R devel - Sep 2015 - segfault with readDCF on R 3.1.2 on AIX 6.1 when using install.packages

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

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

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
me.

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.

Thanks.

-- Vinh


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:
>>
>> 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