问题
I'm setting up a new laptop running Gentoo and wish to install R (as I do on all of my computers!).
However, I've hit a bit of a problem when it comes to installing packages.
I first tried to:
> install.packages(c("ggplot2", "plyr", "reshape2"))
And it duly downloaded all of the packages and its dependencies. However they didn't install reporting.
Error in library(data.table) : there is no package called ‘data.table’
Calls: .First -> library
Execution halted
Error in library(data.table) : there is no package called ‘data.table’
Calls: .First -> library
Execution halted
Error in library(data.table) : there is no package called ‘data.table’
Calls: .First -> library
Execution halted
Error in library(data.table) : there is no package called ‘data.table’
Calls: .First -> library
Execution halted
Error in library(data.table) : there is no package called ‘data.table’
Calls: .First -> library
Execution halted
Error in library(data.table) : there is no package called ‘data.table’
Calls: .First -> library
Execution halted
Error in library(data.table) : there is no package called ‘data.table’
Calls: .First -> library
Execution halted
Error in library(data.table) : there is no package called ‘data.table’
Calls: .First -> library
Not a problem I'll just install the data.table package, unfortunately...
> install.packages("data.table")
trying URL 'http://cran.uk.r-project.org/src/contrib/data.table_1.8.2.tar.gz'
Content type 'application/x-gzip' length 818198 bytes (799 Kb)
opened URL
==================================================
downloaded 799 Kb
Error in library(data.table) : there is no package called ‘data.table’
Calls: .First -> library
Execution halted
The downloaded source packages are in
‘/tmp/RtmpbQtALj/downloaded_packages’
Updating HTML index of packages in '.Library'
Making packages.html ... done
Warning message:
In install.packages("data.table") :
installation of package ‘data.table’ had non-zero exit status
And there is no indication of why installation failed at all, so I've no idea how to go about solving this? A traceback() isn't available either.
GCC is installed and configured as the output of gcc-config shows (and the fact that I can install other software from source no problem).
# gcc-config -l
[1] x86_64-pc-linux-gnu-4.6.3 *
Stumped as to how to go about solving this one. Any thoughts or ideas on how to get more information out of install.packages() welcome.
EDIT : contents of .First as requested....
> .First
function ()
{
library(data.table)
library(foreign)
library(ggplot2)
library(Hmisc)
library(lattice)
library(plyr)
library(rms)
library(xtable)
cat("\nWelcome at", date(), "\n")
}
EDIT 2 : No Rprofile.site but there is /usr/lib64/R/library/base/R/Rprofile which has....
# cat /usr/lib64/R/library/base/R/Rprofile
### This is the system Rprofile file. It is always run on startup.
### Additional commands can be placed in site or user Rprofile files
### (see ?Rprofile).
### Notice that it is a bad idea to use this file as a template for
### personal startup files, since things will be executed twice and in
### the wrong environment (user profiles are run in .GlobalEnv).
.GlobalEnv <- globalenv()
attach(NULL, name = "Autoloads")
.AutoloadEnv <- as.environment(2)
assign(".Autoloaded", NULL, envir = .AutoloadEnv)
T <- TRUE
F <- FALSE
R.version <- structure(R.Version(), class = "simple.list")
version <- R.version # for S compatibility
## for backwards compatibility only
R.version.string <- R.version$version.string
## NOTA BENE: options() for non-base package functionality are in places like
## --------- ../utils/R/zzz.R
options(keep.source = interactive())
options(warn = 0)
# options(repos = c(CRAN="@CRAN@"))
# options(BIOC = "http://www.bioconductor.org")
options(timeout = 60)
options(encoding = "native.enc")
options(show.error.messages = TRUE)
## keep in sync with PrintDefaults() in ../../main/print.c :
options(scipen = 0)
options(max.print = 99999)# max. #{entries} in internal printMatrix()
options(add.smooth = TRUE)# currently only used in 'plot.lm'
options(stringsAsFactors = TRUE)
if(!interactive() && is.null(getOption("showErrorCalls")))
options(showErrorCalls = TRUE)
local({dp <- Sys.getenv("R_DEFAULT_PACKAGES")
if(identical(dp, "")) # marginally faster to do methods last
dp <- c("datasets", "utils", "grDevices", "graphics",
"stats", "methods")
else if(identical(dp, "NULL")) dp <- character(0)
else dp <- strsplit(dp, ",")[[1]]
dp <- sub("[[:blank:]]*([[:alnum:]]+)", "\\1", dp) # strip whitespace
options(defaultPackages = dp)
})
