
47 |
48 | row.names(shadow) <- shadow[, "Package"]
49 | shadow$Version <- as.package_version(shadow$Version)
50 | shadow$Shadow.Version <- as.package_version(shadow$Shadow.Version)
51 | newer <- shadow[, "Version"] < shadow[, "Shadow.Version"]
52 | shadow <- cbind(shadow, Shadow.Newer = newer)
53 | shadow
54 | }
55 |
56 | list_inst <- function() {
57 | libs <- unique(c(.Library.site, .Library))
58 | inst <- unique(row.names(utils::installed.packages(libs)))
59 | inst
60 | }
61 |
62 | list_deps <- function(packages, db, which, recursive) {
63 | deps <- tools::package_dependencies(packages, db, which, recursive)
64 | deps <- unique(unlist(deps, use.names=FALSE))
65 | deps
66 | }
67 |
68 | # get package dependencies
69 | pkg_deps <- function(pkgs, dependencies, db, all=TRUE) {
70 | pkgs <- unique(pkgs)
71 | deps <- list_deps(pkgs, db, c("Depends", "Imports"), recursive=TRUE)
72 | if (!all)
73 | deps <- c(deps, list_deps(pkgs, db, "LinkingTo", recursive=FALSE))
74 | if (isTRUE(dependencies) || "Suggests" %in% dependencies)
75 | deps <- c(deps, list_deps(pkgs, db, "Suggests", recursive=FALSE))
76 | if ("Enhances" %in% dependencies)
77 | deps <- c(deps, list_deps(pkgs, db, "Enhances", recursive=FALSE))
78 | deps <- unique(c(setdiff(deps, list_inst()), if (all) pkgs))
79 | deps
80 | }
81 |
82 | # get LinkingTo-only dependencies for src packages
83 | hard_deps <- function(pkgs, db, mask) {
84 | srcs <- c(pkgs$bins[mask], pkgs$srcs)
85 | deps <- list_deps(srcs, db, "LinkingTo", recursive=FALSE)
86 | deps <- setdiff(deps, c(list_inst(), pkgs$bins, pkgs$srcs))
87 | deps
88 | }
89 |
90 | # adapted from install.packages
91 | # get available binaries and pkgs with later versions available
92 | check_versions <- function(pkgs, db) {
93 | dbb <- available_sys()
94 | row.names(dbb) <- tolower(row.names(dbb))
95 |
96 | bins <- pkgs[tolower(pkgs) %in% row.names(dbb)]
97 | srcs <- pkgs[! pkgs %in% bins]
98 |
99 | binvers <- dbb[tolower(bins), "Version"]
100 | srcvers <- sapply(bins, function(bin) # may not be in db
101 | if (bin %in% row.names(db)) db[bin, "Version"] else "0")
102 |
103 | later <- as.numeric_version(binvers) < srcvers
104 |
105 | list(bins=bins, srcs=srcs, binvers=binvers, srcvers=srcvers, later=later)
106 | }
107 |
108 | # consider as "later" packages with the same version installed from remotes
109 | remotes_as_newer <- function(pkgs, lib) {
110 | for (i in which(as.numeric_version(pkgs$binvers) == pkgs$srcvers))
111 | if (!is.na(utils::packageDescription(pkgs$bins[i], lib, "RemoteSha")))
112 | pkgs$later[i] <- TRUE
113 | pkgs
114 | }
115 |
116 | # adapted from install.packages
117 | # determine whether later versions should be preferred
118 | ask_user <- function(later, bins, binvers, srcvers) {
119 | if (!any(later)) return(later)
120 |
121 | msg <- ngettext(
122 | sum(later),
123 | "There is a binary version available but the source version is later",
124 | "There are binary versions available but the source versions are later")
125 | cat("\n", paste(strwrap(msg, indent = 2, exdent = 2), collapse = "\n"),
126 | ":\n", sep = "")
127 | print(data.frame(`binary` = binvers, `source` = srcvers,
128 | row.names = bins, check.names = FALSE)[later, ])
129 | cat("\n")
130 | action <- getOption("install.packages.compile.from.source", "interactive")
131 | if (action == "interactive" && interactive()) {
132 | msg <- gettext("Do you prefer later versions from sources?")
