I am running R 3.5.1 on ubuntu 18.04, installed via apt. When I run R
from the bash prompt, I get (reinstalling r-base doesn't help)
> devtools::install_github("goranbrostrom/eha", build_vignettes =
TRUE)
*** caught segfault ***
address 0x68456, cause 'memory not mapped'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(name)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(loadNamespace(name), error = function(e) stop(e))
8: getNamespace(ns)
9: asNamespace(ns)
10: getExportedValue(pkg, name)
11: curl::new_handle
12: handle(name)
13: handle_find(url)
14: handle_url(handle, url, ...)
15: httr::GET(url, path = path, httr::write_disk(path = tmp), auth)
16: remote_package_name.github_remote(remote)
17: remote_package_name(remote)
18: install_remote(..., quiet = quiet)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch(install_remote(..., quiet = quiet), error = function(e) {
if (!quiet) { message("Installation failed: ",
conditionMessage(e)) } FALSE})
23: FUN(X[[i]], ...)
24: vapply(remotes, try_install_remote, ..., FUN.VALUE = logical(1))
25: install_remotes(remotes, quiet = quiet, ...)
26: devtools::install_github("goranbrostrom/eha", build_vignettes =
TRUE)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 3
Segmentation fault (core dumped)
-----------------------------------------------------------------
devtools is version 1.13.6 in all cases.
However, running the same in RStudio: No problem.
The same setup, but on ubuntu 16.04 (another computer): No problem.
On my Mac: No problem.
Is it ubuntu, devtools, or me? If it is me, what can I do?
G?ran
Just as one more datapoint: I cannot reproduce the segfault, with
R 3.5.1 on (L)Ubuntu 18.04. (I use the Ubuntu package, i.e. I did not
build from source.)
regards
Enrico
Quoting G?ran Brostr?m <goran.brostrom at umu.se>:
> I am running R 3.5.1 on ubuntu 18.04, installed via apt. When I run
> R from the bash prompt, I get (reinstalling r-base doesn't help)
>
>> devtools::install_github("goranbrostrom/eha", build_vignettes
= TRUE)
>
> *** caught segfault ***
> address 0x68456, cause 'memory not mapped'
>
> Traceback:
> 1: dyn.load(file, DLLpath = DLLpath, ...)
> 2: library.dynam(lib, package, package.lib)
> 3: loadNamespace(name)
> 4: doTryCatch(return(expr), name, parentenv, handler)
> 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 6: tryCatchList(expr, classes, parentenv, handlers)
> 7: tryCatch(loadNamespace(name), error = function(e) stop(e))
> 8: getNamespace(ns)
> 9: asNamespace(ns)
> 10: getExportedValue(pkg, name)
> 11: curl::new_handle
> 12: handle(name)
> 13: handle_find(url)
> 14: handle_url(handle, url, ...)
> 15: httr::GET(url, path = path, httr::write_disk(path = tmp), auth)
> 16: remote_package_name.github_remote(remote)
> 17: remote_package_name(remote)
> 18: install_remote(..., quiet = quiet)
> 19: doTryCatch(return(expr), name, parentenv, handler)
> 20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 21: tryCatchList(expr, classes, parentenv, handlers)
> 22: tryCatch(install_remote(..., quiet = quiet), error = function(e)
> { if (!quiet) { message("Installation failed: ",
> conditionMessage(e)) } FALSE})
> 23: FUN(X[[i]], ...)
> 24: vapply(remotes, try_install_remote, ..., FUN.VALUE = logical(1))
> 25: install_remotes(remotes, quiet = quiet, ...)
> 26: devtools::install_github("goranbrostrom/eha", build_vignettes
= TRUE)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection: 3
> Segmentation fault (core dumped)
> -----------------------------------------------------------------
> devtools is version 1.13.6 in all cases.
>
> However, running the same in RStudio: No problem.
>
> The same setup, but on ubuntu 16.04 (another computer): No problem.
>
> On my Mac: No problem.
>
> Is it ubuntu, devtools, or me? If it is me, what can I do?
>
> G?ran
>
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
--
Enrico Schumann
Lucerne, Switzerland
http://enricoschumann.net
On 6 July 2018 at 12:31, Enrico Schumann wrote: | Just as one more datapoint: I cannot reproduce the segfault, with | R 3.5.1 on (L)Ubuntu 18.04. (I use the Ubuntu package, i.e. I did not | build from source.) I have been a little too busy and have not yet upgraded to 18.04 so I can't attempt to replicate -- but it _looks_ just like a garden variety binary mismatch. We _know_ R 3.5.* requires _all_ binary packages to be reinstalled and it is easy to miss one. So unless G?ran shows us a generally reproducible bug I will suspect that this is simply a local deployment issue. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org