--- re-building ‘reproducible-vignette.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/SNPfiltR.Rcheck/vign_test/SNPfiltR/vignettes/reproducible-vignette_files/figure-html/unnamed-chunk-4-1.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 13277 bytes Input file size = 13367 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10812 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 = 10812 Output IDAT size = 10812 bytes (2465 bytes decrease) Output file size = 10890 bytes (2477 bytes = 18.53% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/SNPfiltR.Rcheck/vign_test/SNPfiltR/vignettes/reproducible-vignette_files/figure-html/unnamed-chunk-5-1.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 12893 bytes Input file size = 12983 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10134 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 = 10134 Output IDAT size = 10134 bytes (2759 bytes decrease) Output file size = 10212 bytes (2771 bytes = 21.34% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/SNPfiltR.Rcheck/vign_test/SNPfiltR/vignettes/reproducible-vignette_files/figure-html/unnamed-chunk-6-1.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22414 bytes Input file size = 22516 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17792 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 = 17792 Output IDAT size = 17792 bytes (4622 bytes decrease) Output file size = 17870 bytes (4646 bytes = 20.63% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/SNPfiltR.Rcheck/vign_test/SNPfiltR/vignettes/reproducible-vignette_files/figure-html/unnamed-chunk-6-2.png 384x288 pixels, 8 bits/pixel, 250 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8137 bytes Input file size = 8977 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7717 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 = 7717 Output IDAT size = 7717 bytes (420 bytes decrease) Output file size = 7795 bytes (1182 bytes = 13.17% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/SNPfiltR.Rcheck/vign_test/SNPfiltR/vignettes/reproducible-vignette_files/figure-html/unnamed-chunk-6-3.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19076 bytes Input file size = 19178 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14792 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 = 14792 Output IDAT size = 14792 bytes (4284 bytes decrease) Output file size = 14870 bytes (4308 bytes = 22.46% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/SNPfiltR.Rcheck/vign_test/SNPfiltR/vignettes/reproducible-vignette_files/figure-html/unnamed-chunk-6-4.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 9056 bytes Input file size = 9146 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7102 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 = 7102 Output IDAT size = 7102 bytes (1954 bytes decrease) Output file size = 7180 bytes (1966 bytes = 21.50% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/SNPfiltR.Rcheck/vign_test/SNPfiltR/vignettes/reproducible-vignette_files/figure-html/unnamed-chunk-7-1.png 384x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 43628 bytes Input file size = 43766 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36765 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 = 36765 Output IDAT size = 36765 bytes (6863 bytes decrease) Output file size = 36843 bytes (6923 bytes = 15.82% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang-ASAN/SNPfiltR.Rcheck/vign_test/SNPfiltR/vignettes/reproducible-vignette_files/figure-html/unnamed-chunk-7-2.png 384x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 10471 bytes Input file size = 11341 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9824 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 = 9824 Output IDAT size = 9824 bytes (647 bytes decrease) Output file size = 9902 bytes (1439 bytes = 12.69% decrease) ================================================================= ==3055591==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x5160005cd8b0 at pc 0x7f873b607fe0 bp 0x7ffe7dae7930 sp 0x7ffe7dae7928 READ of size 16 at 0x5160005cd8b0 thread T0 #0 0x7f873b607fdf in bytesToDouble /tmp/RtmpNNPUz9/R.INSTALL3cef1f2b1bd39c/adegenet/src/snpbin.c:225:19 #1 0x7f873b609ca5 in snpbin2freq /tmp/RtmpNNPUz9/R.INSTALL3cef1f2b1bd39c/adegenet/src/snpbin.c:332:5 #2 0x7f873b609ca5 in snpbin_dotprod_freq /tmp/RtmpNNPUz9/R.INSTALL3cef1f2b1bd39c/adegenet/src/snpbin.c:447:5 #3 0x7f873b5f6a42 in GLdotProd /tmp/RtmpNNPUz9/R.INSTALL3cef1f2b1bd39c/adegenet/src/GLfunctions.c:42:14 #4 0x564ab74af067 in do_dotCode /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c #5 0x564ab7550b4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122:14 #6 0x564ab7542f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #7 0x564ab754146a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #8 0x564ab758af3c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #9 0x564ab758a101 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #10 0x564ab7541eb9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #11 0x564ab7541eb9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #12 0x564ab75a135e in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3945:13 #13 0x564ab7550b4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122:14 #14 0x564ab7542f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #15 0x564ab754146a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #16 0x564ab7543811 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #17 0x564ab7541664 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187:6 #18 0x564ab75a2573 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3988:9 #19 0x564ab764e389 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1410:11 #20 0x564ab7556636 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142:15 #21 0x564ab7542f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #22 0x564ab754146a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #23 0x564ab7543811 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #24 0x564ab7541664 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187:6 #25 0x564ab7543811 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #26 