* using log directory ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/SuperLearner.Rcheck’ * using R Under development (unstable) (2025-12-12 r89163) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2) GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘SuperLearner/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SuperLearner’ version ‘2.0-29’ * 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 ‘SuperLearner’ can be installed ... [41s/42s] OK * checking package directory ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [60s/61s] OK * checking tests ... [18s/19s] ERROR Running ‘testthat.R’ [17s/17s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(SuperLearner) Loading required package: nnls Loading required package: gam Loading required package: splines Loading required package: foreach Loaded gam 1.22-7 Super Learner Version: 2.0-29 Package created on 2024-02-06 > > test_check("SuperLearner") ================================================================= ==260915==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x7e227010f018 at pc 0x7bd257619c8d bp 0x7ffdd11a2e30 sp 0x7ffdd11a2e28 READ of size 8 at 0x7e227010f018 thread T0 #0 0x7bd257619c8c in regRF /tmp/RtmpMafIQX/R.INSTALLead384000b385/randomForest/src/regrf.c:115 #1 0x0000007678ce in do_dotCode /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:2256 #2 0x0000008cc332 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #3 0x0000008b957b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #4 0x0000008598f2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #5 0x00000086f63a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #6 0x0000008736fa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #7 0x000000a94683 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #8 0x000000a94683 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #9 0x000000a98480 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #10 0x000000a9a405 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513 #11 0x000000a9b026 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #12 0x0000008d9541 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #13 0x0000008b957b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #14 0x0000008598f2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #15 0x00000086f63a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #16 0x0000008736fa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #17 0x000000859f93 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #18 0x000000859f93 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #19 0x0000006262c5 in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2789 #20 0x0000008cc332 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #21 0x0000008b957b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #22 0x0000008598f2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x00000086f63a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #24 0x0000008736fa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #25 0x000000875017 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #26 0x000000875017 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2456 #27 0x00000049a176 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75 #28 0x000000a93476 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #29 0x0000008d9541 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #30 0x0000008b957b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #31 0x0000008598f2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x00000086f63a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #33 0x0000008736fa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #34 0x000000859f93 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #35 0x000000859f93 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #36 0x00000088838e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563 #37 0x00000085a3b6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #38 0x00000086de3b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992 #39 0x00000085a3b6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #40 0x00000085a3b6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #41 0x000000890a23 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #42 0x0000008cc332 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #43 0x0000008b957b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #44 0x0000008598f2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #45 0x00000086f63a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #46 0x0000008736fa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #47 0x000000875017 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #48 0x000000875017 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2456 #49 0x00000049a176 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75 #50 0x000000a93476 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #51 0x0000008d9541 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #52 0x0000008b957b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #53 0x0000008598f2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #54 0x00000086f63a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #55 0x0000008736fa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #56 0x000000859f93 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #57 0x000000859f93 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #58 0x0000009fff08 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #59 0x0000009fff08 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #60 0x000000a0533a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #61 0x000000a0f552 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #62 0x0000004131af in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #63 0x7fd26c4115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #64 0x7fd26c4116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #65 0x000000413b74 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b74) (BuildId: 162da4155cf0b7e57a4e8bd0b5eda527e8633566) 0x7e227010f018 is located 0 bytes after 7960-byte region [0x7e227010d100,0x7e227010f018) allocated by thread T0 here: #0 0x7fd26dce6f0b in malloc (/lib64/libasan.so.8+0xe6f0b) (BuildId: 7f1aa7e2e600e8c9d54ce6e3d36f3d31bfe7949a) #1 0x000000a197cb in GetNewPage /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:998 #2 0x000000a6e901 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2717 #3 0x00000060af60 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609 #4 0x00000060af60 in do_is /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2033 #5 0x0000008cc332 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #6 