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

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