Algorithms for lasso and fused-lasso problems: implementation of the lars algorithm for lasso and fusion penalization and EM-based algorithms for (logistic) lasso and fused-lasso penalization.
run the following workflow https://github.com/modal-inria/HDPenReg/actions/workflows/R-CMD-check-cpp.yml with clang-asan container to generate the error
* using log directory ‘/data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg.Rcheck’
* using R Under development (unstable) (2023-03-27 r84069)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
clang version 16.0.0
GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘HDPenReg/DESCRIPTION’ ... OK
* this is package ‘HDPenReg’ version ‘0.94.9’
* package encoding: UTF-8
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package ‘HDPenReg’ can be installed ... [15m/28m] OK
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
* checking package directory ... OK
* checking whether the package can be loaded ... [12s/43s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/27s] OK
* checking whether the package can be unloaded cleanly ... [13s/34s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/21s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/29s] OK
* checking loading without being on the library search path ... [12s/15s] OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [75s/178s] ERROR
Running examples in ‘HDPenReg-Ex.R’ failed
The error most likely occurred in:
> ### Name: HDcvlars
> ### Title: cross validation
> ### Aliases: HDcvlars
>
> ### ** Examples
>
> dataset <- simul(50, 10000, 0.4, 10, 50, matrix(c(0.1, 0.8, 0.02, 0.02), nrow = 2))
> result <- HDcvlars(dataset$data, dataset$response, 5)
=================================================================
==3531110==ERROR: AddressSanitizer: container-overflow on address 0x623000221010 at pc 0x7f44f92f87da bp 0x7ffcf58ac7d0 sp 0x7ffcf58ac7c8
READ of size 8 at 0x623000221010 thread T0
#0 0x7f44f92f87d9 in HD::PathState::l1norm() const /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/../lars/PathState.h:72:53
#1 0x7f44f92f87d9 in HD::Path::l1norm() const /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/../lars/Path.h:72:40
#2 0x7f44f92d5038 in HD::Lars::predict(STK::CArray<double, 2147483647, 2147483647, true> const&, double, bool, STK::CArrayVector<double, 2147483647, true>&) /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Lars.cpp:804:24
#3 0x7f44f934b0df in .omp_outlined._debug__ /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Cvlars.cpp:304:15
#4 0x7f44f934b0df in .omp_outlined. /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Cvlars.cpp:263:4
#5 0x7f44fc3c90e2 in __kmp_invoke_microtask (/usr/local/clang/lib64/libomp.so+0xb80e2) (BuildId: 8eba3d0f3145b19407156ac55f322da7c26ffb38)
#6 0x7f44fc34ca35 in __kmp_fork_call (/usr/local/clang/lib64/libomp.so+0x3ba35) (BuildId: 8eba3d0f3145b19407156ac55f322da7c26ffb38)
#7 0x7f44fc33d2c3 in __kmpc_fork_call (/usr/local/clang/lib64/libomp.so+0x2c2c3) (BuildId: 8eba3d0f3145b19407156ac55f322da7c26ffb38)
#8 0x7f44f9347de7 in HD::Cvlars::run2() /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Cvlars.cpp:263:4
#9 0x7f44f92966fd in cvlarsmain /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/larsRmain.cpp:241:10
#10 0x5626f0b0cca1 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c
#11 0x5626f0b5be75 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1551:11
#12 0x5626f0c76c5e in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7399:14
#13 0x5626f0c5fec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#14 0x5626f0cc1ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#15 0x5626f0cbe386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#16 0x5626f0c607b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1140:12
#17 0x5626f0cd0240 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3250:8
#18 0x5626f0c6026d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1092:12
#19 0x5626f0d9f945 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:262:2
#20 0x5626f0da3170 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11
#21 0x5626f0da2f66 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1200:5
#22 0x5626f0da32b2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1207:5
#23 0x5626f08c572c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5
#24 0x7f450c62950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
#25 0x7f450c6295c8 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
#26 0x5626f07ec314 in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x310314)
0x623000221010 is located 2832 bytes inside of 6000-byte region [0x623000220500,0x623000221c70)
allocated by thread T0 here:
#0 0x5626f08c310d in operator new(unsigned long) /data/gannet/ripley/Sources2/LLVM/16.0/llvm-project/compiler-rt/lib/asan/asan_new_delete.cpp:95:3
#1 0x7f44f9315f74 in void* std::__1::__libcpp_operator_new[abi:v160000]<unsigned long>(unsigned long) /usr/local/clang16/bin/../include/c++/v1/new:266:10
#2 0x7f44f9315f74 in std::__1::__libcpp_allocate[abi:v160000](unsigned long, unsigned long) /usr/local/clang16/bin/../include/c++/v1/new:292:10
#3 0x7f44f9315f74 in std::__1::allocator<HD::PathState>::allocate[abi:v160000](unsigned long) /usr/local/clang16/bin/../include/c++/v1/__memory/allocator.h:115:38
#4 0x7f44f9315f74 in std::__1::__allocation_result<std::__1::allocator_traits<std::__1::allocator<HD::PathState> >::pointer> std::__1::__allocate_at_least[abi:v160000]<std::__1::allocator<HD::PathState> >(std::__1::allocator<HD::PathState>&, unsigned long) /usr/local/clang16/bin/../include/c++/v1/__memory/allocate_at_least.h:55:19
#5 0x7f44f9315f74 in std::__1::__split_buffer<HD::PathState, std::__1::allocator<HD::PathState>&>::__split_buffer(unsigned long, unsigned long, std::__1::allocator<HD::PathState>&) /usr/local/clang16/bin/../include/c++/v1/__split_buffer:323:29
#6 0x7f44f9314bc5 in std::__1::vector<HD::PathState, std::__1::allocator<HD::PathState> >::reserve(unsigned long) /usr/local/clang16/bin/../include/c++/v1/vector:1503:53
#7 0x7f44f930fab8 in HD::Path::Path(int) /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Path.cpp:45:11
#8 0x7f44f92c3c41 in HD::Lars::Lars(STK::CArray<double, 2147483647, 2147483647, true> const&, STK::CArrayVector<double, 2147483647, true> const&, int, bool, double) /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Lars.cpp:83:13
#9 0x7f44f934af83 in .omp_outlined._debug__ /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Cvlars.cpp:298:17
