[Rd] segfault with readDCF on R 3.1.2 on AIX 6.1 when using install.packages
vinhdizzo at gmail.com
Mon Sep 21 19:49:57 CEST 2015
Here's an update:
I checked the ChangeLog for R, and it seems like readDCF was changed
in 3.0.2. I went on a whim and copied src/main/dcf.c from R 2.15.3
over to 3.2.2, and R compiled fine and install.packages now work for
This is probably not ideal, but it at least makes R usable on AIX for
me. Would definitely like to help figure out what's wrong with the
new dcf.c on AIX.
On Mon, Sep 21, 2015 at 10:01 AM, Vinh Nguyen <vinhdizzo at gmail.com> wrote:
> 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:
>> debug: if (!all) return(.Internal(readDCF(file, fields, keep.white)))
>> debug: return(.Internal(readDCF(file, fields, keep.white)))
>> *** 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
>> 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
>> I went back and compiled older versions of R to see if this error
>> exists. On R 3.0.3, I get:
>> install.packages('ggplot2', dep=TRUE, repo='http://cran.stat.ucla.edu')
>> debug: z <- res0 <- tryCatch(read.dcf(file = tmpf), error = identity)
>> 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
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