* using log directory ‘/data/gannet/ripley/R/packages/tests-clang-ASAN/SlaPMEG.Rcheck’ * using R Under development (unstable) (2025-01-09 r87552) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 19.1.6 flang-new version 19.1.6 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘SlaPMEG/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SlaPMEG’ version ‘1.0.2’ * 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 ‘SlaPMEG’ can be installed ... [132s/163s] OK * checking package directory ... OK * checking whether the package can be loaded ... [39s/47s] OK * checking whether the package can be loaded with stated dependencies ... [42s/54s] OK * checking whether the package can be unloaded cleanly ... [39s/44s] OK * checking whether the namespace can be loaded with stated dependencies ... [41s/44s] OK * checking whether the namespace can be unloaded cleanly ... [42s/45s] OK * checking loading without being on the library search path ... [43s/47s] OK * checking examples ... [48s/55s] ERROR Running examples in ‘SlaPMEG-Ex.R’ failed The error most likely occurred in: > ### Name: pairslapmeg > ### Title: Testing pathways using SLaPMEG (shared latent process mixed > ### effects model and Globaltest) for longitudinal Omics data based on > ### pairwise estimation approach (a computational solution for latrge > ### pathways) > ### Aliases: pairslapmeg > > ### ** Examples > > > > # simulate data with 15 omics > testdata<-simslapmeg(nY=25, ntime=3, nsubj = 30, seed=123) > head(testdata) ID time group Y1 Y2 Y3 Y4 Y5 Y6 1 1 1 0 2.977698 2.509604 5.291550 8.848022 1.557810 5.985848 2 1 2 0 6.064517 4.750857 8.207306 6.434223 8.083080 5.091904 3 1 3 0 9.051023 5.401653 10.589329 11.187737 11.795346 6.112518 4 2 1 1 3.424484 6.150878 9.158543 8.301348 6.023678 3.368641 5 2 2 1 8.885819 10.877560 11.648935 11.409409 7.657008 7.742970 6 2 3 1 14.035576 13.658098 18.288682 16.535436 13.427194 14.926327 Y7 Y8 Y9 Y10 Y11 Y12 Y13 1 2.404243 9.047661 1.739978 6.338122 4.819147 5.352517 4.910611 2 7.859247 9.306517 4.454465 8.561131 8.102554 6.557261 5.259962 3 7.937847 13.130536 6.955808 10.070836 10.701122 8.643793 7.950818 4 3.987205 4.044989 4.826116 2.794645 6.935294 3.739476 5.186586 5 9.435294 8.211624 9.111832 5.272689 5.722398 6.704656 12.640938 6 13.596401 13.929860 13.262494 13.749133 10.311474 12.029277 15.255177 Y14 Y15 Y16 Y17 Y18 Y19 Y20 1 5.961024 5.605164 6.769332 5.124660 2.584225 4.698821 1.883005 2 3.579911 5.482432 6.421360 7.689649 6.843658 5.360052 6.006416 3 9.198733 8.551225 8.354538 10.798769 7.778663 8.516744 5.659267 4 3.277386 3.440615 4.863408 3.412033 5.057267 4.455025 5.441549 5 6.186292 8.082832 9.097246 7.103231 9.040060 13.927091 8.279761 6 10.696039 12.101611 13.296919 11.685124 8.602294 16.633904 14.183550 Y21 Y22 Y23 Y24 Y25 1 1.643846 5.319555 6.311868 4.010848 3.617374 2 3.925207 6.092139 7.937606 9.426779 5.502391 3 6.091471 7.436385 9.579301 6.586056 8.316584 4 4.999083 1.834089 3.303630 7.418006 5.502022 5 8.521774 7.490923 8.592331 9.338018 6.428974 6 16.552743 13.576288 9.661444 19.282093 14.977833 > > #fit slapmeg to test for the differential expression of a pathway of size 15 > slapmegfit<- pairslapmeg(Y1+Y2+Y6+Y7+Y8~time, ~1, grouping="group", subject="ID", data=testdata) ================================================================= ==3063806==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x525023e78818 at pc 0x55e2ba586d05 bp 0x7ffd1d03c200 sp 0x7ffd1d03b9b8 READ of size 16 at 0x525023e78818 thread T0 #0 0x55e2ba586d04 in memmove /data/gannet/ripley/Sources/LLVM/19/latest/compiler-rt/lib/asan/../sanitizer_common/sanitizer_common_interceptors_memintrinsics.inc:98:3 #1 0x7fcee8ec79db in Fortran::runtime::Assign(Fortran::runtime::Descriptor&, Fortran::runtime::Descriptor const&, Fortran::runtime::Terminator&, int) assign.cpp #2 0x7fcee8ec824b in _FortranAAssign (/data/gannet/ripley/R/clang-ASAN/lib/libRblas.so+0x9c24b) #3 0x7fcecad130d6 in loglikmultlcmm_ (/data/gannet/ripley/R/test-clang/lcmm/libs/lcmm.so+0x1130d6) #4 0x55e2ba75aeb8 in do_dotCode /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c #5 0x55e2ba7f4b4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122:14 #6 0x55e2ba7e6f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #7 0x55e2ba7e546a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #8 0x55e2ba82ef3c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #9 0x55e2ba82e101 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #10 0x55e2ba837f14 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #11 0x55e2ba837f14 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2460:8 #12 0x55e2ba8c2537 in do_mapply /data/gannet/ripley/R/svn/R-devel/src/main/mapply.c:113:13 #13 