Installing devtools package in R - r

Trying to install devtools package is resulting in a segmentation error? Can any one help me what i might be doing wrong or a possible solution to the issue ? Also while loading the devtools it throws an error.
install.packages("devtools")
Installing package into ‘/Users/srao1/Library/R/3.3/library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.revolutionanalytics.com/src/contrib/devtools_1.12.0.tar.gz'
Content type 'application/octet-stream' length 466618 bytes (455 KB)
==================================================
downloaded 455 KB
* installing *source* package ‘devtools’ ...
** package ‘devtools’ successfully unpacked and MD5 sums checked
** libs
gcc -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c devtools.c -o devtools.o
gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib/R/lib -L/usr/local/lib -o devtools.so devtools.o -L/usr/local/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation
installing to /Users/srao1/Library/R/3.3/library/devtools/libs
** R
** inst
** preparing package for lazy loading
*** caught segfault ***
address 0x18, cause 'memory not mapped'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
4: asNamespace(ns)
5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
6: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
7: asNamespace(ns)
8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
9: loadNamespace(package, lib.loc, keep.source, partial = TRUE)
10: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
11: suppressPackageStartupMessages(loadNamespace(package, lib.loc, keep.source, partial = TRUE))
12: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source, compress = compress)
13: makeLazyLoading(pkg_name, lib, keep.source = keep.source)
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: tryCatchList(expr, classes, parentenv, handlers)
17: 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 <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
18: try({ suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE)) makeLazyLoading(pkg_name, lib, keep.source = keep.source)})
19: do_install_source(pkg_name, instdir, pkg, desc)
20: do_install(pkg)
21: tools:::.install_packages()
An irrecoverable exception occurred. R is aborting now ...
/usr/local/lib/R/bin/INSTALL: line 34: 75279 Done echo 'tools:::.install_packages()'
75280 Segmentation fault: 11 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
My Session info
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin14.3.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base

Related

Why can't install tidymodels package in Jupyter notebook?

My Rstudio is 4.0.4 version, however, it showed that the package was built under R verision 3.6.3.
And I can not use this package. How to solove this problem?
library(tidymodels)
Warning message:
"package 'tidymodels' was built under R version 3.6.3"
Error: package or namespace load failed for 'tidymodels' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace 'recipes' 0.1.5 is being loaded, but >= 0.1.16 is required
Traceback:
1. library(tidymodels)
2. tryCatch({
. attr(package, "LibPath") <- which.lib.loc
. ns <- loadNamespace(package, lib.loc)
. env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
. }, error = function(e) {
. P <- if (!is.null(cc <- conditionCall(e)))
. paste(" in", deparse(cc)[1L])
. else ""
. msg <- gettextf("package or namespace load failed for %s%s:\n %s",
. sQuote(package), P, conditionMessage(e))
. if (logical.return)
. message(paste("Error:", msg), domain = NA)
. else stop(msg, call. = FALSE, domain = NA)
. })
3. tryCatchList(expr, classes, parentenv, handlers)
4. tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. value[[3L]](cond)
6. stop(msg, call. = FALSE, domain = NA)
That's a warning. The actual error shows beneath:
Error: package or namespace load failed for 'tidymodels' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace 'recipes' 0.1.5 is being loaded, but >= 0.1.16 is required
And it is very clear: you need a more recent version of recipes which you can get through install.packages. It could be that a newer version of the package is not available for your R version, in which case you'll need to install RTools (assuming windows, otherwise not required) and do an installation from source.

macOS fresh install of R - devtools are giving segfault error -

I've done a fresh reinstall of R 3.6 on a macOS Mojava v 10.14.6
I've install clang 7 here from the provided installer /usr/local/clang7
I have xcode
But there's something wrong with the install that I can seem to figure out
.libPaths()
[1] "/Users/annaleigh/Library/R/3.6/library"
[2] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library"
> install.packages("devtools")
Installing package into ‘/Users/annaleigh/Library/R/3.6/library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/devtools_2.2.1.tgz'
Content type 'application/x-gzip' length 339075 bytes (331 KB)
==================================================
downloaded 331 KB
The downloaded binary packages are in
/var/folders/xr/lmkkh0p10t948k1n104z1jsh0000gn/T//Rtmpf54J79/downloaded_packages
> library(devtools)
\Loading required package: usethis
*** caught segfault ***
address 0x2c2e0, cause 'memory not mapped'
However the usethis library seem to load fine
> library(usethis)
> library(devtools)
*** caught segfault ***
address 0x2c2e0, cause 'memory not mapped'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
4: asNamespace(ns)
5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
6: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
7: asNamespace(ns)
8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
9: loadNamespace(package, lib.loc)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
14: library(devtools)
Answer found here:
https://github.com/r-lib/devtools/issues/1292
"Finally looked at .libPath() and realized that both instances of R were looking at the user library before the system library. So if the packages were linked to different system libraries from the compiled versions (OS X Sierra and El Capitan in my case) this could create the seg fault.
Removing libraries in the user library ~/user/Library/R/version# fixed the issue (with installing to different locations)"

