--- re-building ‘short-creek.qmd’ using html  processing file: short-creek.qmd ================================================================= ==4190217==ERROR: AddressSanitizer: container-overflow on address 0x7d736f4d0080 at pc 0x55fb0c778044 bp 0x7be355e3b510 sp 0x7be355e3acc8 READ of size 904 at 0x7d736f4d0080 thread T3  #0 0x55fb0c778043 in memcpy /data/gannet/ripley/Sources2/LLVM/21/latest/compiler-rt/lib/asan/../sanitizer_common/sanitizer_common_interceptors_memintrinsics.inc:117:5 #1 0x7be35bfc2258 in std::__1::function&, epiworld::Model*)> epiworld::distribute_tool_to_entities(std::__1::vector>, bool)::'lambda'(epiworld::Tool&, epiworld::Model*)::operator()(epiworld::Tool&, epiworld::Model*) const (/data/gannet/ripley/R/test-clang/epiworldR/libs/epiworldR.so+0xa2258) #2 0x7be35be89b85 in std::__1::__function::__value_func&, epiworld::Model*)>::operator()[abi:ne210108](epiworld::Tool&, epiworld::Model*&&) const /usr/local/clang21/bin/../include/c++/v1/__functional/function.h:274:12 #3 0x7be35be89b85 in std::__1::function&, epiworld::Model*)>::operator()(epiworld::Tool&, epiworld::Model*) const /usr/local/clang21/bin/../include/c++/v1/__functional/function.h:772:10 #4 0x7be35be89b85 in epiworld::Tool::distribute(epiworld::Model*) /data/gannet/ripley/R/test-clang/epiworldR/include/epiworld/tool-meat.hpp:563:9 #5 0x7be35be89b85 in epiworld::Model::dist_tools() /data/gannet/ripley/R/test-clang/epiworldR/include/epiworld/model-meat.hpp:815:15 #6 0x7be35be89b85 in epiworld::Model::reset() /data/gannet/ripley/R/test-clang/epiworldR/include/epiworld/model-meat.hpp:2069:5 #7 0x7be35becf88d in epiworld::epimodels::ModelMeaslesMixing::reset() /data/gannet/ripley/R/test-clang/epiworldR/include/epiworld/models/measlesmixing.hpp:518:18 #8 0x7be35be85322 in epiworld::Model::run(unsigned long long, int) /data/gannet/ripley/R/test-clang/epiworldR/include/epiworld/model-meat.hpp:1471:5 #9 0x7be35becf71d in epiworld::epimodels::ModelMeaslesMixing::run(unsigned long long, int) /data/gannet/ripley/R/test-clang/epiworldR/include/epiworld/models/measlesmixing.hpp:508:18 #10 0x7be35bfaaf34 in epiworld::Model::run_multiple(unsigned long long, unsigned long long, int, std::__1::function*)>, bool, bool, int) (.omp_outlined.136) model.cpp #11 0x7fe3728d1128 in __kmp_invoke_microtask (/usr/local/clang21/lib/x86_64-unknown-linux-gnu/libomp.so+0xa8128) #12 0x7fe37284d91e (/usr/local/clang21/lib/x86_64-unknown-linux-gnu/libomp.so+0x2491e) #13 0x7fe37284c57d (/usr/local/clang21/lib/x86_64-unknown-linux-gnu/libomp.so+0x2357d) #14 0x7fe3728b0b77 (/usr/local/clang21/lib/x86_64-unknown-linux-gnu/libomp.so+0x87b77) #15 0x55fb0c7769f6 in asan_thread_start(void*) /data/gannet/ripley/Sources2/LLVM/21/latest/compiler-rt/lib/asan/asan_interceptors.cpp:239:28 #16 0x7fe37207f1d3 in start_thread (/lib64/libc.so.6+0x711d3) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #17 0x7fe372101ceb in __GI___clone3 (/lib64/libc.so.6+0xf3ceb) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) 0x7d736f4d0080 is located 0 bytes inside of 1024-byte region [0x7d736f4d0080,0x7d736f4d0480) allocated by thread T3 here:  #0 0x55fb0c779114 in malloc /data/gannet/ripley/Sources2/LLVM/21/latest/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x7fe36fc1f2fb in operator new(unsigned long) (/lib64/libstdc++.so.6+0x1f2fb) (BuildId: a34f3756a2aefc3d2b7ae49335dfdd1b4555be43) Thread T3 created by T0 here:  #0 0x55fb0c75d371 in pthread_create /data/gannet/ripley/Sources2/LLVM/21/latest/compiler-rt/lib/asan/asan_interceptors.cpp:250:3 #1 0x7fe3728b01e2 (/usr/local/clang21/lib/x86_64-unknown-linux-gnu/libomp.so+0x871e2) HINT: if you don't care about these errors you may set ASAN_OPTIONS=detect_container_overflow=0. If you suspect a false positive see also: https://github.com/google/sanitizers/wiki/AddressSanitizerContainerOverflow. SUMMARY: AddressSanitizer: container-overflow (/data/gannet/ripley/R/test-clang/epiworldR/libs/epiworldR.so+0xa2258) in std::__1::function&, epiworld::Model*)> epiworld::distribute_tool_to_entities(std::__1::vector>, bool)::'lambda'(epiworld::Tool&, epiworld::Model*)::operator()(epiworld::Tool&, epiworld::Model*) const Shadow bytes around the buggy address: 0x7d736f4cfe00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d736f4cfe80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d736f4cff00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d736f4cff80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d736f4d0000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7d736f4d0080:[fc]fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x7d736f4d0100: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x7d736f4d0180: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x7d736f4d0200: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x7d736f4d0280: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x7d736f4d0300: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc Shadow byte legend (one shadow byte represents 8 application bytes): Addressable: 00 Partially addressable: 01 02 03 04 05 06 07 Heap left redzone: fa Freed heap region: fd Stack left redzone: f1 Stack mid redzone: f2 Stack right redzone: f3 Stack after return: f5 Stack use after scope: f8 Global redzone: f9 Global init order: f6 Poisoned by user: f7 Container overflow: fc Array cookie: ac Intra object redzone: bb ASan internal: fe Left alloca redzone: ca Right alloca redzone: cb ==4190217==ABORTING Error: processing vignette 'short-creek.qmd' failed with diagnostics: ! Error running quarto CLI from R. Caused by error in `quarto_render()`: ✖ Error returned by quarto CLI. ----------------------------- processing file: short-creek.qmd ================================================================= ==4190217==ERROR: AddressSanitizer: container-overflow on address 0x7d736f4d0080 at pc 0x55fb0c778044 bp 0x7be355e3b510 sp 0x7be355e3acc8 READ of size 904 at 0x7d736f4d0080 thread T3 #0 0x55fb0c778043 in memcpy /data/gannet/ripley/Sources2/LLVM/21/latest/compiler-rt/lib/asan/../sanitizer_common/sanitizer_common_interceptors_memintrinsics.inc:117:5 #1 0x7be35bfc2258 in std::__1::function&, epiworld::Model*)> epiworld::distribute_tool_to_entities(std::__1::vector>, bool)::'lambda'(epiworld::Tool&, epiworld::Model*)::operator()(epiworld::Tool&, epiworld::Model*) const (/data/gannet/ripley/R/test-clang/epiworldR/libs/epiworldR.so+0xa2258) #2 0x7be35be89b85 in std::__1::__function::__value_func&, epiworld::Model*)>::operator()[abi:ne210108](epiworld::Tool&, epiworld::Model*&&) const /usr/local/clang21/bin/../include/c++/v1/__functional/function.h:274:12 #3 0x7be35be89b85 in std::__1::function&, epiworld::Model*)>::operator()(epiworld::Tool&, epiworld::Model*) const /usr/local/clang21/bin/../include/c++/v1/__functional/function.h:772:10 #4 0x7be35be89b85 in epiworld::Tool::distribute(epiworld::Model*) /data/gannet/ripley/R/test-clang/epiworldR/include/epiworld/tool-meat.hpp:563:9 #5 0x7be35be89b85 in epiworld::Model::dist_tools() /data/gannet/ripley/R/test-clang/epiworldR/include/epiworld/model-meat.hpp:815:15 #6 0x7be35be89b85 in epiworld::Model::reset() /data/gannet/ripley/R/test-clang/epiworldR/include/epiworld/model-meat.hpp:2069:5 #7 0x7be35becf88d in epiworld::epimodels::ModelMeaslesMixing::reset() /data/gannet/ripley/R/test-clang/epiworldR/include/epiworld/models/measlesmixing.hpp:518:18 #8 0x7be35be85322 in epiworld::Model::run(unsigned long long, int) /data/gannet/ripley/R/test-clang/epiworldR/include/epiworld/model-meat.hpp:1471:5 #9 0x7be35becf71d in epiworld::epimodels::ModelMeaslesMixing::run(unsigned long long, int) /data/gannet/ripley/R/test-clang/epiworldR/include/epiworld/models/measlesmixing.hpp:508:18 #10 0x7be35bfaaf34 in epiworld::Model::run_multiple(unsigned long long, unsigned long long, int, std::__1::function*)>, bool, bool, int) (.omp_outlined.136) model.cpp #11 0x7fe3728d1128 in __kmp_invoke_microtask (/usr/local/clang21/lib/x86_64-unknown-linux-gnu/libomp.so+0xa8128) #12 0x7fe37284d91e (/usr/local/clang21/lib/x86_64-unknown-linux-gnu/libomp.so+0x2491e) #13 0x7fe37284c57d (/usr/local/clang21/lib/x86_64-unknown-linux-gnu/libomp.so+0x2357d) #14 0x7fe3728b0b77 (/usr/local/clang21/lib/x86_64-unknown-linux-gnu/libomp.so+0x87b77) #15 0x55fb0c7769f6 in asan_thread_start(void*) /data/gannet/ripley/Sources2/LLVM/21/latest/compiler-rt/lib/asan/asan_interceptors.cpp:239:28 #16 0x7fe37207f1d3 in start_thread (/lib64/libc.so.6+0x711d3) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #17 0x7fe372101ceb in __GI___clone3 (/lib64/libc.so.6+0xf3ceb) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) 0x7d736f4d0080 is located 0 bytes inside of 1024-byte region [0x7d736f4d0080,0x7d736f4d0480) allocated by thread T3 here: #0 0x55fb0c779114 in malloc /data/gannet/ripley/Sources2/LLVM/21/latest/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x7fe36fc1f2fb in operator new(unsigned long) (/lib64/libstdc++.so.6+0x1f2fb) (BuildId: a34f3756a2aefc3d2b7ae49335dfdd1b4555be43) Thread T3 created by T0 here: #0 0x55fb0c75d371 in pthread_create /data/gannet/ripley/Sources2/LLVM/21/latest/compiler-rt/lib/asan/asan_interceptors.cpp:250:3 #1 0x7fe3728b01e2 (/usr/local/clang21/lib/x86_64-unknown-linux-gnu/libomp.so+0x871e2) HINT: if you don't care about these errors you may set ASAN_OPTIONS=detect_container_overflow=0. If you suspect a false positive see also: https://github.com/google/sanitizers/wiki/AddressSanitizerContainerOverflow. SUMMARY: AddressSanitizer: container-overflow (/data/gannet/ripley/R/test-clang/epiworldR/libs/epiworldR.so+0xa2258) in std::__1::function&, epiworld::Model*)> epiworld::distribute_tool_to_entities(std::__1::vector>, bool)::'lambda'(epiworld::Tool&, epiworld::Model*)::operator()(epiworld::Tool&, epiworld::Model*) const Shadow bytes around the buggy address: 0x7d736f4cfe00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d736f4cfe80: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d736f4cff00: fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x7d736f4cff80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7d736f4d0000: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x7d736f4d0080:[fc]fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x7d736f4d0100: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x7d736f4d0180: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x7d736f4d0200: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x7d736f4d0280: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x7d736f4d0300: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc Shadow byte legend (one shadow byte represents 8 application bytes): Addressable: 00 Partially addressable: 01 02 03 04 05 06 07 Heap left redzone: fa Freed heap region: fd Stack left redzone: f1 Stack mid redzone: f2 Stack right redzone: f3 Stack after return: f5 Stack use after scope: f8 Global redzone: f9 Global init order: f6 Poisoned by user: f7 Container overflow: fc Array cookie: ac Intra object redzone: bb ASan internal: fe Left alloca redzone: ca Right alloca redzone: cb ==4190217==ABORTING Caused by error: ! System command 'quarto' failed --- failed re-building ‘short-creek.qmd’ SUMMARY: processing the following file failed: ‘short-creek.qmd’ Error: Vignette re-building failed. Execution halted