133 | res <- utils::askYesNo(msg)
134 | if (is.na(res)) stop("Cancelled by user")
135 | if (!isTRUE(res)) later <- FALSE
136 | } else if (action == "never") {
137 | cat(" Binaries will be preferred\n")
138 | later <- FALSE
139 | }
140 |
141 | later
142 | }
143 |
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/NEWS.md:
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1 | # bspm devel
2 |
3 | - Fix "invalid escape sequence" SyntaxWarning (@pekkarr in #84).
4 | - Catch and show early errors (e.g. no backend found) in root mode.
5 |
6 | # bspm 0.5.7
7 |
8 | - Restrict D-Bus service configuration to installations in Linux machines
9 | with admininistrative privileges.
10 |
11 | # bspm 0.5.6
12 |
13 | - Move to cran4linux org on GitHub, update URLs.
14 | - Try binary installation of build-only dependencies for source packages
15 | (#82 addressing #81).
16 |
17 | # bspm 0.5.5
18 |
19 | - Fix test to feed character input to `numeric_version`.
20 |
21 | # bspm 0.5.4
22 |
23 | - Fix DNF backend to ensure that the system configuration is used (228407a).
24 | - Minor documentation improvements.
25 |
26 | # bspm 0.5.3
27 |
28 | - Add workaround for underscores in Arch package versions (#71).
29 | - Fix BioArchLinux instructions in README.
30 | - Fix discovery of installed system packages in Arch (#73).
31 |
32 | # bspm 0.5.2
33 |
34 | - Fix package deduplication in dependency getter (#68 addressing #67).
35 | - Rename scripts manual page to `bspm-scripts`.
36 |
37 | # bspm 0.5.1
38 |
39 | - Add support for littler in scripts (@eddelbuettel in #64).
40 | - Refactor + fixes + improve testing (#66 addressing #63).
41 |
42 | # bspm 0.5.0
43 |
44 | - New function `moveto_sys()` moves existing user packages to the system
45 | library to avoid _package shadowing_; the associated script `mass_move`
46 | enables mass-calling this function for several users and/or libraries to
47 | facilitate `bspm` deployment in multitenant servers (#60 addressing #59).
48 | - New function `shadowed_packages()` analyzes the library tree and reports
49 | which packages, one per row, are shadowed by others (#62 addressing #58).
50 | - Add new `options(bspm.version.check=FALSE)` (true by default) to globally
51 | enable `binary-source` installation type (#61).
52 | - Add a specific manual page `bspm-options` documenting all supported options.
53 | - Add support for the installation of binary Suggests and Enhances if they are
54 | supplied to the `dependencies` argument of `install.packages`.
55 | `LinkingTo` now is omitted for binary packages as documented (#32).
56 |
57 | # bspm 0.4.2
58 |
59 | - Fix error forwarding in root mode (#54).
60 | - Fix installation error when `type="binary-source"` is set and
61 | a package without binary version available is requested (#56).
62 | - Fix installation error in `options(pkgType="both")` mode (default) when an
63 | available binary is not available as source (#57).
64 |
65 | # bspm 0.4.1
66 |
67 | - New `type="binary-source"` option (or _fast mode_) tries to install as many
68 | binaries as possible (requested packages and dependencies), and then falls
69 | back to source installation (per @eddelbuettel's wish).
70 | - Fix the call to `available.packages()` when the `repos` argument is specified
71 | (#52 addressing #51).
72 |
73 | # bspm 0.4.0
74 |
75 | - New function `available_sys()` returns a matrix of available packages with
76 | `"Package"`, `"Version"`, and `"Repository"` (#47 addressing #41).
77 | - Honor `type` option, set by default to `"both"`, which means 'use binary
78 | if available and current, otherwise try source' (#48 addressing #46).
79 | As a consequence, the option `bspm.always.install.deps` has been removed.
80 |
81 | # bspm 0.3.10
82 |
83 | - Check backend availability on `enable()`, and trigger a warning if the
84 | service is required but not found. This check can be disabled by setting
85 | `options(bspm.backend.check=FALSE)` (#40).
86 |
87 | # bspm 0.3.9
88 |
89 | - Force `sudo` unconditionally also with autodetection (#27, #28).
90 | - Call `update_cache` in DNF install transactions (#29).
91 | - Add ALPM backend (#35 addressing #34).
92 | - Fix repeated installation issue in APT backend (#36).
93 |
94 | # bspm 0.3.8
95 |
96 | - Fix spurious error with `options(bspm.always.install.deps=TRUE)` (#25).
97 | - Ensure that `options(bspm.sudo=TRUE)` forces `sudo` unconditionally (#28).
98 | - Add new `options(bspm.sudo.autodetect=TRUE)` (not set by default) to enable
99 | passwordless `sudo` autodetection on every call (#27).
100 |
101 | # bspm 0.3.7
102 |
103 | - Fix spurious error with `options(bspm.always.install.deps=TRUE)` (#24).
104 |
105 | # bspm 0.3.6
106 |
107 | - Make APT call fail if there are unmet dependencies (#20).
108 | - Add new `options(bspm.always.install.deps=TRUE)` (not set by default) to
109 | always try to install recursive hard dependencies of packages from system
110 | repositories even if the requested package is not available (#14, #23).
111 | - Add a note about SELinux (#19).
112 |
113 | # bspm 0.3.5
114 |
115 | - Fix noise when `busctl` is installed but there's no system bus (docker) (#12).
116 | - Workaround issue with file permissions under `/tmp` (#13).
117 | - Fix compatibility with Python 3.6 (#16 addressing #15).
118 | - Workaround PATH for old versions of APT/dpkg (#17 addressing #15).
119 | - Prioritize `options(bspm.sudo=TRUE)` over DBus calls (as part of #16), so that
120 | any DBus error or incompatibility can be at least bypassed with `sudo`.
121 |
122 | # bspm 0.3.4
123 |
124 | - Fix installation issue reported by CRAN on Solaris.
125 |
126 | # bspm 0.3.3
127 |
128 | - Cosmetic changes suggested by CRAN.
129 | - Small configure fix.
130 |
131 | # bspm 0.3.2
132 |
133 | - Implement functions to discover new prefixes dynamically (#3).
134 | - Fall back to `sudo` if no root permissions nor D-Bus service are available.
135 | - More documentation, some examples, and testing.
136 |
137 | # bspm 0.3.1
138 |
139 | - Simplified installation, because D-Bus files are always in the same place.
140 | - Support for multiple prefixes and exclusions (#1).
141 | - Improve APT cache management (#4).
142 | - Fix newlines in APT output (#5).
143 | - Load D-Bus variables locally instead of in the global environment (#6).
144 |
145 | # bspm 0.3.0
146 |
147 | - New package name, as suggested by @eddelbuettel; improved title & description.
148 | - Allow root user to talk directly to the system package manager, without D-Bus.
149 |
150 | # PackageManager 0.2.1
151 |
152 | - Add APT backend.
153 |
154 | # PackageManager 0.2.0
155 |
156 | - Initial fork from cran2copr project, reworked to make it extensible.
157 | - Currently, only DNF backend supported.
158 |
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2 | Call Internal Scripts — bspm-scripts • bspm
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48 |
49 | Internal scripts can be called via Rscript (see examples).
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43 | ![]()
Authors and Citation
44 |
45 |
46 |
54 |
55 |
56 | Citation
57 | Source: DESCRIPTION
58 |
59 | Ucar I (2024).
60 | bspm: Bridge to System Package Manager.
61 | R package version 0.5.7, https://cran4linux.github.io/bspm/.
62 |
63 | @Manual{,
64 | title = {bspm: Bridge to System Package Manager},
65 | author = {Iñaki Ucar},
66 | year = {2024},
67 | note = {R package version 0.5.7},
68 | url = {https://cran4linux.github.io/bspm/},
69 | }
70 |
71 |
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87 |
88 |
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90 |
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43 | ![]()
Function reference
44 |
45 |
46 |
53 |
54 |
55 |
56 |
57 | -
58 |
59 |
bspm-options
60 |
61 | - Package Options
62 |
-
63 |
64 |
bspm-package
65 |
66 | - bspm: Bridge to System Package Manager
67 |
-
68 |
69 |
bspm-scripts
70 |
71 | - Call Internal Scripts
72 |
-
78 |
79 |
install_sys() remove_sys() moveto_sys() available_sys() discover()
80 |
81 | - Manage Packages from System Repositories
82 |
-
83 |
84 |
shadowed_packages()
85 |
86 | - Find Shadowed Packages
87 |
88 |
89 |
90 |
91 |
100 |
101 |
102 |
103 |
104 |
105 |
106 |
107 |
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1 |
2 | Package Options — bspm-options • bspm
8 | Skip to contents
9 |
10 |
11 |
43 |
44 |
49 |
50 |
51 | List of options() supported to configure bspm's behavior.
