dipetkov
commented
7 years ago I updated to R 3.4.0 and fixed code to pass R CMD check without warnings. (Previous version resulted in the warning described here: https://github.com/RcppCore/Rcpp/issues/636.)
That was a warning, not an error, so I am not sure whether it will solve your problem (which occurs in the cpp code not in the native R code).
Here is my session info:
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
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] grDevices graphics stats utils methods base
other attached packages:
[1] rEEMSplots_0.0.0.9000
loaded via a namespace (and not attached):
[1] compiler_3.4.0 RcppEigen_0.3.3.3.0 Matrix_1.2-10
[4] tools_3.4.0 sp_1.2-4 Rcpp_0.12.10
[7] raster_2.5-8 grid_3.4.0 rgeos_0.3-23
[10] lattice_0.20-35 
jbemmels
Hi, I have successfully installed, but have not been able to run the R package rEEMSplots. Whether I use data files generated myself by running runeems_snps, or if I use the example files that come with the rEEMSplots package, I always encounter a segmentation fault.
I do not understand what the error message means or how to fix it. Searching online said this type of error might indicate a problem with the code. I am using R version 3.4.0 on Mac OS X 10.11.6 El Capitan.
Here is an example of the error output to the R console using the example scripts and example files provided with the rEEMSplots documentation. Any help or suggestions would be greatly appreciated. Thank you very much! - Jordan
The error message:
Input projection: Output projection:
Using the default DarkOrange to Blue color scheme, with 'white' as the midpoint color. It combines two color schemes from the 'dichromat' package, which itself is based on a collection of color schemes for scientific data graphics: Light A and Bartlein PJ (2004). The End of the Rainbow? Color Schemes for Improved Data Graphics. EOS Transactions of the American Geophysical Union, 85(40), 385. See also http://geog.uoregon.edu/datagraphics/color_scales.htm
Using 'euclidean' distance to assign interpolation points to Voronoi tiles.
Processing the following EEMS output directories : /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rEEMSplots/extdata/EEMS-example Plotting effective migration surface (posterior mean of m rates) /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rEEMSplots/extdata/EEMS-example
caught segfault address 0x18, cause 'memory not mapped'
Traceback: 1: .Call("rEEMSplots_tiles2contours_standardize", PACKAGE = "rEEMSplots", tiles, rates, seeds, marks, distm) 2: tiles2contours_standardize(tiles, rates, cbind(xseed, yseed), marks, dimns$dist.metric) 3: transform.rates(dimns, tiles, rates, xseed, yseed, zero_mean) 4: average.eems.contours(mcmcpath, dimns, longlat, plot.params, is.mrates = TRUE, plot.xy = m.plot.xy) 5: eems.plots(mcmcpath = eems.results.to.plot, plotpath = paste(name.figures.to.save, "-default", sep = ""), longlat = TRUE)
Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: