我的系统（服务器）中安装了大约4000个R软件包，其中大多数已经过时，因为它们是在R-3.0.0之前构建的。现在我知道
update.packages(checkBuilt=TRUE, ask=FALSE)
会更新我的所有套餐，但这太慢了。问题是用户不使用大多数软件包，现在他们要求我更新他们使用的软件包（比如字段）。现在如果我跑
install.packages("fields")
即使字段依赖于地图，它也只会更新包字段而不更新包映射。因此，当我尝试加载包字段时：
library("fields")
我收到错误消息
Error: package ‘maps’ was built before R 3.0.0: please re-install it
有没有办法升级字段，以便它还会自动更新包字段取决于？
答案 0 :(得分：14)
正如Ben在评论中指出的那样，您需要获取fields的依赖关系，然后过滤掉优先级为"Base"或"Recommended"的包，然后将该包列表传递给install.packages()来处理安装。类似的东西：
instPkgPlusDeps <- function(pkg, install = FALSE,
which = c("Depends", "Imports", "LinkingTo"),
inc.pkg = TRUE) {
stopifnot(require("tools")) ## load tools
ap <- available.packages() ## takes a minute on first use
## get dependencies for pkg recursively through all dependencies
deps <- package_dependencies(pkg, db = ap, which = which, recursive = TRUE)
## the next line can generate warnings; I think these are harmless
## returns the Priority field. `NA` indicates not Base or Recommended
pri <- sapply(deps[[1]], packageDescription, fields = "Priority")
## filter out Base & Recommended pkgs - we want the `NA` entries
deps <- deps[[1]][is.na(pri)]
## install pkg too?
if (inc.pkg) {
deps = c(pkg, deps)
}
## are we installing?
if (install) {
install.packages(deps)
}
deps ## return dependencies
}
这给出了：
R> instPkgPlusDeps("fields")
Loading required package: tools
[1] "fields" "spam" "maps"
与
匹配> packageDescription("fields", fields = "Depends")
[1] "R (>= 2.13), methods, spam, maps"
如果未实际安装sapply()中的依赖项，则会从deps行收到警告。我认为这些是无害的，因为在这种情况下返回的值是NA，我们用它来表示我们想要安装的包。如果您安装了4000个软件包，我怀疑它会对您产生影响。
默认为不来安装软件包，但只返回依赖项列表。我认为这是最安全的，因为您可能没有意识到隐含的依赖链并最终意外地安装了数百个软件包。如果您愿意安装指示的软件包，请传入install = TRUE。
请注意，我限制搜索的依赖项类型 - 如果您使用which = "most" - 字段，一旦递归解析这些依赖项（包括{{1也是字段）。 Suggests:会查找所有内容，包括which = "all"，这将是一个更大的包列表。有关Enhances:参数的有效输入，请参阅?tools::package_dependencies。
答案 1 :(得分：7)
我的回答建立在Gavin的答案之上......请注意，原始海报user3175783要求提供更智能的update.packages()版本。该功能会跳过安装已更新的软件包。但是Gavin的解决方案安装了一个包及其所有依赖项，无论它们是否是最新的。我使用了Gavin的跳过基础包（实际上不可安装）的提示，并编写了一个解决方案，该解决方案也会跳过最新的包。
主要功能是installPackages()。此函数及其帮助程序执行拓扑排序，这些依赖树以一组给定的包为根。检查结果列表中的包的陈旧性并逐个安装。这是一些示例输出：
> remove.packages("tibble")
Removing package from ‘/home/frederik/.local/lib/x86_64/R/packages’
(as ‘lib’ is unspecified)
> installPackages(c("ggplot2","stringr","Rcpp"), dry_run=T)
## Package digest is out of date ( 0.6.9 < 0.6.10 )
Would have installed package digest
## Package gtable is up to date ( 0.2.0 )
## Package MASS is up to date ( 7.3.45 )
## Package Rcpp is out of date ( 0.12.5 < 0.12.8 )
Would have installed package Rcpp
## Package plyr is out of date ( 1.8.3 < 1.8.4 )
Would have installed package plyr
## Package stringi is out of date ( 1.0.1 < 1.1.2 )
Would have installed package stringi
## Package magrittr is up to date ( 1.5 )
## Package stringr is out of date ( 1.0.0 < 1.1.0 )
Would have installed package stringr
...
