* using log directory ‘/home/hornik/tmp/CRAN_special_gcc-san/NMRphasing.Rcheck’ * using R Under development (unstable) (2024-12-15 r87442) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-8) 14.2.0 GNU Fortran (Debian 14.2.0-8) 14.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘NMRphasing/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NMRphasing’ version ‘1.0.6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘NMRphasing’ can be installed ... [6s/7s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [13s/13s] OK * checking Rd files ... [1s/1s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [1s/1s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [72s/72s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SPC_AAM 18.850 0.120 18.971 SPC_DSM 16.156 0.048 16.213 SPC_ADSM 15.329 0.084 15.424 SPC_EMP 14.802 0.040 14.846 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [5s/5s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘NMRphasing_vignette.rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_special_gcc-san/NMRphasing.Rcheck/vign_test/NMRphasing/vignettes/NMRphasing_vignette_files/figure-html/unnamed-chunk-4-1.png 216x216 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 5609 bytes Input file size = 6467 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4953 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 IDAT size = 4547 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 = 5 IDAT size = 4547 Output IDAT size = 4547 bytes (1062 bytes decrease) Output file size = 4625 bytes (1842 bytes = 28.48% decrease) ================================================================= ==3497999==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x52e000797c48 at pc 0x7fa686fc0a3b bp 0x7ffd6bacbb50 sp 0x7ffd6bacbb48 READ of size 8 at 0x52e000797c48 thread T0 #0 0x7fa686fc0a3a in localMaximumSlidingWindow /home/hornik/tmp/scratch/RtmpYrTn6q/R.INSTALL352e7147e44786/MassSpecWavelet/src/find_local_maximum.c:492 #1 0x7fa6ab25c16c in R_doDotCall /home/hornik/src/R/src/main/dotcode.c:757 #2 0x7fa6ab3fdc56 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8672 #3 0x7fa6ab3d67ff in bcEval /home/hornik/src/R/src/main/eval.c:7505 #4 0x7fa6ab382952 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #5 0x7fa6ab37c602 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #6 0x7fa6ab38132a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #7 0x7fa6ab383231 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #8 0x7fa6ab383231 in Rf_eval /home/hornik/src/R/src/main/eval.c:1280 #9 0x7fa6ab399ce8 in applydefine /home/hornik/src/R/src/main/eval.c:3392 #10 0x7fa6ab383873 in Rf_eval /home/hornik/src/R/src/main/eval.c:1232 #11 0x7fa6ab3aad01 in do_eval /home/hornik/src/R/src/main/eval.c:3945 #12 0x7fa6ab3e9de0 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8122 #13 0x7fa6ab3d67ff in bcEval /home/hornik/src/R/src/main/eval.c:7505 #14 0x7fa6ab382952 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #15 0x7fa6ab44857b in forcePromise.part.0.lto_priv.0 /home/hornik/src/R/src/main/eval.c:976 #16 0x7fa6ab38463e in forcePromise /home/hornik/src/R/src/main/eval.c:956 #17 0x7fa6ab38463e in Rf_eval /home/hornik/src/R/src/main/eval.c:1187 #18 0x7fa6ab3ae0d6 in do_withVisible /home/hornik/src/R/src/main/eval.c:3988 #19 0x7fa6ab59f79a in do_internal /home/hornik/src/R/src/main/names.c:1410 #20 0x7fa6ab3e95c9 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8142 #21 0x7fa6ab3d67ff in bcEval /home/hornik/src/R/src/main/eval.c:7505 #22 0x7fa6ab382952 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #23 0x7fa6ab44857b in forcePromise.part.0.lto_priv.0 /home/hornik/src/R/src/main/eval.c:976 #24 0x7fa6ab38463e in forcePromise /home/hornik/src/R/src/main/eval.c:956 #25 0x7fa6ab38463e in Rf_eval /home/hornik/src/R/src/main/eval.c:1187 #26 0x7fa6ab44857b in forcePromise.part.0.lto_priv.0 /home/hornik/src/R/src/main/eval.c:976 #27 0x7fa6ab3b8fff in forcePromise /home/hornik/src/R/src/main/eval.c:956 #28 0x7fa6ab3b8fff in getvar /home/hornik/src/R/src/main/eval.c:5839 #29 0x7fa6ab3fed18 in bcEval_loop /home/hornik/src/R/src/main/eval.c:7852 #30 0x7fa6ab3d67ff in bcEval /home/hornik/src/R/src/main/eval.c:7505 #31 0x7fa6ab382952 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #32 0x7fa6ab37c602 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #33 0x7fa6ab38132a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #34 0x7fa6ab383231 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #35 0x7fa6ab383231 in Rf_eval /home/hornik/src/R/src/main/eval.c:1280 #36 0x7fa6ab3aad01 in do_eval /home/hornik/src/R/src/main/eval.c:3945 #37 0x7fa6ab3e9de0 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8122 #38 0x7fa6ab3d67ff in bcEval /home/hornik/src/R/src/main/eval.c:7505 #39 0x7fa6ab382952 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #40 0x7fa6ab37c602 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #41 0x7fa6ab38132a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #42 0x7fa6ab383231 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #43 0x7fa6ab383231 in Rf_eval /home/hornik/src/R/src/main/eval.c:1280 #44 