Hi Brent, In case you aren't aware, Winston Chang has some Docker images that build R with ASAN and UBSAN, using gcc and clang: https://github.com/wch/r-debug
This doesn't directly address your question, but I hope it might be helpful. Best, Josh On Thu, Feb 15, 2024 at 12:15 PM Brent G Ewing <b...@uw.edu> wrote: > > Hi, > > I want to build a Docker container with R and various R packages built and > installed with the gcc address sanitizer enabled. I am working on a Debian > Bookworm system running on an x86_64 architecture. > > I start with the Docker file at > > https://github.com/rocker-org/r-devel-san/blob/master/Dockerfile > > I added -fsanitize=address to compiler and linker variables in the > Dockerfile. I also import into the image a Makevars file with the contents > > CC=gcc -std=gnu99 -fsanitize=address -fno-omit-frame-pointer > CXX=g++ -fsanitize=address -fno-omit-frame-pointer > FC=gfortran -fsanitize=address > LDFLAGS=-fsanitize=address > > Finally, the Docker file installs additional Debian object libraries and R > packages that I want to test. > > When the package build gets to testing whether the package can be > installed, an error message appears saying > > ==ASan runtime does not come first in initial library list; you should > either link runtime to your application or manually preload it with > LD_PRELOAD. > > For example, > > ESC[0mESC[91m** building package indices > ESC[0mESC[91m** installing vignettes > ESC[0mESC[91m** testing if installed package can be loaded from temporary > location > ESC[0m==684==ASan runtime does not come first in initial library list; you > should either link runtime to your application or manually preload it with > LD_PRELOAD. > ESC[91mERROR: loading failed > ESC[0mESC[91m* removing ‘/usr/local/lib/R/site-library/utf8’ > ESC[0mESC[91m* installing *source* package ‘isoband’ ... > ESC[0mESC[91m** package ‘isoband’ successfully unpacked and MD5 sums checked > ESC[0mESC[91m** using staged installation > ESC[0mESC[91m** libs > > I've tried preloading various libasan.so files that I find on the system > but the loader says that it cannot load them. > > My questions are > > 1. is it possible to build and install R and packages (in a container) with > the gcc address sanitizer enabled? > 2. if it is, how do I do it? > 3. is this ld_preload message relevant? If so, to which file does it refer? > Is there an ASAN runtime library file that I need to specify, and if so, > what is the path to it? > > I appreciate your consideration and assistance. > > Thank you. > Brent > > P.S. The build-related commands in the Docker file (including my address > sanitizer additions) are > > RUN cd /tmp/R-devel \ > && R_PAPERSIZE=letter \ > R_BATCHSAVE="--no-save --no-restore" \ > R_BROWSER=xdg-open \ > PAGER=/usr/bin/pager \ > PERL=/usr/bin/perl \ > R_UNZIPCMD=/usr/bin/unzip \ > R_ZIPCMD=/usr/bin/zip \ > R_PRINTCMD=/usr/bin/lpr \ > LIBnn=lib \ > AWK=/usr/bin/awk \ > CC="gcc -std=gnu99 -fsanitize=address -fsanitize=undefined > -fno-omit-frame-pointer" \ > CFLAGS="-fno-omit-frame-pointer -g -O2 -Wall -pedantic > -mtune=native" \ > FFLAGS="-g -O2 -mtune=native" \ > FCFLAGS="-g -O2 -mtune=native" \ > CXX="g++ -fsanitize=address -fsanitize=undefined,bounds-strict > -fno-omit-frame-pointer" \ > CXXFLAGS="-fsanitize=address -g -O2 -Wall -pedantic > -mtune=native" \ > CXX11FLAGS="-fsanitize=address -g -O2 -Wall -pedantic > -mtune=native" \ > CXX14FLAGS="-fsanitize=address -g -O2 -Wall -pedantic > -mtune=native" \ > CXX17FLAGS="-fsanitize=address -g -O2 -Wall -pedantic > -mtune=native" \ > LDFLAGS="-fsanitize=address" \ > MAIN_LDFLAGS="-fsanitize=address -fsanitize=undefined -pthread" \ > F77="gfortran -fsanitize=undefined" \ > FC="gfortran -fsanitize=undefined" \ > FCFLAGS="-g -O2 -mtune=native" \ > FFLAGS="-g -O2 -mtune=native" \ > ./configure --enable-R-shlib \ > --without-blas \ > --without-lapack \ > --with-readline \ > --without-recommended-packages \ > --program-suffix=dev \ > --disable-openmp \ > && make \ > && make install \ > && make clean > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian -- Joshua Ulrich | about.me/joshuaulrich FOSS Trading | www.fosstrading.com _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
