ms609/actions/asan#271
Merged
Merged
Conversation
The "AddressSanitizer tests" job has been failing on every push for several weeks with: ==PID==Shadow memory range interleaves with an existing memory mapping. ASan cannot proceed correctly. ABORTING. This is google/sanitizers#856 / llvm/llvm-project#85780. The ubuntu-24.04 runner ships a kernel with vm.mmap_rnd_bits=32; ASan's shadow memory layout cannot accommodate that much ASLR entropy and aborts at startup. Setting vm.mmap_rnd_bits=28 (the canonical workaround) gives ASan a clean shadow region. Only "AddressSanitizer tests" is affected on this repo today, because testthat::test_local() loads more shared libraries before ASan allocates its shadow than the examples/vignettes subjobs do. Applying the sysctl unconditionally to all three configurations is harmless and avoids future drift.
Setting vm.mmap_rnd_bits=28 alone was applied successfully (logs confirm 'vm.mmap_rnd_bits = 28') but ASan still aborted with the ELF_ET_DYN_BASE diagnostic - the kernel's load address for PIE binaries on ubuntu-24.04 collides with ASan's shadow regardless of mmap entropy. Disable system-wide ASLR for the runner VM to give ASan a stable, low-address layout.
The previous attempt set sysctl vm.mmap_rnd_bits=28 and
kernel.randomize_va_space=0, both confirmed applied on the runner.
ASan still aborted with the ELF_ET_DYN_BASE diagnostic, indicating
the failure is not about ASLR entropy.
Log analysis showed the abort happens AFTER 'library(TreeTools)'
succeeds (the 'Creating a generic function' messages from TreeTools
loading print, then ASan aborts). That timing rules out a parent-R
startup failure: libasan must be initialising late, when R dlopen()s
the package's instrumented .so.
The 'Initialize ASan configuration' step had
export LD_PRELOAD=\$(gcc -print-file-name=libasan.so)
inside a subshell, so the variable did not persist to the Rscript
step. Without LD_PRELOAD, libasan is only pulled in via the package's
.so dependency, by which point R's heap, libR.so, and (for the tests
subjob) testthat's full dependency stack already occupy the address
range ASan needs for its shadow region. examples and vignettes
happened to leave enough room; tests did not.
Set LD_PRELOAD inline on the Rscript command so libasan loads at
process startup, before any other shared object. Keep the
mmap_rnd_bits sysctl as defence in depth; drop the more invasive
randomize_va_space=0 now that the root cause is addressed.
The LD_PRELOAD fix in the previous commit moved ASan past the shadow-memory abort, but leak detection now fires on: - libcrypto.so.3 / libssl.so.3 / libxml2.so.2 one-time init memory - xml2 R package allocations from HTML parsing - /usr/bin/sed (a 1-byte allocation in sed itself, called by some test-discovery step) None of these are TreeTools bugs and none are actionable from this codebase. CRAN's own gcc-ASAN setup runs with detect_leaks=0 for the same reason - LSan in an R session pulls in too much third-party state to be useful. We retain valgrind for leak coverage.
Replace the bespoke 95-line vanilla-runner workflow (manual Makevars, LD_PRELOAD, sysctl workarounds, R install steps) with the container- based approach used by sibling package TreeSearch. The r-hub gcc-asan image ships an ASan-instrumented R, so all sanitizer setup is handled inside the composite action. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Retain the simplified ms609/actions/asan@main approach over the bespoke vanilla-runner steps that came in from main. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.