## Package lazyeval is out of date ( 0.1.10 < 0.2.0 )
Would have installed package lazyeval
## Package tibble is not currently installed, installing
Would have installed package tibble
## Package ggplot2 is out of date ( 2.1.0 < 2.2.0 )
Would have installed package ggplot2
这里是代码，抱歉长度：
library(tools)
# Helper: a "functional" interface depth-first-search
fdfs = function(get.children) {
rec = function(root) {
cs = get.children(root);
out = c();
for(c in cs) {
l = rec(c);
out = c(out, setdiff(l, out));
}
c(out, root);
}
rec
}
# Entries in the package "Priority" field which indicate the
# package can't be upgraded. Not sure why we would exclude
# recommended packages, since they can be upgraded...
#excl_prio = c("base","recommended")
excl_prio = c("base")
# Find the non-"base" dependencies of a package.
nonBaseDeps = function(packages,
ap=available.packages(),
ip=installed.packages(), recursive=T) {
stopifnot(is.character(packages));
all_deps = c();
for(p in packages) {
# Get package dependencies. Note we are ignoring version
# information
deps = package_dependencies(p, db = ap, recursive = recursive)[[1]];
ipdeps = match(deps,ip[,"Package"])
# We want dependencies which are either not installed, or not part
# of Base (e.g. not installed with R)
deps = deps[is.na(ipdeps) | !(ip[ipdeps,"Priority"] %in% excl_prio)];
# Now check that these are in the "available.packages()" database
apdeps = match(deps,ap[,"Package"])
notfound = is.na(apdeps)
if(any(notfound)) {
notfound=deps[notfound]
stop("Package ",p," has dependencies not in database: ",paste(notfound,collapse=" "));
}
all_deps = union(deps,all_deps);
}
all_deps
}
# Return a topologically-sorted list of dependencies for a given list
# of packages. The output vector contains the "packages" argument, and
# recursive dependencies, with each dependency occurring before any
# package depending on it.
packageOrderedDeps = function(packages, ap=available.packages()) {
# get ordered dependencies
odeps = sapply(packages,
fdfs(function(p){nonBaseDeps(p,ap=ap,recursive=F)}))
# "unique" preserves the order of its input
odeps = unique(unlist(odeps));
# sanity checks
stopifnot(length(setdiff(packages,odeps))==0);
seen = list();
for(d in odeps) {
ddeps = nonBaseDeps(d,ap=ap,recursive=F)
stopifnot(all(ddeps %in% seen));
seen = c(seen,d);
}
as.vector(odeps)
}
# Checks if a package is up-to-date.
isPackageCurrent = function(p,
ap=available.packages(),
ip=installed.packages(),
verbose=T) {
if(verbose) msg = function(...) cat("## ",...)
else msg = function(...) NULL;
aprow = match(p, ap[,"Package"]);
iprow = match(p, ip[,"Package"]);
if(!is.na(iprow) && (ip[iprow,"Priority"] %in% excl_prio)) {
msg("Package ",p," is a ",ip[iprow,"Priority"]," package\n");
return(T);
}
if(is.na(aprow)) {
stop("Couldn't find package ",p," among available packages");
}
if(is.na(iprow)) {
msg("Package ",p," is not currently installed, installing\n");
F;
} else {
iv = package_version(ip[iprow,"Version"]);
av = package_version(ap[aprow,"Version"]);
if(iv < av) {
msg("Package ",p," is out of date (",
as.character(iv),"<",as.character(av),")\n");
F;
} else {
msg("Package ",p," is up to date (",
as.character(iv),")\n");
T;
}
}
}
# Like install.packages, but skips packages which are already
# up-to-date. Specify dry_run=T to just see what would be done.
installPackages =
function(packages,
ap=available.packages(), dry_run=F,
want_deps=T) {
stopifnot(is.character(packages));
ap=tools:::.remove_stale_dups(ap)
ip=installed.packages();
ip=tools:::.remove_stale_dups(ip)
if(want_deps) {
packages = packageOrderedDeps(packages, ap);
}
for(p in packages) {
curr = isPackageCurrent(p,ap,ip);
if(!curr) {
if(dry_run) {
cat("Would have installed package ",p,"\n");
} else {
install.packages(p,dependencies=F);
}
}
}
}
# Convenience function to make sure all the libraries we have loaded
# in the current R session are up-to-date (and to update them if they
# are not)
updateAttachedLibraries = function(dry_run=F) {
s=search();
s=s[grep("^package:",s)];
s=gsub("^package:","",s)
installPackages(s,dry_run=dry_run);
}