* using log directory ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/STGS.Rcheck’ * using R Under development (unstable) (2025-01-08 r87545) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘STGS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘STGS’ version ‘0.1.0’ * 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 ‘STGS’ can be installed ... [60s/67s] OK * checking package directory ... OK * checking whether the package can be loaded ... [18s/19s] OK * checking whether the package can be loaded with stated dependencies ... [18s/19s] OK * checking whether the package can be unloaded cleanly ... [18s/20s] OK * checking whether the namespace can be loaded with stated dependencies ... [18s/19s] OK * checking whether the namespace can be unloaded cleanly ... [18s/19s] OK * checking loading without being on the library search path ... [18s/19s] OK * checking examples ... [87s/95s] ERROR Running examples in ‘STGS-Ex.R’ failed The error most likely occurred in: > ### Name: STGS.rf > ### Title: Genomic Selection using Random Forest > ### Aliases: STGS.rf > > ### ** Examples > > > library(STGS) > > data(wheat_data) > > X<-wheat_data[,1:100] > > Y<-as.data.frame(wheat_data[,101]) > > r<-0.25 > > STGS.rf(X,Y,r) ================================================================= ==2119275==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x52500c354818 at pc 0x7f6d00d3fc50 bp 0x7fff0fa7ae20 sp 0x7fff0fa7ae18 READ of size 8 at 0x52500c354818 thread T0 #0 0x7f6d00d3fc4f in regRF /tmp/RtmpRJlmoa/R.INSTALL3c5b986f246cea/randomForest/src/regrf.c:115 #1 0x74f7c4 in do_dotCode /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:2256 #2 0x8a2ae3 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #3 0x873caf in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #4 0x83aa12 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #5 0x8459e2 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #6 0x83938a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #7 0xa4f09b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #8 0xa4f09b in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #9 0xa53257 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #10 0xf493b0 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:523 #11 0xa54ec6 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #12 0x8afb5d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142 #13 0x873caf in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #14 0x83aa12 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #15 0x8459e2 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #16 0x83938a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #17 0x83b096 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #18 0x83b096 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #19 0x9c4e19 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #20 0x9c4e19 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #21 0x9c631b in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1219 #22 0x9d0892 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1226 #23 0x4290cf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #24 0x7f6d17c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #25 0x7f6d17c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #26 0x429ab4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x429ab4) (BuildId: b25c18b29da9020de134f39d59f7dee05849d9e9) 0x52500c354818 is located 0 bytes after 7960-byte region [0x52500c352900,0x52500c354818) allocated by thread T0 here: #0 0x7f6d194f7997 in malloc ../../../../latest/libsanitizer/asan/asan_malloc_linux.cpp:69 #1 0x9e0e5c in GetNewPage /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:998 #2 0xa2da7e in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2868 #3 0xc17d1e in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:607 #4 0xc17d1e in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2036 #5 0xc150ba in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #6 0xc150ba in ReadItem_Iterative /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1837 #7 0xc150ba in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1963 #8 0xc150ba in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #9 0xc150ba in ReadItem_Iterative /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1837 #10 0xc150ba in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1963 #11 0xc150ba in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #12 0xc150ba in ReadItem_Iterative /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1837 #13 0xc150ba in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1963 #14 0xc150ba in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #15 0xc150ba in ReadItem_Iterative /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1837 #16 0xc150ba in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1963 #17 0xc150ba in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #18 0xc150ba in ReadItem_Iterative /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1837 #19 0xc150ba in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1963 #20 0xc150ba in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #21 0xc150ba in ReadItem_Iterative /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1837 #22 0xc150ba in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1963 #23 0xc150ba in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #24 0xc150ba in ReadItem_Iterative /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1837 #25 0xc150ba in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1963 #26 0xc150ba in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #27 0xc150ba in ReadItem_Iterative /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1837 #28 0xc150ba in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1963 #29 0xc150ba in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #30 0xc150ba in ReadItem_Iterative /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1837 #31 0xc150ba in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1963 #32 0xc1fef0 in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #33 0xc1fef0 in ReadBCConsts /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2197 #34 0xc1fef0 in ReadBC1 /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2214 #35 0xc18262 in ReadBC /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2225 #36 0xc18262 in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2056 #37 0xc163fb in ReadItem_Iterative /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1863 #38 0xc163fb in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1963 #39 0xc16b68 in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #40 0xc16b68 in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2051 #41 0xc16b68 in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #42 0xc16b68 in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2051 #43 0xc20653 in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #44 0xc20653 in R_Unserialize /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2277 #45 0xc2f121 in R_unserialize /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:3005 #46 0xc31a37 in do_lazyLoadDBfetch /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:3317 #47 0x8a2ae3 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #48 0x873caf in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #49 0x83aa12 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #50 0x8459e2 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #51 0x83938a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #52 0x83b096 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #53 0x83b096 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #54 0xc2aadd in CallHook /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2578 #55 0xc14f7b in PersistentRestore /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:826 #56 0xc14f7b in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:1895 #57 0xc16b68 in ReadItem /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2120 #58 0xc16b68 in ReadItem_Recursive /data/gannet/ripley/R/svn/R-devel/src/main/serialize.c:2051 SUMMARY: AddressSanitizer: heap-buffer-overflow /tmp/RtmpRJlmoa/R.INSTALL3c5b986f246cea/randomForest/src/regrf.c:115 in regRF Shadow bytes around the buggy address: 0x52500c354580: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52500c354600: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52500c354680: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52500c354700: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52500c354780: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x52500c354800: 00 00 00[fa]fa fa fa fa fa fa fa fa fa fa fa fa 0x52500c354880: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52500c354900: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52500c354980: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52500c354a00: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52500c354a80: 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 ==2119275==ABORTING * DONE Status: 1 ERROR