0x7fa6ab37c602 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #45 0x7fa6ab38132a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #46 0x7fa6ab3ea28a in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #47 0x7fa6ab3ea28a in bcEval_loop /home/hornik/src/R/src/main/eval.c:8093 #48 0x7fa6ab3d67ff in bcEval /home/hornik/src/R/src/main/eval.c:7505 #49 0x7fa6ab382952 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #50 0x7fa6ab37c602 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #51 0x7fa6ab38132a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #52 0x7fa6ab383231 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #53 0x7fa6ab383231 in Rf_eval /home/hornik/src/R/src/main/eval.c:1280 #54 0x7fa6ab51c5bc in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:265 #55 0x7fa6ab51c5bc in R_ReplConsole /home/hornik/src/R/src/main/main.c:317 #56 0x7fa6ab52bdf3 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1219 #57 0x562ab744f0c9 in main /home/hornik/src/R/src/main/Rmain.c:29 #58 0x7fa6a9833d67 in __libc_start_call_main ../sysdeps/nptl/libc_start_call_main.h:58 #59 0x7fa6a9833e24 in __libc_start_main_impl ../csu/libc-start.c:360 #60 0x562ab744f110 in _start (/home/hornik/tmp/R-d-gcc-xtra/bin/exec/R+0x1110) (BuildId: 66592a328da23f759444d5aec64b7ce5ae5a5f76) 0x52e000797c48 is located 0 bytes after 47176-byte region [0x52e00078c400,0x52e000797c48) allocated by thread T0 here: #0 0x7fa6acef4c77 in malloc ../../../../src/libsanitizer/asan/asan_malloc_linux.cpp:69 #1 0x7fa6ab584dd7 in Rf_allocVector3 /home/hornik/src/R/src/main/memory.c:2890 #2 0x7fa6ab83be1c in Rf_allocVector /home/hornik/src/R/src/include/Rinlinedfuns.h:607 #3 0x7fa6ab83be1c in MatrixSubset /home/hornik/src/R/src/main/subset.c:330 #4 0x7fa6ab83be1c in do_subset_dflt /home/hornik/src/R/src/main/subset.c:892 #5 0x7fa6ab3e1bcc in bcEval_loop /home/hornik/src/R/src/main/eval.c:8269 #6 0x7fa6ab3d67ff in bcEval /home/hornik/src/R/src/main/eval.c:7505 #7 0x7fa6ab382952 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #8 0x7fa6ab37c602 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #9 0x7fa6ab38132a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #10 0x7fa6ab383231 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #11 0x7fa6ab383231 in Rf_eval /home/hornik/src/R/src/main/eval.c:1280 #12 0x7fa6ab399ce8 in applydefine /home/hornik/src/R/src/main/eval.c:3392 #13 0x7fa6ab383873 in Rf_eval /home/hornik/src/R/src/main/eval.c:1232 #14 0x7fa6ab3aad01 in do_eval /home/hornik/src/R/src/main/eval.c:3945 #15 0x7fa6ab3e9de0 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8122 #16 0x7fa6ab3d67ff in bcEval /home/hornik/src/R/src/main/eval.c:7505 #17 0x7fa6ab382952 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #18 0x7fa6ab44857b in forcePromise.part.0.lto_priv.0 /home/hornik/src/R/src/main/eval.c:976 #19 0x7fa6ab38463e in forcePromise /home/hornik/src/R/src/main/eval.c:956 #20 0x7fa6ab38463e in Rf_eval /home/hornik/src/R/src/main/eval.c:1187 #21 0x7fa6ab3ae0d6 in do_withVisible /home/hornik/src/R/src/main/eval.c:3988 #22 0x7fa6ab59f79a in do_internal /home/hornik/src/R/src/main/names.c:1410 #23 0x7fa6ab3e95c9 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8142 #24 0x7fa6ab3d67ff in bcEval /home/hornik/src/R/src/main/eval.c:7505 #25 0x7fa6ab382952 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #26 0x7fa6ab44857b in forcePromise.part.0.lto_priv.0 /home/hornik/src/R/src/main/eval.c:976 #27 0x7fa6ab38463e in forcePromise /home/hornik/src/R/src/main/eval.c:956 #28 0x7fa6ab38463e in Rf_eval /home/hornik/src/R/src/main/eval.c:1187 #29 0x7fa6ab44857b in forcePromise.part.0.lto_priv.0 /home/hornik/src/R/src/main/eval.c:976 #30 0x7fa6ab3b8fff in forcePromise /home/hornik/src/R/src/main/eval.c:956 #31 0x7fa6ab3b8fff in getvar /home/hornik/src/R/src/main/eval.c:5839 #32 0x7fa6ab3fed18 in bcEval_loop /home/hornik/src/R/src/main/eval.c:7852 #33 0x7fa6ab3d67ff in bcEval /home/hornik/src/R/src/main/eval.c:7505 #34 0x7fa6ab382952 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #35 0x7fa6ab37c602 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 SUMMARY: AddressSanitizer: heap-buffer-overflow /home/hornik/tmp/scratch/RtmpYrTn6q/R.INSTALL352e7147e44786/MassSpecWavelet/src/find_local_maximum.c:492 in localMaximumSlidingWindow Shadow bytes around the buggy address: 0x52e000797980: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52e000797a00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52e000797a80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52e000797b00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52e000797b80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x52e000797c00: 00 00 00 00 00 00 00 00 00[fa]fa fa fa fa fa fa 0x52e000797c80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52e000797d00: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52e000797d80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52e000797e00: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52e000797e80: 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 ==3497999==ABORTING * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR