我在我的电脑系统（一台服务器）上安装了大约4000个R软件包，其中大部分已经过时，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)
我希望更新所有的包，但那太慢了。问题在于用户并没有使用大部分的包，时不时地他们会要求我更新一个他们需要使用的包（比如说fields）。如果我运行
install.packages("fields")
library("fields")
我收到了一个错误信息
Error: package ‘maps’ was built before R 3.0.0: please re-install it
有没有一种方法可以升级字段，以便它还可以自动更新取决于其的包字段？
如Ben在他的评论中指出的那样，您需要获取fields的依赖项，然后过滤掉Priority为"Base"或"Recommended"的软件包，然后将该软件包列表传递给install.packages()来进行安装处理。类似于：
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
}
这样就得到了：
R> instPkgPlusDeps("fields")
Loading required package: tools
[1] "fields" "spam" "maps"
与之匹配
> packageDescription("fields", fields = "Depends")
[1] "R (>= 2.13), methods, spam, maps"
如果在sapply()行中依赖于deps的软件包未安装，则会收到警告。但是，我认为这些警告是无害的，因为在这种情况下返回的值是NA，我们使用它来指示我们想要安装的软件包。如果您已安装了4000个软件包，则不太可能受到影响。
默认情况下不会安装软件包，只会返回依赖项列表。我觉得这样做最安全，因为您可能没有意识到所暗示的依赖关系链，并最终意外安装数百个软件包。如果您愿意安装所指示的软件包，请传递install = TRUE。
请注意，我限制了搜索的依赖类型 - 如果使用which = "most"，则会出现问题 - fields中有超过300个这样的依赖项，一旦您递归解析这些依赖关系（其中包括Suggests:字段），就会不断膨胀。 which = "all"将查找所有内容，包括Enhances:，这将再次是一个更大的软件包列表。有关which参数的有效输入，请参见?tools::package_dependencies。
install.packages(deps)编辑为install.packages(c(pkg,deps))。 - user3175783update.packages()版本。该函数跳过已经更新的包的安装。但是，Gavin的解决方案会安装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跳过基本包的提示(它们实际上不能被安装)，并编写了一个跳过最新包的方案。installPackages()。这个函数及其辅助函数对以给定一组包为根的依赖树进行拓扑排序。结果列表中的包会被检查是否过时，并逐一安装。下面是一些示例输出:> 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## Package digest is out of date ( 0.6.9 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
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);
}
Error in nonBaseDeps(p, ap = ap, recursive = F) : Package dplyr has dependencies not in database: methods utils Calls: installPackages ... sapply -> lapply -> FUN -> get.children -> nonBaseDeps Execution halted
你知道是什么原因导致的吗？不过从@Gavin那里获取的版本可以正常运行。 - understorey
update.packages(checkBuilt=TRUE, ask=FALSE)。 - Dirk Eddelbuettelap <- available.packages(); pkgs <- tools::package_dependencies("fields",db=ap,recursive=TRUE)开始。然后你需要过滤掉内置和推荐的包，并安装其余的包。（这不涉及依赖图的顺序，但可能适用于你的情况。） - Ben Bolker>，而应该使用缩进4个空格的代码/预格式化标记。 - Gavin Simpsonwhich参数。如果我使用fields并设置which = "most"，你将需要安装近400个软件包！对于一些更受欢迎的软件包，您可能需要安装大块的CRAN，这种情况下，您可以在周末从CRAN更新所有内容。 - Gavin Simpsonupdate.packages()函数更好，即使它存在一些限制？您为什么认为编写新的软件包安装函数是试图“重新设计或重写R的软件包系统”？这难道不是试图改进 R 的包系统吗？我们使用的函数，如package_dependencies()和installed.packages()难道不是专门为此目的而提供的吗？ - Metamorphic