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; > sumis.na(tmp$M)) [1] 717 > sumis.na(tmp$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 [[alternative HTML version deleted]]