0x564ab756ed31 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5839:6 #27 0x564ab756ed31 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7852:20 #28 0x564ab7542f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #29 0x564ab754146a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #30 0x564ab758af3c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #31 0x564ab758a101 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #32 0x564ab7541eb9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #33 0x564ab7541eb9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #34 0x564ab75a135e in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3945:13 #35 0x564ab7550b4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122:14 #36 0x564ab7542f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #37 0x564ab754146a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #38 0x564ab758af3c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #39 0x564ab758a101 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #40 0x564ab7541eb9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #41 0x564ab7541eb9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #42 0x564ab758af3c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #43 0x564ab758a101 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #44 0x564ab7566f32 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #45 0x564ab7566f32 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8093:16 #46 0x564ab7542f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #47 0x564ab754146a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #48 0x564ab758af3c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #49 0x564ab758a101 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #50 0x564ab7541eb9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #51 0x564ab7541eb9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #52 0x564ab761866a in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265:2 #53 0x564ab761ada0 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #54 0x564ab761ada0 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1219:5 #55 0x564ab761ae32 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1226:5 #56 0x564ab732712c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #57 0x7f8747c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #58 0x7f8747c295c8 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #59 0x564ab7247404 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x157404) 0x5160005cd8b0 is located 0 bytes after 560-byte region [0x5160005cd680,0x5160005cd8b0) allocated by thread T0 here: #0 0x564ab72e43d9 in calloc /data/gannet/ripley/Sources/LLVM/19/latest/compiler-rt/lib/asan/asan_malloc_linux.cpp:75:3 #1 0x7f873b609bca in snpbin_dotprod_freq /tmp/RtmpNNPUz9/R.INSTALL3cef1f2b1bd39c/adegenet/src/snpbin.c:443:23 #2 0x7f873b5f6a42 in GLdotProd /tmp/RtmpNNPUz9/R.INSTALL3cef1f2b1bd39c/adegenet/src/GLfunctions.c:42:14 #3 0x564ab74af067 in do_dotCode /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c #4 0x564ab7550b4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122:14 #5 0x564ab7542f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #6 0x564ab754146a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #7 0x564ab758af3c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #8 0x564ab758a101 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #9 0x564ab7541eb9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #10 0x564ab7541eb9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #11 0x564ab75a135e in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3945:13 #12 0x564ab7550b4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122:14 #13 0x564ab7542f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #14 0x564ab754146a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #15 0x564ab7543811 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #16 0x564ab7541664 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187:6 #17 0x564ab75a2573 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3988:9 #18 0x564ab764e389 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1410:11 #19 0x564ab7556636 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142:15 #20 0x564ab7542f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #21 0x564ab754146a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #22 0x564ab7543811 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #23 0x564ab7541664 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187:6 #24 0x564ab7543811 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #25 0x564ab756ed31 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5839:6 #26 0x564ab756ed31 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7852:20 #27 0x564ab7542f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #28 0x564ab754146a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #29 0x564ab758af3c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #30 0x564ab758a101 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #31 0x564ab7541eb9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #32 0x564ab7541eb9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 SUMMARY: AddressSanitizer: heap-buffer-overflow /tmp/RtmpNNPUz9/R.INSTALL3cef1f2b1bd39c/adegenet/src/snpbin.c:225:19 in bytesToDouble Shadow bytes around the buggy address: 0x5160005cd600: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x5160005cd680: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x5160005cd700: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x5160005cd780: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x5160005cd800: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x5160005cd880: 00 00 00 00 00 00[fa]fa fa fa fa fa fa fa fa fa 0x5160005cd900: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x5160005cd980: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x5160005cda00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x5160005cda80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x5160005cdb00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 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 ==3055591==ABORTING