0x55e2ba7f4b4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122:14 #14 0x55e2ba7e6f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #15 0x55e2ba7e546a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #16 0x55e2ba82ef3c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #17 0x55e2ba82e101 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #18 0x55e2ba7e5eb9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #19 0x55e2ba7e5eb9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #20 0x55e2ba8409d0 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3571:8 #21 0x55e2ba7e59b3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #22 0x55e2ba8bc66a in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265:2 #23 0x55e2ba8beda0 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #24 0x55e2ba8beda0 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1219:5 #25 0x55e2ba8bee32 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1226:5 #26 0x55e2ba5cb12c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #27 0x7fcee822950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #28 0x7fcee82295c8 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #29 0x55e2ba4eb404 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x157404) 0x525023e78818 is located 0 bytes after 7960-byte region [0x525023e76900,0x525023e78818) allocated by thread T0 here: #0 0x55e2ba58820f in malloc /data/gannet/ripley/Sources/LLVM/19/latest/compiler-rt/lib/asan/asan_malloc_linux.cpp:68:3 #1 0x55e2ba8e1c67 in GetNewPage /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:998:12 #2 0x55e2ba8c6f5f in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2713:6 #3 0x55e2ba7b0842 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:607:12 #4 0x55e2ba7b0842 in do_missing /data/gannet/ripley/R/svn/R-devel/src/main/envir.c:2460:17 #5 0x55e2ba7fa636 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142:15 #6 0x55e2ba7e6f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #7 0x55e2ba7e546a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #8 0x55e2ba7e7811 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #9 0x55e2ba7e541e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193:2 #10 0x55e2ba7f4b4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122:14 #11 0x55e2ba7e6f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #12 0x55e2ba7e546a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #13 0x55e2ba82ef3c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #14 0x55e2ba82e101 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #15 0x55e2ba7e8e28 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #16 0x55e2ba8f8b87 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #17 0x55e2ba8f7618 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:509:10 #18 0x55e2ba8f9df3 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #19 0x55e2ba7fa636 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142:15 #20 0x55e2ba7e6f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #21 0x55e2ba7e546a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #22 0x55e2ba82ef3c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #23 0x55e2ba82e101 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #24 0x55e2ba7e8e28 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #25 0x55e2ba8f8b87 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #26 0x55e2ba8f7618 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:509:10 #27 0x55e2ba8f9df3 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #28 0x55e2ba7fa636 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142:15 #29 0x55e2ba7e6f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #30 0x55e2ba7e546a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 SUMMARY: AddressSanitizer: heap-buffer-overflow assign.cpp in Fortran::runtime::Assign(Fortran::runtime::Descriptor&, Fortran::runtime::Descriptor const&, Fortran::runtime::Terminator&, int) Shadow bytes around the buggy address: 0x525023e78580: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x525023e78600: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x525023e78680: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x525023e78700: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x525023e78780: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x525023e78800: 00 00 00[fa]fa fa fa fa fa fa fa fa fa fa fa fa 0x525023e78880: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x525023e78900: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x525023e78980: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x525023e78a00: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x525023e78a80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 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 ==3063806==ABORTING * DONE Status: 1 ERROR