From vinhdizzo at gmail.com  Mon Sep 21 19:01:12 2015
From: vinhdizzo at gmail.com (Vinh Nguyen)
Date: Mon, 21 Sep 2015 10:01:12 -0700
Subject: [Rd] segfault with readDCF on R 3.1.2 on AIX 6.1 when using
	install.packages
In-Reply-To: <CA+2Dmwgowjk9+qKcVQOPXRaGpER5wu+UtqZ=pJrJmaNS1DDpdw@mail.gmail.com>
References: <CA+2Dmwgowjk9+qKcVQOPXRaGpER5wu+UtqZ=pJrJmaNS1DDpdw@mail.gmail.com>
Message-ID: <CA+2DmwigXqx_ymW85qzgL7JvyM6tHyzyqSNjWcazow+JROZZ+g@mail.gmail.com>

Hi there,

I just wanted to follow up on this readDCF issue with install.packages
on AIX on R 3.*.  I'm happy to help try potential solutions or debug
if anyone could point me in the right direction.

To re-cap, it appears readDCF is segfault'ing since R 3.* on AIX.
This was not the case up until R 2.15.3.  This makes install.packages
not usable.  Thanks.

-- Vinh


On Tue, Nov 11, 2014 at 10:23 AM, Vinh Nguyen <vinhdizzo at gmail.com> wrote:
> Dear list (re-posting from r-help as r-devel is probably more appropriate),
>
> I was able to successfully compile R on our AIX box at work using the
> GNU compilers following the instructions on the R Administration
> guide.  The output can be seen at here
> (https://gist.github.com/nguyenvinh/504321ea9c89d8919bef) and yields
> no errors .
>
> However, I get a segfault whenever I try to use the install.packages
> function to install packages.  Using debug, I was able to trace it to
> the readDCF function:
>
> Browse[2]>
> debug: if (!all) return(.Internal(readDCF(file, fields, keep.white)))
> Browse[2]>
> debug: return(.Internal(readDCF(file, fields, keep.white)))
> Browse[2]>
>
>  *** caught segfault ***
> address 4, cause 'invalid permissions'
>
> 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:
>
> Was curious if anyone has a clue on why such error exists or what I
> could do to fix it?  I'm able to install packages via R CMD INSTALL,
> but I would hate to have to manually determine dependencies, download
> the source for each package, and install them "by hand" via R CMD
> INSTALL.
>
> I went back and compiled older versions of R to see if this error
> exists.  On R 3.0.3, I get:
>
> debug(available.packages)
> install.packages('ggplot2', dep=TRUE, repo='http://cran.stat.ucla.edu')
> ...
> Browse[2]>
> debug: z <- res0 <- tryCatch(read.dcf(file = tmpf), error = identity)
> Browse[2]>
> Error: segfault from C stack overflow
>
> On R 2.15.3, I do not see the error.
>
> Would be great to get this resolved.  Thank you for your help.
>
> -- Vinh



[Rd] segfault with readDCF on R 3.1.2 on AIX 6.1 when using install.packages
Vinh Nguyen