52 | In general, these should be set before calling any package function.
53 |
54 |
55 |
56 |
57 | Options specific to bspm
58 |
59 |
60 | bspm.backend.check:logical, default TRUE. If false,
62 | the initial check on enable() is not performed.
bspm.version.check:logical, default TRUE. If false,
66 | as many binaries are installed as possible without any version check,
67 | and then installation from source is used as a fallback.
bspm.sudo.autodetect:logical, default FALSE. If true,
71 | enables autodetection and selection of password-less sudo.
bspm.sudo:logical, default FALSE. If true, forces
75 | sudo unconditionally as the preferred mechanism.
79 |
80 | Options from base R
81 |
82 |
83 | These are used in the same way as in base R. See options for
84 | a detailed description.
askYesNo
install.packages.compile.from.source
87 |
88 |
90 |
91 |
92 |
101 |
102 |
103 |
104 |
105 |
106 |
107 |
108 |
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2 | bspm: Bridge to System Package Manager — bspm-package • bspm
18 | Skip to contents
19 |
20 |
21 |
53 |
54 |
59 |
60 |
61 | Enables binary package installations on Linux distributions.
62 | Provides functions to manage packages via the distribution's package
63 | manager. Also provides transparent integration with R's install.packages
64 | and a fallback mechanism. When installed as a system package, interacts
65 | with the system's package manager without requiring administrative
66 | privileges via an integrated D-Bus service; otherwise, uses sudo.
67 | Currently, the following backends are supported: DNF, APT, ALPM.
68 |
69 |
70 |
71 |
75 |
76 | See also
77 | manager, integration,
78 | bspm-scripts, bspm-options
79 |
80 |
84 |
85 |
87 |
88 |
89 |
98 |
99 |
100 |
101 |
102 |
103 |
104 |
105 |
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1 |
2 | Find Shadowed Packages — shadowed_packages • bspm
8 | Skip to contents
9 |
10 |
11 |
43 |
44 |
49 |
50 |
51 | Find packages that are shadowed by others in library locations
52 | with a higher priority.
53 |
54 |
55 |
59 |
60 |
61 | Arguments
62 | - lib.loc
63 | character vector describing the location of the R library
64 | trees to search through, or NULL for all known trees
65 | (see .libPaths).
68 |
69 | Value
70 |
71 |
72 | A data.frame with one row per package, row names the package
73 | names and column names (currently) "Package", "LibPath", "Version",
74 | "Shadow.LibPath", "Shadow.Version", "Shadow.Newer".
75 |
76 |
77 | Details
78 | R supports setting several locations for library trees. This is a
79 | powerful feature, but many times packages end up installed in multiple
80 | locations, and in such cases R silently uses the one in the path with the
81 | highest priority (appearing first in .libPaths), thus
82 | shadowing packages in locations with a lower priority.
83 | For bspm installations, this means that outdated user packages may
84 | break system libraries. This utility reports packages that are shadowed
85 | (one per row) with information on which location ("Shadow.LibPath")
86 | and version ("Shadow.Version") has priority over it.
87 | The moveto_sys method is a great complement to move such
88 | outdated versions to the system libraries.
89 |
90 |
94 |
95 |
97 |
98 |
99 |
108 |
109 |
110 |
111 |
112 |
113 |
114 |
115 |
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70 |
71 |
72 |
83 |
62 | ![]()
65 |
66 | Content not found. Please use links in the navbar.
67 |
68 | Page not found (404)
63 | 64 |
42 |
47 |
48 |
70 |
71 |
72 |
49 |
51 |
52 |
53 |
54 |
69 | Internal scripts can be called via Rscript (see examples).
