[R-SIG-Mac] consistent segfault

[Dan Tenenbaum]

----- Original Message -----
> From: "Richard M. Heiberger" <rmh at temple.edu>
> To: r-sig-mac at 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 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
> 
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