[R-pkg-devel] How to check memory access (understanding Section 4.3 WRE)

[Marius Hofert]

Hi,

I tried to understand how to check memory access of an R package with
C code; see https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Checking-memory-access

I'm about 90% sure I understood WRE Section 4.3.2 about valgrind. In essence:
1) When configuring R before make, use the configure flags '-C
--with-valgrind-instrumentation=2 --with-system-valgrind-headers'
   to get a memory-profiling-enabled version of R. This I found on
https://www.stats.ox.ac.uk/pub/bdr/memtests/README.txt
   and it's also described at the bottom of
https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Configuration-options
2) Then use 'R CMD check --use-valgrind' or directly check examples via
   'R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < mypkg-Ex.R'
I also seems to work (but reports false positives for Mac as others
have reported).

I'm still struggling with 4.3.3, see
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-Address-Sanitizer.
It says "The simplest way to make use of this is to build a version of
R with something like..." and
CC="gcc -std=gnu99 -fsanitize=address"
CFLAGS="-fno-omit-frame-pointer -g -O2 -Wall -pedantic -mtune=native"
I set these flags via 'configure CC="gcc -std=gnu99
-fsanitize=address" CFLAGS="-fno-omit-frame-pointer -g -O2 -Wall
-pedantic -mtune=native"' before 'make'. I used R-devel for it and the
installation was fine. Is there any option 'R CMD check' would need to
obtain (like the '--use-valgrind' above)? 'R CMD check mypkg.tar.gz'
doesn't seem to do any memory access checking. Would I also need to
set "MAIN_LDFLAGS=-fsanitize=address" for configure? (it's a bit
unclear from WRE whether this applies to both of the approaches
mentioned or just to the one based on Makevars)

I also tried the second approach based on "~/.R/Makevars" and put the
following in "~/.R/Makevars" as suggested in WRE:
CC = gcc -std=gnu99 -fsanitize=address -fno-omit-frame-pointer
CXX = g++ -fsanitize=address -fno-omit-frame-pointer
F77 = gfortran -fsanitize=address
FC = gfortran -fsanitize=address
'R CMD check mypkg.tar.gz' then fails and 00install.out shows (on
macOS 10.13.5, R-3.5.0 here):

* installing *source* package ‘mypkg’ ...
** libs
...
* R
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
sh: line 1: 14016 Abort trap: 6
'/usr/local/R/R-3.5.0_build/bin/R' --no-save --slave 2>&1 <
'/var/folders/cb/drz6kv896317dzbg52flzn_r0000gn/T//RtmpTha0EH/file369f755a95ad'
==14016==ERROR: Interceptors are not working. This may be because
AddressSanitizer is loaded too late (e.g. via dlopen). Please launch
the executable with:
DYLD_INSERT_LIBRARIES=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/9.1.0/lib/darwin/libclang_rt.asan_osx_dynamic.dylib
"interceptors not installed" && 0
ERROR: loading failed
* removing ‘/Users/mhofert/pro/mypkg/mypkg.Rcheck/mypkg’
Any ideas where the 'DYLD_INSERT_LIBRARIES' should go?

Thanks & cheers,
Marius