After upgrading to version R 3.0.X, I began to get quite frequent, non-reproducible segfault errors, similar to those that were discovered by this user. I have never had one of these errors before with R 2.XX. For example, this is session information for a long block of code that just caused an error. However, after R failed, I ran the entire block of code again and there was no error.
R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] klaR_0.6-8 ggplot2_0.9.3.1 labdsv_1.5-0 MASS_7.3-26 mgcv_1.7-22 [6] cluster_1.14.4 sparcl_1.0.3 FD_1.0-11 vegan_2.0-7 permute_0.7-0 [11] geometry_0.3-3 magic_1.5-4 abind_1.4-0 ape_3.0-8 ade4_1.5-2 [16] plyr_1.8 loaded via a namespace (and not attached): [1] class_7.3-7 colorspace_1.2-2 dichromat_2.0-0 digest_0.6.3 [5] e1071_1.6-1 grid_3.0.1 gtable_0.1.2 labeling_0.1 [9] lattice_0.20-15 Matrix_1.0-12 munsell_0.4 nlme_3.1-109 [13] proto_0.3-10 RColorBrewer_1.0-5 reshape2_1.2.2 scales_0.2.3 [17] stringr_0.6.2
Sometimes R completely freezes, and I have to do a force shutdown, but in other cases it allows me to exit with kernel dump options or save the workspace.
Someone in another post suggested setting options(CBoundsCheck=T) , and this seemed to work for a while, but I still often encounter errors.
I do not think that these errors are related to any particular type of computation or function, since I received it the day after the start of a new session and set only the working directory and parameters. The code that caused the error and system information will look like this:
#Set my working directory setwd("~/Documents/School Spring 2013/Quaternary Dissasembly/Functional Diversity Basefile 3")
Any help anyone can give me to find and correct the error, or the incorrect settings that I have, would be greatly appreciated. Thanks.
-M
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