Hi Brent,
On 15 February 2024 at 10:14, Brent G Ewing 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 That container has been building weekly quite reliably for a few years now. The variant at https://github.com/rocker-org/r-devel-san-clang was dormant for a while (first an error during R package build, later a missing package) and was just resurrected and builds again. And then there is of course Winston's 'sumo' container with several builds layerd into one. I use that too: https://github.com/wch/r-debug | 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 Sure -- but I found this finicky in the past: certain combinations lead to cases that did not build or errored. So I recommend following the set that Brian Ripley has at https://www.stats.ox.ac.uk/pub/bdr/memtests/README.txt | 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. Maybe try removing 'address' and see what happens? | My questions are | | 1. is it possible to build and install R and packages (in a container) with | the gcc address sanitizer enabled? Yes. The two Docker contains show how to. | 2. if it is, how do I do it? Follow the container recipe? Use the container? Eg I just pulled up the rocker/r-devel-san, giving 'bash' as the command / entry point, and (having mounted my local directory too) said 'RD CMD INSTALL digest_0.6.34.tar.gz'. That install the package under the instrumented R(-devel) version. Tests should now use SAN. I have fixed bugs that way. | 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 think it is relevant but you must have ended up with a non-working combination. I no longer recall why I removed 'address'. It may have been something like this, or something else. `git blame` tells me I did so in 2018. It's been a while. As I said, these things _are_ finicky. So I recommend - starting from a known working container (see above) - establish a baseline by testing a package which has a _known_ true positive - for which I wrote a package: https://cran.r-project.org/package=sanitizers - given the baseline make the mods you want to make and re-test you still get the true positive Hope this helps, Dirk | 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 -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