#10 0x7f44f934af83 in .omp_outlined. /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Cvlars.cpp:263:4
#11 0x7f44fc3c90e2 in __kmp_invoke_microtask (/usr/local/clang/lib64/libomp.so+0xb80e2) (BuildId: 8eba3d0f3145b19407156ac55f322da7c26ffb38)
#12 0x7f44fc34ca35 in __kmp_fork_call (/usr/local/clang/lib64/libomp.so+0x3ba35) (BuildId: 8eba3d0f3145b19407156ac55f322da7c26ffb38)
#13 0x7f44fc33d2c3 in __kmpc_fork_call (/usr/local/clang/lib64/libomp.so+0x2c2c3) (BuildId: 8eba3d0f3145b19407156ac55f322da7c26ffb38)
#14 0x7f44f9347de7 in HD::Cvlars::run2() /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Cvlars.cpp:263:4
#15 0x7f44f92966fd in cvlarsmain /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/larsRmain.cpp:241:10
#16 0x5626f0b0cca1 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c
#17 0x5626f0b5be75 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1551:11
#18 0x5626f0c76c5e in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7399:14
#19 0x5626f0c5fec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#20 0x5626f0cc1ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#21 0x5626f0cbe386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#22 0x5626f0c607b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1140:12
#23 0x5626f0cd0240 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3250:8
#24 0x5626f0c6026d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1092:12
#25 0x5626f0d9f945 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:262:2
#26 0x5626f0da3170 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11
#27 0x5626f0da2f66 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1200:5
#28 0x5626f0da32b2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1207:5
#29 0x5626f08c572c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5
#30 0x7f450c62950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
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/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/../lars/PathState.h:72:53 in HD::PathState::l1norm() const
Shadow bytes around the buggy address:
0x623000220d80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x623000220e00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x623000220e80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x623000220f00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x623000220f80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 fc fc
=>0x623000221000: fc fc[fc]fc fc fc fc fc fc fc fc fc fc fc fc fc
0x623000221080: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc
0x623000221100: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc
0x623000221180: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc
0x623000221200: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc
0x623000221280: 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
==3531110==ABORTING
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [78s/174s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘HDPenReg.Rnw’ using Sweave
Loading required package: rtkore
Loading required package: Rcpp
Attaching package: ‘rtkore’
The following object is masked from ‘package:Rcpp’:
LdFlags
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
=================================================================
==3548796==ERROR: AddressSanitizer: container-overflow on address 0x6230000d0de0 at pc 0x7f53614f87da bp 0x7fffb8c2e550 sp 0x7fffb8c2e548
READ of size 8 at 0x6230000d0de0 thread T0
#0 0x7f53614f87d9 in HD::PathState::l1norm() const /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/../lars/PathState.h:72:53
#1 0x7f53614f87d9 in HD::Path::l1norm() const /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/../lars/Path.h:72:40
#2 0x7f53614d5038 in HD::Lars::predict(STK::CArray<double, 2147483647, 2147483647, true> const&, double, bool, STK::CArrayVector<double, 2147483647, true>&) /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Lars.cpp:804:24
#3 0x7f536154b0df in .omp_outlined._debug__ /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Cvlars.cpp:304:15
#4 0x7f536154b0df in .omp_outlined. /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Cvlars.cpp:263:4
#5 0x7f536468b0e2 in __kmp_invoke_microtask (/usr/local/clang/lib64/libomp.so+0xb80e2) (BuildId: 8eba3d0f3145b19407156ac55f322da7c26ffb38)
#6 0x7f53646140e7 in __kmp_invoke_task_func (/usr/local/clang/lib64/libomp.so+0x410e7) (BuildId: 8eba3d0f3145b19407156ac55f322da7c26ffb38)
#7 0x7f536460e777 in __kmp_fork_call (/usr/local/clang/lib64/libomp.so+0x3b777) (BuildId: 8eba3d0f3145b19407156ac55f322da7c26ffb38)
#8 0x7f53645ff2c3 in __kmpc_fork_call (/usr/local/clang/lib64/libomp.so+0x2c2c3) (BuildId: 8eba3d0f3145b19407156ac55f322da7c26ffb38)
#9 0x7f5361547de7 in HD::Cvlars::run2() /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Cvlars.cpp:263:4
#10 0x7f53614966fd in cvlarsmain /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/larsRmain.cpp:241:10
#11 0x55e6e0a7dca1 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c
#12 0x55e6e0acce75 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1551:11
#13 0x55e6e0be7c5e in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7399:14
#14 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#15 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#16 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#17 0x55e6e0bd17b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1140:12
#18 0x55e6e0c41240 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3250:8
#19 0x55e6e0bd126d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1092:12
#20 0x55e6e0c482ec in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3625:13
#21 0x55e6e0be7c5e in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7399:14
#22 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#23 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#24 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#25 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#26 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#27 0x55e6e0c2c90e in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:833:8
#28 0x55e6e0bd181d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1040:9
#29 0x55e6e0c4a1cf in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3677:9
#30 0x55e6e0d5f9a6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1404:11
#31 0x55e6e0bda504 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7419:15
