R help - Nov 2014 - segfault with readDCF on R 3.1.2 on AIX 6.1 when using install.packages

Dear list,

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.  Would be great to get this resolved.  Thank you for your
help.

-- Vinh

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.

Thanks!

-- Vinh


On Tue, Nov 11, 2014 at 8:10 AM, Vinh Nguyen <vinhdizzo at gmail.com>
wrote:
> Dear list,
>
> 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.  Would be great to get this resolved.  Thank you for your
> help.
>
> -- Vinh

Perhaps you are not using a compatible compiler. I believe this is off-topic for
this mailing list, though.. see the Posting Guide.
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Sent from my phone. Please excuse my brevity.

On November 11, 2014 8:10:49 AM PST, Vinh Nguyen <vinhdizzo at gmail.com>
wrote:
>Dear list,
>
>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.  Would be great to get this resolved.  Thank you for your
>help.
>
>-- Vinh
>
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>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.