[R] Problems installing gputools

[Noah Silverman]

Hi,

I have some surprising trouble installing the gputools package.

This is a linux box running Fedora with an Nvidia GeForce GTX 260 card
and R 2.12.1

I had gputools running on it for the past several months. Wanting to
update to the newest version, I simply executed
install.packages("gputools") from within R. This should mean that the
problem isn't in the hardware or OS.

Errors were produced when compiling and the new version failed to
install. Even worse, my existing version is now broken.

I've included some relevant terminal output below my signature.

Any suggestions would be greatly appreciated!

Thanks,

--
Noah


---------------------------------------------------------------------------------------
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

*** caught segfault ***
address 0x8, cause 'memory not mapped'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
keep.source)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if
(!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <-
sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in",
dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg,
"\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type =
"w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") if (w > LONG) prefix <- paste(prefix, "\n ", sep = "") }
else prefix <- "Error : " msg <- paste(prefix, conditionMessage(e),
"\n", sep = "") .Internal(seterrmessage(msg[1L])) if (!silent &&
identical(getOption("show.error.messages"), TRUE)) { cat(msg, file =
stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg,
class = "try-error"))})
8: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc),
keep.source = keep.source) dataPath <- file.path(which.lib.loc, package,
"data") env <- attachNamespace(ns, pos = pos, dataPath = dataPath, deps)})
9: library(pkg_name, lib.loc = lib, character.only = TRUE,
logical.return = TRUE)
10: withCallingHandlers(expr, packageStartupMessage = function(c)
invokeRestart("muffleMessage"))
11: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
character.only = TRUE, logical.return = TRUE))
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(expr, error = function(e) { call <- conditionCall(e) if
(!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <-
sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in",
dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg,
"\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type =
"w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b") if (w > LONG) prefix <- paste(prefix, "\n ", sep = "") }
else prefix <- "Error : " msg <- paste(prefix, conditionMessage(e),
"\n", sep = "") .Internal(seterrmessage(msg[1L])) if (!silent &&
identical(getOption("show.error.messages"), TRUE)) { cat(msg, file =
stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg,
class = "try-error"))})
16: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
character.only = TRUE, logical.return = TRUE)))
17: do_install_source(pkg_name, instdir, pkg, desc)
18: do_install(pkg)
19: tools:::.install_packages()
aborting ...
/usr/local/lib64/R/bin/INSTALL: line 34: 26393 Done echo
'tools:::.install_packages()'
26394 Segmentation fault (core dumped) | R_DEFAULT_PACKAGES=
LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}

The downloaded packages are in
‘/tmp/Rtmpbi9cKk/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning message:
In install.packages("gputools") :
installation of package 'gputools' had non-zero exit status