Can't get working R 3.6.3 and 4.2.3 with DESEq2 if compiled by AMD CLANG at Ubuntu 22.04 x64
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lokapal • 0
@lokapal-10101
Last seen 9 months ago
Russia

I've tried to compiled both R and some modules (namely DESeq2) by AMD optimizing compiler AMD clang version 14.0.6 (CLANG: AOCC_4.0.0-Build#434 2022_10_28) (based on LLVM Mirror.Version.14.0.6) with no success. configure was run by the bash script:

#!/bin/sh
export CXX=clang++
export CC=clang
./configure \
     --prefix=/opt/R/4.2.3 \
     --disable-R-profiling \
     --with-blas \
     --with-lapack \
     --with-tcltk \
     --without-x

Makeconf was tuned to add -march=native -mtune=native for all compilers, and compilation of R both 3.6.3 and 4.2.3 went smoothly. make check tests passed, no discrepancies observed. Bioconductor 3.16 for R 4.2.3 and Bioconductor 3.10 for R 3.6.3 were installed. Through Bioconductors DESeq2 and all dependent modules have been installed. Nevertheless when I try to run tested at the other computer DESEq2 script I get "C stack overflow" in both R's (3.6.3 and 4.2.3). After full re-compilation of R 4.2.3 and re-installation of modules with default Ubuntu 22.04 gcc-11 all passed smoothly.

So, it's the question - can anybody successfully compiled DESeq2 and many other useful Bioconductor modules with AMD CLANG? Which compiler options can be a remedy in this case? Thanks in advance

CLANG DESeq2 • 462 views
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