* using log directory ‘/data/gannet/ripley/R/packages/tests-clang-ASAN/SuperLearner.Rcheck’ * using R Under development (unstable) (2025-12-12 r89163) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 21.1.7 flang version 21.1.7 * 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 ... [32s/32s] 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 ... [46s/47s] OK * checking tests ... [14s/15s] ERROR Running ‘testthat.R’ [13s/13s] 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") ================================================================= ==333321==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x7dc21ab39818 at pc 0x7b7201b5ae29 bp 0x7fff92dfeaf0 sp 0x7fff92dfeae8 READ of size 8 at 0x7dc21ab39818 thread T0 #0 0x7b7201b5ae28 in regRF /tmp/RtmpBu21DK/R.INSTALL279b017543e8b6/randomForest/src/regrf.c:115:21 #1 0x55dc4c659cb2 in do_dotCode /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c #2 0x55dc4c6feb89 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114:14 #3 0x55dc4c6f1844 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #4 0x55dc4c6efd6a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #5 0x55dc4c737cfc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #6 0x55dc4c736ec1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #7 0x55dc4c6f36f8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #8 0x55dc4c801b74 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #9 0x55dc4c800684 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513:10 #10 0x55dc4c802dd3 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #11 0x55dc4c704383 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134:15 #12 0x55dc4c6f1844 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #13 0x55dc4c6efd6a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #14 0x55dc4c737cfc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #15 0x55dc4c736ec1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #16 0x55dc4c6f07b9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #17 0x55dc4c6f07b9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #18 0x55dc4c5ac57c in do_docall /data/gannet/ripley/R/svn/R-devel/src/main/coerce.c:2789:12 #19 0x55dc4c6feb89 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114:14 #20 0x55dc4c6f1844 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #21 0x55dc4c6efd6a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #22 0x55dc4c737cfc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #23 0x55dc4c736ec1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #24 0x55dc4c740994 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #25 0x55dc4c740994 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2456:8 #26 0x55dc4c500e01 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75:8 #27 0x55dc4c7fb189 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411:11 #28 0x55dc4c704383 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134:15 #29 0x55dc4c6f1844 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #30 0x55dc4c6efd6a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #31 0x55dc4c737cfc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #32 0x55dc4c736ec1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #33 0x55dc4c6f07b9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #34 0x55dc4c6f07b9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #35 0x55dc4c7493e7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563:8 #36 0x55dc4c6f02b3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #37 0x55dc4c746569 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992:10 #38 0x55dc4c6f02b3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #39 0x55dc4c6f02b3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #40 0x55dc4c74e65a in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955:9 #41 0x55dc4c6feb89 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114:14 #42 0x55dc4c6f1844 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #43 0x55dc4c6efd6a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #44 0x55dc4c737cfc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #45 0x55dc4c736ec1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #46 0x55dc4c740994 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #47 0x55dc4c740994 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2456:8 #48 0x55dc4c500e01 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75:8 #49 0x55dc4c7fb189 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411:11 #50 0x55dc4c704383 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134:15 #51 0x55dc4c6f1844 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #52 0x55dc4c6efd6a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #53 0x55dc4c737cfc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #54 0x55dc4c736ec1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #55 0x55dc4c6f07b9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #56 0x55dc4c6f07b9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #57 0x55dc4c7c4681 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:15 #58 0x55dc4c7c6ed0 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #59 0x55dc4c7c6ed0 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #60 0x55dc4c7c6f62 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #61 0x55dc4c4ce13c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #62 0x7f7216e115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #63 0x7f7216e116a7 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #64 0x55dc4c3e67e4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17e4) 0x7dc21ab39818 is located 0 bytes after 7960-byte region [0x7dc21ab37900,0x7dc21ab39818) allocated by thread T0 here: #0 0x55dc4c48b104 in malloc /data/gannet/ripley/Sources2/LLVM/21/latest/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x55dc4c7e9bf7 in GetNewPage /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:998:12 #2 0x55dc4c7cf04f in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2717:6 #3 0x55dc4c70a366 in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:609:12 #4 0x55dc4c70a366 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7678:14 #5 0x55dc4c6f1844 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #6 0x55dc4c6efd6a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #7 0x55dc4c6f2101 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #8 0x55dc4c6efd1e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193:2 #9 0x55dc4c7048d2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8008:16 #10 0x55dc4c6f1844 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #11 0x55dc4c6efd6a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #12 0x55dc4c737cfc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #13 0x55dc4c736ec1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #14 0x55dc4c740994 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #15 0x55dc4c740994 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2456:8 #16 0x55dc4c500e01 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75:8 #17 0x55dc4c7fb189 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411:11 #18 0x55dc4c704383 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134:15 #19 0x55dc4c6f1844 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #20 0x55dc4c6efd6a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #21 0x55dc4c737cfc in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:22 #22 0x55dc4c736ec1 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #23 0x55dc4c6f07b9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #24 0x55dc4c6f07b9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #25 0x55dc4c6f24a2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3661:12 #26 0x55dc4c6f044e in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1251:6 #27 0x55dc4c741c0b in do_if /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2700:5 #28 0x55dc4c6f02b3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #29 0x55dc4c74e65a in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955:9 #30 0x55dc4c6feb89 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114:14 #31 0x55dc4c6f1844 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497:16 #32 0x55dc4c6efd6a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 SUMMARY: AddressSanitizer: heap-buffer-overflow /tmp/RtmpBu21DK/R.INSTALL279b017543e8b6/randomForest/src/regrf.c:115:21 in regRF Shadow bytes around the buggy address: 0x7dc21ab39580: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7dc21ab39600: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7dc21ab39680: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7dc21ab39700: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7dc21ab39780: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x7dc21ab39800: 00 00 00[fa]fa fa fa fa fa fa fa fa fa fa fa fa 0x7dc21ab39880: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7dc21ab39900: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7dc21ab39980: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7dc21ab39a00: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7dc21ab39a80: 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 ==333321==ABORTING * checking package vignettes ... OK * checking re-building of vignette outputs ... [10m/10m] 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-clang-ASAN/SuperLearner.Rcheck/vign_test/SuperLearner/vignettes/Guide-to-SuperLearner_files/figure-html/predict-1.png 672x480 pixels, 8 bits/pixel, 225 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 5892 bytes Input file size = 6657 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4556 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 4527 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 = 4527 Output IDAT size = 4527 bytes (1365 bytes decrease) Output file size = 4605 bytes (2052 bytes = 30.82% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/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 = 9695 bytes Input file size = 10565 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8022 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7964 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 = 7964 Output IDAT size = 7964 bytes (1731 bytes decrease) Output file size = 8042 bytes (2523 bytes = 23.88% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/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 = 7076 bytes Input file size = 7931 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6047 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 = 6047 Output IDAT size = 6047 bytes (1029 bytes decrease) Output file size = 6125 bytes (1806 bytes = 22.77% 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