#32 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#33 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#34 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#35 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#36 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#37 0x55e6e0c2c90e in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:833:8
#38 0x55e6e0c62f46 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5420:15
#39 0x55e6e0c62f46 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5461:14
#40 0x55e6e0c04bea in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7151:20
#41 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#42 0x55e6e0c2c90e in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:833:8
#43 0x55e6e0c62f46 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5420:15
#44 0x55e6e0c62f46 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5461:14
#45 0x55e6e0c04bea in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7151:20
#46 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#47 0x55e6e0c2c90e in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:833:8
#48 0x55e6e0c62f46 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5420:15
#49 0x55e6e0c62f46 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5461:14
#50 0x55e6e0c04bea in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7151:20
#51 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#52 0x55e6e0c2c90e in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:833:8
#53 0x55e6e0c62f46 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5420:15
#54 0x55e6e0c62f46 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5461:14
#55 0x55e6e0c04bea in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7151:20
#56 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#57 0x55e6e0c2c90e in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:833:8
#58 0x55e6e0c62f46 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5420:15
#59 0x55e6e0c62f46 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5461:14
#60 0x55e6e0c04bea in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7151:20
#61 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#62 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#63 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#64 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#65 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#66 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#67 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#68 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#69 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#70 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#71 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#72 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#73 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#74 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#75 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#76 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#77 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#78 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#79 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#80 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#81 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#82 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#83 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#84 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#85 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#86 0x55e6e0c2c90e in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:833:8
#87 0x55e6e0c62f46 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5420:15
#88 0x55e6e0c62f46 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5461:14
#89 0x55e6e0c04bea in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7151:20
#90 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#91 0x55e6e0c2c90e in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:833:8
#92 0x55e6e0c62f46 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5420:15
#93 0x55e6e0c62f46 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5461:14
#94 0x55e6e0c04bea in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7151:20
#95 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#96 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#97 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#98 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#99 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#100 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#101 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#102 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#103 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#104 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#105 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#106 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#107 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#108 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#109 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#110 0x55e6e0bd17b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1140:12
#111 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#112 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#113 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#114 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#115 0x55e6e0c2c90e in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:833:8
#116 0x55e6e0c62f46 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5420:15
#117 0x55e6e0c62f46 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5461:14
#118 0x55e6e0c04bea in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7151:20
#119 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#120 0x55e6e0c2c90e in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:833:8
#121 0x55e6e0c62f46 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5420:15
#122 0x55e6e0c62f46 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5461:14
#123 0x55e6e0c04bea in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7151:20
#124 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#125 0x55e6e0c2c90e in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:833:8
#126 0x55e6e0c62f46 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5420:15
#127 0x55e6e0c62f46 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5461:14
