On 7 November 2025 at 15:14, Peter Carbonetto wrote: | However, I was not able to reproduce the exact errors Dirk obtained by | running the R code purl'ed from the single_cell_rnaseq_basic.Rmd vignette. | I thought that this might work: | | R -d valgrind --vanilla < single_cell_rnaseq_basic.R | | but this did not produce any of the "runtime errors" such as: | | /usr/local/lib/R/site-library/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7043:26: | runtime error: reference binding to null pointer of type 'const double' | | Dirk, could you please share the exact R or Rscript command you ran to | obtain these errors? In addition, do I need to install fastTopics and the | other R packages in a specific way as well? That is, are there special | flags (perhaps existing somewhere in | https://www.stats.ox.ac.uk/pub/bdr/memtests/README.txt) that are needed to | activate these extra debugging checks?
You want 'RD', not 'R'. From the container's github repo README.mdL Note that the instrumented version of R is available on the path as Rdevel, symbolically linked as RD, and that the instrumented versions of Rscript is Rscriptdevel with symbolic link RDscript. Based on the R-devel sources, they use the sanitizer setup that is the focuse here whereas the R and Rscript binaries come from the standard binary package and correspond to R-release without any sanitizer instrumentation. So use RD and RDscript to inspect undefined behavior. Also not sure why you added '-d valgrind'. That is a very fine tool, but its use tends to be independent of ASAN/UBSAN and result in separate reports. Best, Dirk -- dirk.eddelbuettel.com | @eddelbuettel | [email protected] ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
