Hi
Loading the CRAN binary version of the tkrplot package version 0.0-23 causes a segfault of R version 3.2.2 on OS X 10.11.1 too.
Installing form sources solves the problem.
Still no idea ?
Jean
[MacPro:~] jthioulo% R
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
R est un logiciel libre livr? sans AUCUNE GARANTIE.
Vous pouvez le redistribuer sous certaines conditions.
Tapez 'license()' ou 'licence()' pour plus de d?tails.
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Tapez 'contributors()' pour plus d'information et
'citation()' pour la fa?on de le citer dans les publications.
Tapez 'demo()' pour des d?monstrations, 'help()' pour l'aide
en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
Tapez 'q()' pour quitter R.
[Sauvegarde de la session pr?c?dente restaur?e]
sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (El Capitan)
locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
install.packages("tkrplot")
essai de l'URL 'http://cran.univ-lyon1.fr/bin/macosx/mavericks/contrib/3.2/tkrplot_0.0-23.tgz'
Content type 'application/x-gzip' length 24752 bytes (24 KB)
==================================================
downloaded 24 KB
Les packages binaires t?l?charg?s sont dans
/var/folders/qg/wgr2ssj52259lkbxq2z_dwwc0000gn/T//RtmpWSrqzX/downloaded_packages
library(tkrplot)
Le chargement a n?cessit? le package : tcltk
*** caught segfault ***
address 0x998, cause 'memory not mapped'
Traceback:
1: structure(.External(.C_dotTclObjv, objv), class = "tclObj")
2: .Tcl.objv(.Tcl.args.objv(...))
3: tcl("load", file, "Rplot")
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(tcl("load", file, "Rplot"), error = function(e) warning("loading Rplot failed", call. = FALSE))
8: fun(libname, pkgname)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(fun(libname, pkgname), error = identity)
13: runHook(".onLoad", env, package.lib, package)
14: loadNamespace(package, c(which.lib.loc, lib.loc))
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: 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))})
19: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc)) env <- attachNamespace(ns, pos = pos, deps)})
20: library(tkrplot)
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: 4
[MacPro:~] jthioulo% R
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
R est un logiciel libre livr? sans AUCUNE GARANTIE.
Vous pouvez le redistribuer sous certaines conditions.
Tapez 'license()' ou 'licence()' pour plus de d?tails.
R est un projet collaboratif avec de nombreux contributeurs.
Tapez 'contributors()' pour plus d'information et
'citation()' pour la fa?on de le citer dans les publications.
Tapez 'demo()' pour des d?monstrations, 'help()' pour l'aide
en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
Tapez 'q()' pour quitter R.
[Sauvegarde de la session pr?c?dente restaur?e]
install.packages("tkrplot", type="source")
essai de l'URL 'http://cran.univ-lyon1.fr/src/contrib/tkrplot_0.0-23.tar.gz'
Content type 'application/x-gzip' length 39037 bytes (38 KB)
==================================================
downloaded 38 KB
* installing *source* package ?tkrplot? ...
** package ?tkrplot? correctement d?compress? et sommes MD5 v?rifi?es
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC "-mtune=native -g -O2 -Wall -pedantic -Wconversion" -c tcltkimg.c -o tcltkimg.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o tkrplot.so tcltkimg.o -L/usr/local/lib -ltcl8.6 -L/usr/local/lib -ltk8.6 -L/usr/X11/lib -lX11 -Wl,-weak-lXss -lXext -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/tkrplot/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (tkrplot)
Les packages source t?l?charg?s sont dans
?/private/var/folders/qg/wgr2ssj52259lkbxq2z_dwwc0000gn/T/RtmpuiZDOB/downloaded_packages?
library(tkrplot)
Le chargement a n?cessit? le package : tcltk
Save workspace image? [y/n/c]: y
[MacPro:~] jthioulo%
Le 11 juil. 2015 ? 00:54, Dan Tenenbaum <dtenenba at fredhutch.org> a ?crit :
Hi,
loading the tkrplot package (version 0.0-23) causes a segfault. This only seems to happen on Mavericks, not Snow Leopard, Linux, or Windows.
library(tkrplot)
Loading required package: tcltk
*** caught segfault ***
address 0x998, cause 'memory not mapped'
Traceback:
1: structure(.External(.C_dotTclObjv, objv), class = "tclObj")
2: .Tcl.objv(.Tcl.args.objv(...))
3: tcl("load", file, "Rplot")
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(tcl("load", file, "Rplot"), error = function(e) warning("loading Rplot failed", call. = FALSE))
8: fun(libname, pkgname)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(fun(libname, pkgname), error = identity)
13: runHook(".onLoad", env, package.lib, package)
14: loadNamespace(package, c(which.lib.loc, lib.loc))
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: 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))})
19: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc)) env <- attachNamespace(ns, pos = pos, deps)})
20: library(tkrplot)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
My sessionInfo() is:
sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)
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 ideas?
Thanks,
Dan