R SIG Debian - Jan 2017 - Taking determinant of a matrix of NAs results in intermittent memory corruption

-----Original Message-----
From: Dirk Eddelbuettel [mailto:dirk.eddelbuettel at gmail.com] On Behalf Of
Dirk Eddelbuettel
Sent: Thursday, 19 January 2017 12:41 PM
To: Klint Gore
Cc: Dirk Eddelbuettel; r-sig-debian at r-project.org
Subject: RE: [R-sig-Debian] Taking determinant of a matrix of NAs results in
intermittent memory corruption


On 19 January 2017 at 01:26, Klint Gore wrote:
| >So this converges towards 'old versions bad, new versions fine' ?
| 
| Probably.  Old version of what, I don't know.  Openblas is 0.2.8-6ubuntu1
on 14.04 lts which is current.
> Sorry, what part of '14.04' is current?
>
> Ubuntu is at 16.10. And release 16.04, which as a LTS replaces the LTS
14.04 you use, also passes.  Can you upgrade?
That version of the openblas package is the latest currently available for 14.04
LTS from the official ubuntu repository.  14.04 LTS is "supported" by
Canonical until 2019.

Also, I'm just confirming that I can repeat it.  It's not an issue for
me as it's never happened other than the contrived example.  If someone
brought it to my attention, I'd probably follow your original though and ask
them if they really wanted the determinant of an unassigned matrix as it sounds
like not a useful thing to do.  Using rnorm to initialise the matrix works fine.

I'd suggest the OP pursue it with the linux mint people as it's directly
affecting him and it occurs in their "supported" version.

Klint.

On 19 January 2017 at 02:49, Klint Gore wrote:
| -----Original Message-----
| From: Dirk Eddelbuettel [mailto:dirk.eddelbuettel at gmail.com] On Behalf Of
Dirk Eddelbuettel
| > Sorry, what part of '14.04' is current?
| >
| > Ubuntu is at 16.10. And release 16.04, which as a LTS replaces the LTS
14.04 you use, also passes.  Can you upgrade?
| 
| That version of the openblas package is the latest currently available for
14.04 LTS from the official ubuntu repository.  14.04 LTS is
"supported" by Canonical until 2019.

Well but aren't you confusing or conflating two things here? I am only
harping on this as it is r-sig-debian. "Supported" by Canonical means
that
should a security bug require an update to a component of your installation,
you may get it from their repo. No more, no less.

Otherwise, the focus is on _stability_ -- hence no changes whatsoever. [1] 

Which in turn means old, known bugs like the one we are talking about here
will NOT get fixed.  It is a trade-off: some people value the stability, some
people value the fixes and new features.  
 
| Also, I'm just confirming that I can repeat it.  It's not an issue for
me as it's never happened other than the contrived example.  If someone
brought it to my attention, I'd probably follow your original though and ask
them if they really wanted the determinant of an unassigned matrix as it sounds
like not a useful thing to do.  Using rnorm to initialise the matrix works fine.
| 
| I'd suggest the OP pursue it with the linux mint people as it's
directly affecting him and it occurs in their "supported" version.

Agreed.

Dirk

[1] Eg the R version in 14.04 is forever fixed at version 3.0.2 as far as the
'official Ubuntu repository' is concerned. 
| 
| 

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

Thank you Dirk, Klint, and Rolf for your time and attention.

I tried booting off a flash drive loaded with (the most recent) Linux Mint 18.1,
enabled a CRAN Ubuntu mirror as a software source, installed the latest R from
CRAN, and was unable to reproduce the issue.

La_version() gave me 3.6.0, and the output of system(paste("lsof -p",
Sys.getpid(), "| grep -iE '(blas|lapack)'")) also indicated
that R was using the 3.6.0 versions of liblapack.so and libopenblas.so


So, I agree that it looks like it was an issue with the shared libraries as
Martin suspected.


Before submitting this bug report, I had assumed that R uses its own versions of
these libraries by default, so I've learned something new as well.

Thanks Martin also for the troubleshooting tips on how to determine what
libraries are being used by R.

I'll update and close the report on the R Bugzilla tracker next.

Best Wishes,

--Ian




________________________________
From: Dirk Eddelbuettel <edd at debian.org>
To: Klint Gore <kgore4 at une.edu.au> 
Cc: "r-sig-debian at r-project.org" <r-sig-debian at
r-project.org>
Sent: Wednesday, January 18, 2017 7:41 PM
Subject: Re: [R-sig-Debian] Taking determinant of a matrix of NAs results in
intermittent memory corruption



On 19 January 2017 at 02:49, Klint Gore wrote:
| -----Original Message-----
| From: Dirk Eddelbuettel [mailto:dirk.eddelbuettel at gmail.com] On Behalf Of
Dirk Eddelbuettel
| > Sorry, what part of '14.04' is current?
| >
| > Ubuntu is at 16.10. And release 16.04, which as a LTS replaces the LTS
14.04 you use, also passes.  Can you upgrade?
| 
| That version of the openblas package is the latest currently available for
14.04 LTS from the official ubuntu repository.  14.04 LTS is
"supported" by Canonical until 2019.

Well but aren't you confusing or conflating two things here? I am only
harping on this as it is r-sig-debian. "Supported" by Canonical means
that
should a security bug require an update to a component of your installation,
you may get it from their repo. No more, no less.

Otherwise, the focus is on _stability_ -- hence no changes whatsoever. [1] 

Which in turn means old, known bugs like the one we are talking about here
will NOT get fixed.  It is a trade-off: some people value the stability, some
people value the fixes and new features.  

| Also, I'm just confirming that I can repeat it.  It's not an issue for
me as it's never happened other than the contrived example.  If someone
brought it to my attention, I'd probably follow your original though and ask
them if they really wanted the determinant of an unassigned matrix as it sounds
like not a useful thing to do.  Using rnorm to initialise the matrix works fine.
| 
| I'd suggest the OP pursue it with the linux mint people as it's
directly affecting him and it occurs in their "supported" version.

Agreed.

Dirk

[1] Eg the R version in 14.04 is forever fixed at version 3.0.2 as far as the
'official Ubuntu repository' is concerned. 
| 
| 

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org


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