42 |
73 |
74 |
75 |
43 | ![]()
45 |
46 |
54 |
55 | Authors and Citation
44 |
56 |
71 | Citation
57 |Source: DESCRIPTION
Ucar I (2024). 60 | bspm: Bridge to System Package Manager. 61 | R package version 0.5.7, https://cran4linux.github.io/bspm/. 62 |
63 |@Manual{,
64 | title = {bspm: Bridge to System Package Manager},
65 | author = {Iñaki Ucar},
66 | year = {2024},
67 | note = {R package version 0.5.7},
68 | url = {https://cran4linux.github.io/bspm/},
69 | }
70 |
42 |
89 |
90 |
91 |
43 | ![]()
45 |
46 | Function reference
44 |
53 |
54 |
55 |
56 |
57 |
88 | -
58 |
59 |
bspm-options60 |
61 | - Package Options 62 |
-
63 |
64 |
bspm-package65 |
66 | - bspm: Bridge to System Package Manager 67 |
-
68 |
69 |
bspm-scripts70 |
71 | - Call Internal Scripts 72 |
-
78 |
79 |
install_sys()remove_sys()moveto_sys()available_sys()discover()80 |
81 | - Manage Packages from System Repositories 82 |
-
83 |
84 |
shadowed_packages()85 |
86 | - Find Shadowed Packages 87 |
44 |
49 |
50 |
90 |
91 |
92 |
51 |
54 |
55 |
56 | List of options() supported to configure bspm's behavior.
52 | In general, these should be set before calling any package function.
57 |
79 | Options specific to bspm
58 | 59 | 60 |bspm.backend.check:
61 | logical, default
TRUE. If false, 62 | the initial check onenable()is not performed.
63 |
64 | bspm.version.check:
65 | logical, default
TRUE. If false, 66 | as many binaries are installed as possible without any version check, 67 | and then installation from source is used as a fallback.
68 |
69 | bspm.sudo.autodetect:
70 | logical, default
FALSE. If true, 71 | enables autodetection and selection of password-lesssudo.
72 |
73 | bspm.sudo:
74 | logical, default
FALSE. If true, forces 75 |sudounconditionally as the preferred mechanism.
76 |
77 |
78 |
80 |
87 |
88 | Options from base R
81 | 82 | 83 |These are used in the same way as in base R. See options for
84 | a detailed description.
askYesNo
85 | install.packages.compile.from.source
86 |
54 |
59 |
60 |
87 |
88 |
89 |
61 |
69 |
70 |
71 |
75 | Enables binary package installations on Linux distributions.
62 | Provides functions to manage packages via the distribution's package
63 | manager. Also provides transparent integration with R's install.packages
64 | and a fallback mechanism. When installed as a system package, interacts
65 | with the system's package manager without requiring administrative
66 | privileges via an integrated D-Bus service; otherwise, uses sudo.
67 | Currently, the following backends are supported: DNF, APT, ALPM.
76 |
79 |
80 |
84 |
85 | See also
77 |manager, integration,
78 | bspm-scripts, bspm-options
44 |
49 |
50 |
97 |
98 |
99 |
51 |
54 |
55 |
59 |
60 | Find packages that are shadowed by others in library locations 52 | with a higher priority.
53 |
61 |
68 | Arguments
62 |- lib.loc 63 |
character vector describing the location of the R library 64 | trees to search through, or
NULLfor all known trees 65 | (see.libPaths).
66 |
67 |
69 |
76 | Value
70 | 71 | 72 |A data.frame with one row per package, row names the package
73 | names and column names (currently) "Package", "LibPath", "Version",
74 | "Shadow.LibPath", "Shadow.Version", "Shadow.Newer".
77 |
90 |
94 |
95 | Details
78 |R supports setting several locations for library trees. This is a
79 | powerful feature, but many times packages end up installed in multiple
80 | locations, and in such cases R silently uses the one in the path with the
81 | highest priority (appearing first in .libPaths), thus
82 | shadowing packages in locations with a lower priority.
For bspm installations, this means that outdated user packages may
84 | break system libraries. This utility reports packages that are shadowed
85 | (one per row) with information on which location ("Shadow.LibPath")
86 | and version ("Shadow.Version") has priority over it.
87 | The moveto_sys method is a great complement to move such
88 | outdated versions to the system libraries.