[BioC] Limma normalization error and loess.R segmentation type fault (windows)

Martin Morgan mtmorgan at fhcrc.org
Wed Sep 5 02:38:12 CEST 2012 

On 09/04/2012 05:25 PM, Marcus Davy wrote:
> I know that it was introduced in R-2.15.1, and the same error also appears
> to also exist on R-2.15.1-patched
> which I have tested this morning. The subversion revision numbers were in
> the limma change log.
>
> I have a specific simple example to illustrate the *first* error which is a
> core dump on windows R-2.15.1, and R-2.15.1-patched
>
> set.seed(42)
> n <- 10
> y <- rnorm(n)
> x <- rnorm(n)
> w <- rep(0, n)
> sessionInfo()
>
> lm.wfit(cbind(1, x), y, w)

under R -d gdb -f test.R there is

 > set.seed(42)
 > n <- 10
 > y <- rnorm(n)
 > x <- rnorm(n)
 > w <- rep(0, n)
 > lm.wfit(cbind(1, x), y, w)

Program received signal SIGFPE, Arithmetic exception.
0x00007ffff4d6d975 in Cdqrls (x=0xc47eb8, y=0xc47d68, tol=0xe29b68)
     at /home/mtmorgan/src/R-devel/src/library/stats/src/lm.c:51
51	    ny = LENGTH(y)/n;  /* n x ny, or a vector */

with

 > R.version.string
[1] "R Under development (unstable) (2012-09-04 r60559)"

so the reproducible example should be reported to R-devel or R-bugs 
https://bugs.r-project.org