#128 0x55e6e0c04bea in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7151:20
#129 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#130 0x55e6e0c2c90e in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:833:8
#131 0x55e6e0c62f46 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5420:15
#132 0x55e6e0c62f46 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5461:14
#133 0x55e6e0c04bea in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7151:20
#134 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#135 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#136 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#137 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#138 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#139 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#140 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#141 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#142 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#143 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#144 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#145 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#146 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#147 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#148 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#149 0x55e6e0bf29c3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7367:12
#150 0x55e6e0bd0ec5 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1013:8
#151 0x55e6e0c32ddd in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#152 0x55e6e0c2f386 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2113:16
#153 0x55e6e0bd17b1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1140:12
#154 0x55e6e0d10945 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:262:2
#155 0x55e6e0d14170 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11
#156 0x55e6e0d13f66 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1200:5
#157 0x55e6e0d142b2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1207:5
#158 0x55e6e083672c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5
#159 0x7f537582950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
#160 0x7f53758295c8 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
#161 0x55e6e075d314 in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x310314)
0x6230000d0de0 is located 2272 bytes inside of 6000-byte region [0x6230000d0500,0x6230000d1c70)
allocated by thread T0 here:
#0 0x55e6e083410d in operator new(unsigned long) /data/gannet/ripley/Sources2/LLVM/16.0/llvm-project/compiler-rt/lib/asan/asan_new_delete.cpp:95:3
#1 0x7f5361515f74 in void* std::__1::__libcpp_operator_new[abi:v160000]<unsigned long>(unsigned long) /usr/local/clang16/bin/../include/c++/v1/new:266:10
#2 0x7f5361515f74 in std::__1::__libcpp_allocate[abi:v160000](unsigned long, unsigned long) /usr/local/clang16/bin/../include/c++/v1/new:292:10
#3 0x7f5361515f74 in std::__1::allocator<HD::PathState>::allocate[abi:v160000](unsigned long) /usr/local/clang16/bin/../include/c++/v1/__memory/allocator.h:115:38
#4 0x7f5361515f74 in std::__1::__allocation_result<std::__1::allocator_traits<std::__1::allocator<HD::PathState> >::pointer> std::__1::__allocate_at_least[abi:v160000]<std::__1::allocator<HD::PathState> >(std::__1::allocator<HD::PathState>&, unsigned long) /usr/local/clang16/bin/../include/c++/v1/__memory/allocate_at_least.h:55:19
#5 0x7f5361515f74 in std::__1::__split_buffer<HD::PathState, std::__1::allocator<HD::PathState>&>::__split_buffer(unsigned long, unsigned long, std::__1::allocator<HD::PathState>&) /usr/local/clang16/bin/../include/c++/v1/__split_buffer:323:29
#6 0x7f5361514bc5 in std::__1::vector<HD::PathState, std::__1::allocator<HD::PathState> >::reserve(unsigned long) /usr/local/clang16/bin/../include/c++/v1/vector:1503:53
#7 0x7f536150fab8 in HD::Path::Path(int) /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Path.cpp:45:11
#8 0x7f53614c3c41 in HD::Lars::Lars(STK::CArray<double, 2147483647, 2147483647, true> const&, STK::CArrayVector<double, 2147483647, true> const&, int, bool, double) /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Lars.cpp:83:13
#9 0x7f536154af83 in .omp_outlined._debug__ /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Cvlars.cpp:298:17
#10 0x7f536154af83 in .omp_outlined. /data/gannet/ripley/R/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/Cvlars.cpp:263:4
#11 0x7f536468b0e2 in __kmp_invoke_microtask (/usr/local/clang/lib64/libomp.so+0xb80e2) (BuildId: 8eba3d0f3145b19407156ac55f322da7c26ffb38)
#12 0x7f53646140e7 in __kmp_invoke_task_func (/usr/local/clang/lib64/libomp.so+0x410e7) (BuildId: 8eba3d0f3145b19407156ac55f322da7c26ffb38)
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/packages/tests-clang-SAN/HDPenReg/src/HDPenReg/lars/../lars/PathState.h:72:53 in HD::PathState::l1norm() const
Shadow bytes around the buggy address:
0x6230000d0b00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x6230000d0b80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x6230000d0c00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x6230000d0c80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x6230000d0d00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
=>0x6230000d0d80: 00 00 00 00 00 00 00 00 fc fc fc fc[fc]fc fc fc
0x6230000d0e00: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc
0x6230000d0e80: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc
0x6230000d0f00: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc
0x6230000d0f80: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc
0x6230000d1000: 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
==3548796==ABORTING
* DONE
Status: 2 ERRORs
Check Details
Version: 0.94.7
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
lars/Lars.cpp:160:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang
Version: 0.94.7
Check: installed package size
Result: NOTE
installed size is 13.9Mb
sub-directories of 1Mb or more:
libs 13.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.94.7
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
EMmain.cpp:49:53: warning: ‘’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
EMmain.cpp:179:53: warning: ‘’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
EMCVmain.cpp:47:53: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
Flavor: r-devel-linux-x86_64-fedora-gcc
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