Re: [R-SIG-Mac] loading tkrplot causes a segfault

2015-07-13 Thread Kevin Ushey
For what it's worth, I can reproduce the issue with the binary
provided by CRAN; however, the package successfully loads for me when
installed from source.

install.packages(tkrplot, type = source)
library(tkrplot) ## no segfault

The error seems to occur as a result of loading the `Rplot` symbol(s)
with the following call (this is what the package's `.onLoad()` tries
to do:

library(tcltk)
tkrPath - system.file(package = tkrplot)
tkrLib - file.path(tkrPath, libs/tkrplot.so)
tcl(load, tkrLib, Rplot)

I can't really speculate further as to what the cause of the error is
-- perhaps `tkrplot`, or some other libraries used, were built with
incompatible compilers?

Kevin

On Mon, Jul 13, 2015 at 11:20 AM, Dan Tenenbaum dtene...@fredhutch.org wrote:


 - Original Message -
 From: THIOULOUSE JEAN jean.thioulo...@univ-lyon1.fr
 To: Dan Tenenbaum dtene...@fredhutch.org
 Cc: r-sig-mac r-sig-mac@r-project.org
 Sent: Friday, July 10, 2015 9:53:18 PM
 Subject: Re: [R-SIG-Mac] loading tkrplot causes a segfault


 Re-install X11 XQuartz (I think that this is in the FAQ).


 Reinstalling XQuartz (and rebooting) had no effect. Any other ideas?

 Thanks,
 Dan


 Jean


  Le 11 juil. 2015 à 00:54, Dan Tenenbaum dtene...@fredhutch.org a
  écrit :
 
  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 - 75Lmsg -
  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
 
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Re: [R-SIG-Mac] loading tkrplot causes a segfault

2015-07-13 Thread David Winsemius

On Jul 10, 2015, at 3:54 PM, Dan Tenenbaum wrote:

 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 - 75Lmsg - 
 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
 

I don't have an answer, but there were a bunch of tk-functions that were 
removed in version 3.0.0, including: tkcmd(), tkfile.dir(), tkfile.tail(), 
tkopen(),tkputs(), tkread()

There was also a news() item that specifically mentioned tkrplot and changes to 
the Windows graphics devices but didn't appear to me to imply anychanges to 
tkrplot.

Something very similar was reported 

From:   Natalija Keck natalija.k...@the-klu.org
Subject:[R-SIG-Mac] loading issue with tkrplot on OS X Yosemite
Date:   May 4, 2015 5:22:37 AM PDT
To: r-sig-mac R r-sig-mac@r-project.org

I don't see a response in my local email not-an-Archive.

I get the same result after installing tkrplot 0.0-23 from CRAN (using the 
binary pkg and installing with the R.app Package Instller)  and running R from 
a terminal session. XQuartz loads and then the seg-fault dialog appears. I've 
got XQuartz 2.7.7 (xorg-server 1.15.2) and the check for updates response for 
a running X11 session says I have the latest version.

-- David.

 
 
 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
 
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David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] loading tkrplot causes a segfault

2015-07-13 Thread Dan Tenenbaum


- Original Message -
 From: THIOULOUSE JEAN jean.thioulo...@univ-lyon1.fr
 To: Dan Tenenbaum dtene...@fredhutch.org
 Cc: r-sig-mac r-sig-mac@r-project.org
 Sent: Friday, July 10, 2015 9:53:18 PM
 Subject: Re: [R-SIG-Mac] loading tkrplot causes a segfault
 
 
 Re-install X11 XQuartz (I think that this is in the FAQ).
 

Reinstalling XQuartz (and rebooting) had no effect. Any other ideas?

Thanks,
Dan


 Jean
 
 
  Le 11 juil. 2015 à 00:54, Dan Tenenbaum dtene...@fredhutch.org a
  écrit :
  
  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 - 75Lmsg -
  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
  
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  R-SIG-Mac@r-project.org
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Re: [R-SIG-Mac] loading tkrplot causes a segfault

2015-07-10 Thread THIOULOUSE JEAN

Re-install X11 XQuartz (I think that this is in the FAQ).

Jean


 Le 11 juil. 2015 à 00:54, Dan Tenenbaum dtene...@fredhutch.org a écrit :
 
 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 - 75Lmsg - 
 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
 
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 R-SIG-Mac@r-project.org
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[R-SIG-Mac] loading tkrplot causes a segfault

2015-07-10 Thread Dan Tenenbaum
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 - 75Lmsg - 
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

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