Martin

>
> Process R exited abnormally with code 148 at Wed Sep 05 12:23:58 2012
>
>
> Try that and see if you get a core dump, if so that makes this bug pretty
> ciritical on windows given that it is for weighted linear model fits. I am
> still checking out R-2.15.1 to identify what revision changes have taken
> place.
>
> Marcus
>
>> sessionInfo()
> R version 2.15.1 Patched (2012-09-01 r60539)
> Platform: i386-w64-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_New Zealand.1252  LC_CTYPE=English_New
> Zealand.1252
> [3] LC_MONETARY=English_New Zealand.1252
> LC_NUMERIC=C
> [5] LC_TIME=English_New Zealand.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
>
> On Wed, Sep 5, 2012 at 9:44 AM, Kasper Daniel Hansen <
> kasperdanielhansen at gmail.com> wrote:
>
>> On Tue, Sep 4, 2012 at 5:38 PM, Marcus Davy <mdavy86 at gmail.com> wrote:
>>> Hi Gordon,
>>> yes, I believe the cause of the crashes are due to changes in the file
>>>
>> http://svn.r-project.org/R/branches/R-2-15-branch/src/library/stats/R/loess.Rwithin
>>> the stats package for R-2.15.1. I will email you a simple example
>>> off list to see if you can reproduce the crash on windows.
>>
>> Markus, a similar problem seem to occur with the charm package.  Have
>> you tracked down the approximate changes to R which causes it (I think
>> the svn revision numbers below are for bioconductor).  Specifically,
>> does it go away in R-2.15.1-patched and/or when was it introduced?
>>
>> Thanks,
>> Kasper
>>
>>>
>>> The change to loessFit to use stats:::simpleLoess appears to be the
>> reason
>>> for the second error message I got when using the development version of
>>> limma on windows.
>>>
>>>> packageDescription("limma")$Version
>>> [1] "3.13.17"
>>>
>>>> changeLog(n=7)
>>> 17 Aug 2012: limma 3.3.17
>>>
>>> - limma license upgraded to GPL-2 instead of LGPL to match R itself.
>>>
>>> - loessFit() no longer makes direct calls to foreign language
>>>    functions in the stats package.  Same values are returned as before,
>>>    but now take 25-30% longer whenever weights are used.
>>>
>>>
>>> svn diff -r 68536:68077
>>>
>>>
>>> cheers,
>>>
>>> Marcus
>>>
>>>
>>> On Tue, Sep 4, 2012 at 10:09 PM, Gordon K Smyth <smyth at wehi.edu.au>
>> wrote:
>>>
>>>> Hi Marcus,
>>>>
>>>> I haven't seen this problem myself.  I've just tried running the Weaver
>>>> case study in the limma User's Guide, and it still runs correctly for
>> me,
>>>> using either R 2.15.1 or R-devel on Windows.
>>>>
>>>> There weren't any changes to that part of the limma code between R
>> 2.14.1
>>>> and R 2.15.1, so the change you are seeing may be in the stats package.
>>>>
>>>> Best wishes
>>>> Gordon
>>>>
>>>> ---------------- original message ---------------
>>>> [BioC] Limma normalization error and loess.R segmentation type fault
>>>> (windows)
>>>> Marcus Davy mdavy86 at gmail.com
>>>> Tue Sep 4 07:11:43 CEST 2012
>>>>
>>>> Is anyone having recent problems after upgrading to R-2.15.1 on windows
>>>> with limma or other bioconductor packages that use loess functions in
>> the
>>>> stats core package.?
>>>>
>>>> The normalization function normalizeWithinArrays(...,
>>>> method=printtiploess) is crashing on two independent windows machines
>>>> since upgrading R from 2.14.1 to 2.15.1 using the stable release
>> packages
>>>> on bioconductor. I have a segmentation type fault of Rgui.exe running
>> this
>>>> code snippet;
>>>>
>>>> system.time(MA <- normalizeWithinArrays(RG, method="printtiploess",
>>>> bc.method="none"))
>>>>
>>>> Process R exited abnormally with code 148 at Tue Sep 04 14:42:30 2012
>>>>
>>>> I can get a more meaningful error if I install the development release
>> of
>>>> limma;
>>>>
>>>> useDevel()
>>>> biocLite("limma")
>>>>
>>>> system.time(MA <- normalizeWithinArrays(RG, method="printtiploess",
>>>> bc.method="none"))
>>>>
>>>> Error in stats:::simpleLoess(y = yobs, x = xobs, weights = wobs, span =
>>>> span,  :
>>>>
>>>>    NA/NaN/Inf in foreign function call (arg 1)
>>>>
>>>> Timing stopped at: 12.34 2.11 14.5
>>>>
>>>> The number of NAs and weights in the offending array are;
>>>>
>>>>   sum(is.na(tmp$M))
>>>>>
>>>> [1] 717
>>>>
>>>>> sum(is.na(tmp$A))
>>>>>
>>>> [1] 717
>>>>
>>>>> table(tmp$weights)
>>>>>
>>>>      0     1
>>>>   8362 10070
>>>>
>>>>
>>>> The error appears to be caused in R core->stats:::simpleLoess (not
>> limma)
>>>> when interfacing C code, and I can see there have been recent commits to
>>>> the stats/loess.R file in the R core subversion repository. In the
>> stable
>>>> release, limma calls normalizeWithinArrays() -> loessFit() >
>>>> .vsimpleLoess(), which appear to have modified to
>>>>
>>>> normalizeWithinArrays() -> loessFit() > stats:::simpleLoess in the
>>>> development release of limma, which explains the error I get with the
>>>> development release of limma.
>>>>
>>>> A colleague independently tested normalizing the one offending
>> microarray
>>>> slide I identified causing the same segmentation type fault on his
>> machine,
>>>> Sorry I have not provided a reproducible example but I can provide an
>> RSave
>>>> to load just that array of data, and the code snippets to reproduce the
>>>> error in an email, this bug appears to be data dependent, windows
>> dependent
>>>> (my example code works fine without crashing on linux using R version
>>>> 2.15.0 and limma 3.12.0) and probably infrequent to achieve.
>>>>
>>>> cheers,
>>>> Marcus
>>>>
>>>>
>>>> ## Stable release
>>>>
>>>>   sessionInfo()
>>>>>
>>>> R version 2.15.1 (2012-06-22)
>>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>>
>>>> locale:
>>>> [1] LC_COLLATE=English_New Zealand.1252  LC_CTYPE=English_New
>> Zealand.1252
>>>> [3] LC_MONETARY=English_New Zealand.1252 LC_NUMERIC=C
>>>> [5] LC_TIME=English_New Zealand.1252
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>> other attached packages:
>>>> [1] Biobase_2.16.0     BiocGenerics_0.2.0 limma_3.12.1
>>>>
>>>> ## development release
>>>> sessionInfo()
>>>>
>>>> R version 2.15.1 (2012-06-22)
>>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>>
>>>> locale:
>>>> [1] LC_COLLATE=English_New Zealand.1252  LC_CTYPE=English_New
>> Zealand.1252
>>>> [3] LC_MONETARY=English_New Zealand.1252 LC_NUMERIC=C
>>>> [5] LC_TIME=English_New Zealand.1252
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>> other attached packages:
>>>> [1] limma_3.13.17
>>>>
>>>>
>> ______________________________**______________________________**__________
>>>> The information in this email is confidential and inte...{{dropped:10}}
>>>
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