segfault 'memory not mapped' error loading 'ape' in R 3.4

I'm getting two different error messages when attempting to load packages using the 'require' or 'library' functions in R 3.4.1. Since the problem has started, I've only been able to load one package (ggplot2), while others (including any phylogenetics-oriented package, e.g. ape) cause the following error:
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: getDLLRegisteredRoutines.DLLInfo(dll, addNames = FALSE)
2: assignNativeRoutines(dlls[[lib]], lib, env, nsInfo$nativeRoutines[[lib]])
3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
4: asNamespace(ns)
5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
6: loadNamespace(package, lib.loc)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
11: library(ape)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
[EDIT: The following error was resolved, see first comment below] When I try to load the package rJava, I get the following error. Other packages that give similar errors:
library(rJava)
Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Users/dummyname/R_libs/rJava/libs/rJava.so':
dlopen(/Users/dummyname/R_libs/rJava/libs/rJava.so, 6): Library not loaded: #rpath/libjvm.dylib
Referenced from: /Users/dummyname/R_libs/rJava/libs/rJava.so
Reason: image not found
I've tried uninstalling all packages, as suggested here:
caught segfault error in R
I also re-installed R. The same error appears after reinstalling packages. Session info is below the error message. Suggestions?
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.1

ggplot2 causing segfault on Mac

There are several reports for this issue all dating 2 to 3 years back:
caught segfault error in R
Problems loading packages (ie. ggplot2) on R 3.2.2 caught segfault address 0x18, cause 'memory not mapped' [duplicate]
Most of them are referring to older system versions and older ggplot2 version. I'm wondering if anybody found alternative solution to the suggested R re-installation (which apparently did not work for everyone)?
I'm on Mac 10.11.6 and when trying to install ggplot2 either from within or outside of R (R CMD INSTALL) I get segfault:
*** caught segfault ***
address 0x18, cause 'memory not mapped'
The same can be reproduced using ggplot2 versions:
1.0.0, 1.0.1, 2.0.0, 2.1.0, 2.2.0
I tested that on fresh R-3.3.2 session. The error occurs during installation, not during loading.
Traceback received:
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
4: asNamespace(ns)
5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
7: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
8: loadNamespace(package, lib.loc, keep.source, partial = TRUE)
9: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
10: suppressPackageStartupMessages(loadNamespace(package, lib.loc, keep.source, partial = TRUE))
11: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source, compress = compress)
12: makeLazyLoading(pkg_name, lib, keep.source = keep.source)
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: tryCatchList(expr, classes, parentenv, handlers)
16: 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 <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
17: try({ suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE)) makeLazyLoading(pkg_name, lib, keep.source = keep.source)})
18: do_install_source(pkg_name, instdir, pkg, desc)
19: do_install(pkg)
20: tools:::.install_packages()
An irrecoverable exception occurred. R is aborting now ...
/Users/username/miniconda3/lib/R/bin/INSTALL: line 34: 2049 Done echo 'tools:::.install_packages()'
2050 Segmentation fault: 11 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
The reproduce, start new R session and install 'ggplot2' with:
$ R
> install.packages('ggplot2')
Session info:
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin11.4.2 (64-bit)
Running under: OS X 10.11.6 (El Capitan)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Any suggestions would be appreciated.

Error with ggplot2 after installing new R

I wanted to install a new version of R.
I downloaded R-3.1.0.pkg and installed it.
I mved my packages from ~/Library/R/3.0 to ~/Library/R/3.1
the new R starts, but when I try to load some packages, I get an error.
This seems to be due to ggplot2. As I can load any package that doesn't depend on ggplot2.
I just reinstalled ggplot2 using install.packges(), but still no luck. R just crashes when I try to load the library.
I performed update.packages(). Is this related to how I migrated my packages?
Also, I seem to have packages in multiple places. Although I think RStudio seems to install all of them in the ~/Library/Frameworks/R.framework/Versions/3.1/Resources/library
thanks
> library(Hmisc)
Loading required package: grid
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2
*** caught segfault ***
address 0x18, cause 'memory not mapped'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
5: loadNamespace(package, c(which.lib.loc, lib.loc))
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: 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 <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
10: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc)) env <- attachNamespace(ns, pos = pos, deps)})
11: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc)
12: .getRequiredPackages2(pkgInfo, quietly = quietly)
13: library(Hmisc

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