[R-pkg-devel] Additional issues: Intel segfault

Murray Efford murr@y@e||ord @end|ng |rom ot@go@@c@nz
Fri Mar 1 08:42:01 CET 2024


I am puzzling over an 'Additional issues' error in the CRAN check results for package secrdesign version 1.8.2 (see https://CRAN.R-project.org/package=secrdesign, and for an updated version https://github.com/MurrayEfford/secrdesign) The issue rises with the Intel(R) oneAPI DPC++/C++ Compiler: 

 *** caught segfault ***
address (nil), cause 'unknown'

The location of the error is obscure: R CMD check suggests it is most likely in the Examples for 'validate', but all code there is wrapped in \dontrun{}. The package makes limited use of RcppArmadillo and BH. It passes all other CRAN checks on several platforms (see GitHub link) and for all I know may now be 'clean'.

valgrind on x86_64-pc-linux-gnu (64-bit) hits an error that I guess is unrelated and not actually a bug 
(the location is a matrix multiplication in a function from package 'secr' that is executed by run.scenarios):

> sims1 <- run.scenarios(nrepl = 2, trapset = traps1, scenarios =
+      scen1, seed = 345, fit = TRUE, extractfn = summary)
vex amd64->IR: unhandled instruction bytes: 0x62 0xE1 0xFF 0x8 0x10 0xC 0xD1 0x62 0xF2 0xF5
vex amd64->IR:   REX=0 REX.W=0 REX.R=0 REX.X=0 REX.B=0
vex amd64->IR:   VEX=0 VEX.L=0 VEX.nVVVV=0x0 ESC=NONE
vex amd64->IR:   PFX.66=0 PFX.F2=0 PFX.F3=0
==1990825== valgrind: Unrecognised instruction at address 0x57d51f0.
==1990825==    at 0x57D51F0: dgemv_n (in /opt/OpenBLAS/lib/libopenblas_skylakexp-r0.3.23.dev.so)
==1990825==    by 0x554BDF9: dgemv_ (in /opt/OpenBLAS/lib/libopenblas_skylakexp-r0.3.23.dev.so)
==1990825==    by 0x4EE2F2C: matprod (array.c:812)
etc.

I would much appreciate any tips on how to proceed. Specifically, how to reproduce and localise the arcane Intel error that prevents me submitting a new version to CRAN, or whether I should submit regardless.

Murray Efford


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