Kyle Meyer <k...@kyleam.com> skribis: > l...@gnu.org (Ludovic Courtès) writes: > >> I can reproduce the bug with: >> >> guix environment --pure --ad-hoc r -- R > > [...] > >> Might be useful to report it upstream? > > Yes. In preparing to do so, I figured that I should reproduce the issue > with a build outside of Guix. However, when I tried with a manual build > on an Arch Linux system, the snippet ran fine. This was with gcc > version 5.2.0, so I switched the gfortran input of openblas over to > gfortran-5, which seems to fix the issue.
Interesting. > While the issue should still be reported upstream, would it be OK to > update the gfortran input to gfortran-5? The problem is that this leads to an R linked against GCC 4.9’s libgcc_s and other run-time support libraries, and also against those of GCC 5.2, via OpenBLAS. I think we’d rather avoid it. An additional data point: --8<---------------cut here---------------start------------->8--- $ guix environment --pure --ad-hoc r valgrind -- R -d valgrind /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/bin/R: line 8: uname: command not found ==3198== Memcheck, a memory error detector ==3198== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al. ==3198== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info ==3198== Command: /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/bin/exec/R ==3198== R version 3.2.2 (2015-08-14) -- "Fire Safety" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > M <- 50 > N <- 500 > eigen(crossprod(matrix(rnorm(M * N), M, N))) ==3198== Invalid read of size 8 ==3198== at 0x8E400E0: dgemv_t_SANDYBRIDGE (in /gnu/store/hw9p1zyn1nh8pbm1cl69nm0i391lk6c7-openblas-0.2.15/lib/libopenblasp-r0.2.15.so) ==3198== by 0x183AED48: dlatrd_ (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libRlapack.so) ==3198== by 0x18461F92: dsytrd_ (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libRlapack.so) ==3198== by 0x184B9540: dsyevr_ (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libRlapack.so) ==3198== by 0x1B742D5E: La_rs (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/modules/lapack.so) ==3198== by 0x1B745B96: mod_do_lapack (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/modules/lapack.so) ==3198== by 0x4F35635: bcEval (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so) ==3198== by 0x4F432DF: Rf_eval (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so) ==3198== by 0x4F48F4B: Rf_applyClosure (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so) ==3198== by 0x4F4345E: Rf_eval (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so) ==3198== by 0x4F6B0D9: Rf_ReplIteration (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so) ==3198== by 0x4F6B430: R_ReplConsole (in /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so) ==3198== Address 0xfb0 is not stack'd, malloc'd or (recently) free'd ==3198== *** caught segfault *** address 0xfb0, cause 'memory not mapped' --8<---------------cut here---------------end--------------->8--- Here this suggests an R issue more than an OpenBLAS problem. Ludo’.