0x0000008b957b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #7 0x0000008598f2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #8 0x000000920c11 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #9 0x00000085ae27 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #10 0x0000008f0bd7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8008 #11 0x0000008b957b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #12 0x0000008598f2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #13 0x00000086f63a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #14 0x0000008736fa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #15 0x000000875017 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #16 0x000000875017 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2456 #17 0x00000049a176 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75 #18 0x000000a93476 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #19 0x0000008d9541 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #20 0x0000008b957b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #21 0x0000008598f2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #22 0x00000086f63a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #23 0x0000008736fa in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #24 0x000000859f93 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #25 0x000000859f93 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #26 0x000000889a24 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3661 #27 0x00000085a77c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1251 #28 0x00000086cd62 in do_if /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2700 #29 0x00000085a3b6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #30 0x000000890a23 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #31 0x0000008cc332 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #32 0x0000008b957b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 SUMMARY: AddressSanitizer: heap-buffer-overflow /tmp/RtmpMafIQX/R.INSTALLead384000b385/randomForest/src/regrf.c:115 in regRF Shadow bytes around the buggy address: 0x7e227010ed80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7e227010ee00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7e227010ee80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7e227010ef00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7e227010ef80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x7e227010f000: 00 00 00[fa]fa fa fa fa fa fa fa fa fa fa fa fa 0x7e227010f080: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e227010f100: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e227010f180: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e227010f200: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7e227010f280: 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 ==260915==ABORTING * checking package vignettes ... OK * checking re-building of vignette outputs ... [10m/11m] ERROR Error(s) in re-building vignettes: --- re-building ‘Guide-to-SuperLearner.Rmd’ using rmarkdown Boston package:MASS R Documentation _H_o_u_s_i_n_g _V_a_l_u_e_s _i_n _S_u_b_u_r_b_s _o_f _B_o_s_t_o_n _D_e_s_c_r_i_p_t_i_o_n: The 'Boston' data frame has 506 rows and 14 columns. _U_s_a_g_e: Boston _F_o_r_m_a_t: This data frame contains the following columns: 'crim' per capita crime rate by town. 'zn' proportion of residential land zoned for lots over 25,000 sq.ft. 'indus' proportion of non-retail business acres per town. 'chas' Charles River dummy variable (= 1 if tract bounds river; 0 otherwise). 'nox' nitrogen oxides concentration (parts per 10 million). 'rm' average number of rooms per dwelling. 'age' proportion of owner-occupied units built prior to 1940. 'dis' weighted mean of distances to five Boston employment centres. 'rad' index of accessibility to radial highways. 'tax' full-value property-tax rate per $10,000. 'ptratio' pupil-teacher ratio by town. 'black' 1000(Bk - 0.63)^2 where Bk is the proportion of blacks by town. 'lstat' lower status of the population (percent). 'medv' median value of owner-occupied homes in $1000s. _S_o_u_r_c_e: Harrison, D. and Rubinfeld, D.L. (1978) Hedonic prices and the demand for clean air. _J. Environ. Economics and Management_ *5*, 81-102. Belsley D.A., Kuh, E. and Welsch, R.E. (1980) _Regression Diagnostics. Identifying Influential Data and Sources of Collinearity._ New York: Wiley. ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/SuperLearner.Rcheck/vign_test/SuperLearner/vignettes/Guide-to-SuperLearner_files/figure-html/predict-1.png 672x480 pixels, 8 bits/pixel, 221 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 5131 bytes Input file size = 5884 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3777 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3776 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 3672 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 3616 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 3616 Output IDAT size = 3616 bytes (1515 bytes decrease) Output file size = 3694 bytes (2190 bytes = 37.22% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/SuperLearner.Rcheck/vign_test/SuperLearner/vignettes/Guide-to-SuperLearner_files/figure-html/predict-2.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 9495 bytes Input file size = 10365 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7852 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7799 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7799 Output IDAT size = 7799 bytes (1696 bytes decrease) Output file size = 7877 bytes (2488 bytes = 24.00% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/SuperLearner.Rcheck/vign_test/SuperLearner/vignettes/Guide-to-SuperLearner_files/figure-html/cv-sl-1.png 480x480 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 6681 bytes Input file size = 7536 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5663 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5663 Output IDAT size = 5663 bytes (1018 bytes decrease) Output file size = 5741 bytes (1795 bytes = 23.82% decrease) Quitting from Guide-to-SuperLearner.Rmd:557-590 [xgboost] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `FUN()`: ! subscript out of bounds --- Backtrace: ▆ 1. ├─base::system.time(...) 2. └─SuperLearner::CV.SuperLearner(...) 3. └─base::lapply(cvList, "[[", "cvAllSL") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Guide-to-SuperLearner.Rmd' failed with diagnostics: subscript out of bounds --- failed re-building ‘Guide-to-SuperLearner.Rmd’ SUMMARY: processing the following file failed: ‘Guide-to-SuperLearner.Rmd’ Error: Vignette re-building failed. Execution halted * DONE Status: 2 ERRORs