[R-SIG-Mac] consistent segfault

[Richard M. Heiberger]

I can consistently get a segfault from Mavericks 3.1 and I suspect it
is from a mismatch
of compiled code.  Can this type of mismatch be detected when the
package is loaded?


When I moved to the Mavericks R distribution, I copied packages from
my 3.0 (SnowLeopard) library and then did an update.packages().  That
gives a segfault.
I did a fresh install of the relevant package and then it worked.
Both listings are below.

A. segfault listing with copied colorspace package

R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.1.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE)
> library(colorspace)
> ?hex
>      hsv = HSV(seq(0, 360, length = 7)[-7], 1, 1)
>      hsv
       H S V
[1,]   0 1 1
[2,]  60 1 1
[3,] 120 1 1
[4,] 180 1 1
[5,] 240 1 1
[6,] 300 1 1
>      hex(hsv)

 *** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: .Call("as_sRGB", from at coords, class(from), .WhitePoint, PACKAGE =
"colorspace")
 2: cbind(R, if (missing(G)) NULL else G, if (missing(B)) NULL else B)
 3: sRGB(.Call("as_sRGB", from at coords, class(from), .WhitePoint,
PACKAGE = "colorspace"), names = dimnames(from at coords)[[1]])
 4: asMethod(object)
 5: as(from, "sRGB")
 6: hex(hsv)

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: 2

Process R finished at Thu Jul 17 07:25:40 2014


B. same R distribution with newer colorspace

R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.1.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE)
> install.packages("colorspace")
--- Please select a CRAN mirror for use in this session ---
trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/macosx/mavericks/contrib/3.1/colorspace_1.2-4.tgz'
Content type 'application/x-gzip' length 391920 bytes (382 Kb)
opened URL
==================================================
downloaded 382 Kb


The downloaded binary packages are in
/var/folders/vq/xl0j17pn29g52mgx7lqxl8d80000gn/T//Rtmp5YxaKt/downloaded_packages
> library(colorspace)
>      hsv = HSV(seq(0, 360, length = 7)[-7], 1, 1)
>      hsv
       H S V
[1,]   0 1 1
[2,]  60 1 1
[3,] 120 1 1
[4,] 180 1 1
[5,] 240 1 1
[6,] 300 1 1
>      hex(hsv)
[1] "#FF0000" "#FFFF00" "#00FF00" "#00FFFF" "#0000FF" "#FF00FF"
> q()

Process R finished at Thu Jul 17 07:34:55 2014



Both colorspace package DESCRIPTION files start with
Package: colorspace
Version: 1.2-4
Date: 2013-09-30

The only difference in the DESCRIPTION file is
Built: R 3.0.2; x86_64-apple-darwin10.8.0; 2014-01-09 19:11:14 UTC; unix
Built: R 3.1.0; x86_64-apple-darwin13.1.0; 2014-04-24 15:04:36 UTC; unix

The files in the libs directory are different