## Expand R_LIBS_* environment variables.
Sys.setenv(R_LIBS_SITE =
.expand_R_libs_env_var(Sys.getenv("R_LIBS_SITE")))
Sys.setenv(R_LIBS_USER =
.expand_R_libs_env_var(Sys.getenv("R_LIBS_USER")))
.First.sys <- function()
{
for(pkg in getOption("defaultPackages")) {
res <- require(pkg, quietly = TRUE, warn.conflicts = FALSE,
character.only = TRUE)
if(!res)
warning(gettextf('package %s in options("defaultPackages") was not found', sQuote(pkg)),
call.=FALSE, domain = NA)
}
}
.OptRequireMethods <- function()
{
if("methods" %in% getOption("defaultPackages")) {
res <- require("methods", quietly = TRUE, warn.conflicts = FALSE,
character.only = TRUE)
if(!res)
warning('package "methods" in options("defaultPackages") was not found', call.=FALSE)
}
}
if(nzchar(Sys.getenv("R_BATCH"))) {
.Last.sys <- function()
{
cat("> proc.time()\n")
print(proc.time())
}
## avoid passing on to spawned R processes
## A system has been reported without Sys.unsetenv, so try this
try(Sys.setenv(R_BATCH=""))
}
###-*- R -*- Unix Specific ----
.Library <- file.path(R.home(), "library")
.Library.site <- Sys.getenv("R_LIBS_SITE")
.Library.site <- if(!nchar(.Library.site)) file.path(R.home(), "site-library") else unlist(strsplit(.Library.site, ":"))
.Library.site <- .Library.site[file.exists(.Library.site)]
invisible(.libPaths(c(unlist(strsplit(Sys.getenv("R_LIBS"), ":")),
unlist(strsplit(Sys.getenv("R_LIBS_USER"), ":")
))))
local({
## we distinguish between R_PAPERSIZE as set by the user and by configure
papersize <- Sys.getenv("R_PAPERSIZE_USER")
if(!nchar(papersize)) {
lcpaper <- Sys.getlocale("LC_PAPER") # might be null: OK as nchar is 0
papersize <- if(nchar(lcpaper))
if(length(grep("(_US|_CA)", lcpaper))) "letter" else "a4"
else Sys.getenv("R_PAPERSIZE")
}
options(papersize = papersize,
printcmd = Sys.getenv("R_PRINTCMD"),
dvipscmd = Sys.getenv("DVIPS", "dvips"),
texi2dvi = Sys.getenv("R_TEXI2DVICMD"),
browser = Sys.getenv("R_BROWSER"),
pager = file.path(R.home(), "bin", "pager"),
pdfviewer = Sys.getenv("R_PDFVIEWER"),
useFancyQuotes = TRUE)
})
## non standard settings for the R.app GUI of the Mac OS X port
if(.Platform$GUI == "AQUA") {
## this is set to let RAqua use both X11 device and X11/TclTk
if (Sys.getenv("DISPLAY") == "")
Sys.setenv("DISPLAY" = ":0")
## this is to allow gfortran compiler to work
Sys.setenv("PATH" = paste(Sys.getenv("PATH"),":/usr/local/bin",sep = ""))
}## end "Aqua"
local({
tests_startup <- Sys.getenv("R_TESTS")
if(nzchar(tests_startup)) source(tests_startup)
})
回答1:
Looks like data.table is not installed for the user that is running the install.packages command. I think wrapping that .First function in if (interactive()) { } would be a good idea in general. Otherwise, you need to install data.table and any other packages that load at startup since install.packages runs the .Rprofile file when starting
来源：https://stackoverflow.com/questions/12861014/problems-installing-r-packages