Here is a solution worked out by the wonderful staff from our scientific computing support team at the Fred Hutchinson Cancer Research Center. I really don't know how Dan did it, but the way he explained to me was that he came across this github repository by Dirk: https://github.com/rocker-org/r-devel-san-clang. There was the Docker file which built the clang-san image, but he did not find the image itself in Docker Hub. So he built it himself and pushed it as dtenenba/r-devel-san-clang.
The issue I encountered with r-debug was related to ulimit. It turns out that it be specific to the machine I was working on. Dan used a different machine and that went away. Using the docker image dtenenba/r-devel-san-clang on that new machine, I was able to install my package, and upon running the test code, to reproduce the memory issue reported by the CRAN team. I then tested whether r-debug might also work on that machine. It sort of did as it returned a memory-related error when I tried RDsan CMD INSTALL mypkg But it is not as helpful as the behavior by dtenenba/r-devel-san-clang. On Fri, Nov 29, 2019 at 1:48 PM Youyi Fong <youyif...@gmail.com> wrote: > Hi Dirk, > > Thanks very much. Following your suggestion, I tried r-debug, following > the readme on https://github.com/wch/r-debug. After starting docker as > recommended, > > docker run --rm -ti --security-opt seccomp=unconfined wch1/r-debug > > I was able to call RD. But calling RDsan or RDcsan resulted in errors: > > root@258bfdfcce6c:/# RDsan > ==17==ERROR: AddressSanitizer failed to allocate 0xdfff0001000 > (15392894357504) bytes at address 2008fff7000 (errno: 12) > ==17==ReserveShadowMemoryRange failed while trying to map 0xdfff0001000 > bytes. Perhaps you're using ulimit -v > Aborted (core dumped) > > > I have also tried rhub before, following this article: > https://cran.r-project.org/web/packages/rhub/vignettes/local-debugging.html As > you indicated, it may have worked for others, but got the following error: > > >>>>>==================== Installing system requirements > 3b3a65d751c026b7629d2038242c92290cf97853525978381b6e59f41c8500d3 > > >>>>>==================== Starting Docker container > 04d6065323ef732bf89c26df7d547efff40774206a0ac6a24b3d9cdb021cb08e > ls: cannot access '/opt/R-*': No such file or directory > > source('https://bioconductor.org/biocLite.R') > Error: With R version 3.5 or greater, install Bioconductor packages using > BiocManager; see https://bioconductor.org/install > Execution halted > Error in run(bash, c(file.path(wd, "rhub-linux.sh"), args), echo = TRUE, : > System command error > > > > This is where I am stuck at right now. > > Thanks, > Youyi > > > On Fri, Nov 29, 2019 at 10:46 AM Dirk Eddelbuettel <e...@debian.org> wrote: > >> >> Youyi, >> >> It looks like you are trying to debug a _current_ SAN / ASAN / UBSAN error >> against your package by leaning on documentation I wrote five years ago >> specifically for another package (called "sanitizers") used to validate >> the >> initial Docker container builds I made (and to ensure the error these >> SAN/ASAN/UBSAN containers were supposed to trigger were triggered). >> >> Today, your quickest bet to launch a sanitizer run may be via the rhub >> platforms. Clearly the easiest to launch ("no download"), but at times a >> little inconsistent. An alternative is the suite of containers >> maintained by >> Winston described at their repo at https://github.com/wch/r-debug at >> available from the Docker Hub. >> >> All that said, exact configurations matters and the fact remains that we >> all >> still haven't managed to automatically provide the configurations used by >> CRAN. There are possible "gaps" between what CRAN uses and what may be >> available pre-built: compiler versions, builds, sanitizer options, ... and >> these can be enough to not replicate an issue. I think I would try >> Winston's >> r-debug next. >> >> Hope this helps, Dirk >> >> -- >> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org >> > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
