- Original Message -
From: Richard M. Heiberger r...@temple.edu
To: r-sig-mac@r-project.org
Sent: Thursday, July 17, 2014 5:03:26 AM
Subject: [R-SIG-Mac] consistent segfault
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().
You can't copy Snow Leopard packages to Mavericks. They are not compatible.
You should remove your installation and then reinstall R, reinstalling the
packages you need
with install.packages().
Dan
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@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@coords, class(from), .WhitePoint,
PACKAGE = colorspace), names = dimnames(from@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/xl0j17pn29g52mgx7lqxl8d8gn/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] #FF #00 #00FF00 #00 #FF #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
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