* 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 ... [11s/11s] 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 ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [2s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] 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 ... [25s/25s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [3s/3s] ERROR Running examples in ‘NMRphasing-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: MPC_AAM > ### Title: MPC_AAM > ### Aliases: MPC_AAM > > ### ** Examples > > data("fdat") > mpc_aam_phased1 <- MPC_AAM(fdat$frequency_domain) ================================================================= ==339618==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x52e0001d3c50 at pc 0x7fdb40df4a3b bp 0x7ffff5c6edb0 sp 0x7ffff5c6eda8 READ of size 8 at 0x52e0001d3c50 thread T0 #0 0x7fdb40df4a3a in localMaximumSlidingWindow /home/hornik/tmp/scratch/Rtmp03Y2PN/R.INSTALL45416696b6de8/MassSpecWavelet/src/find_local_maximum.c:492 #1 0x7fdb5705d1ac in R_doDotCall /home/hornik/src/R/src/main/dotcode.c:757 #2 0x7fdb571fec96 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8672 #3 0x7fdb571d783f in bcEval /home/hornik/src/R/src/main/eval.c:7505 #4 0x7fdb57183992 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #5 0x7fdb5717d642 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #6 0x7fdb5718236a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #7 0x7fdb57184271 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #8 0x7fdb57184271 in Rf_eval /home/hornik/src/R/src/main/eval.c:1280 #9 0x7fdb571a2716 in do_set /home/hornik/src/R/src/main/eval.c:3571 #10 0x7fdb571848b3 in Rf_eval /home/hornik/src/R/src/main/eval.c:1232 #11 0x7fdb5731d5fc in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:265 #12 0x7fdb5731d5fc in R_ReplConsole /home/hornik/src/R/src/main/main.c:317 #13 0x7fdb5732ce33 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1219 #14 0x55d4fd44d0c9 in main /home/hornik/src/R/src/main/Rmain.c:29 #15 0x7fdb55633d67 in __libc_start_call_main ../sysdeps/nptl/libc_start_call_main.h:58 #16 0x7fdb55633e24 in __libc_start_main_impl ../csu/libc-start.c:360 #17 0x55d4fd44d110 in _start (/home/hornik/tmp/R-d-gcc-xtra/bin/exec/R+0x1110) (BuildId: c7fe195d896200455f7f0ce073f110b1c5100f12) 0x52e0001d3c50 is located 0 bytes after 47184-byte region [0x52e0001c8400,0x52e0001d3c50) allocated by thread T0 here: #0 0x7fdb58cf4c77 in malloc ../../../../src/libsanitizer/asan/asan_malloc_linux.cpp:69 #1 0x7fdb57385e17 in Rf_allocVector3 /home/hornik/src/R/src/main/memory.c:2890 #2 0x7fdb5763ce8c in Rf_allocVector /home/hornik/src/R/src/include/Rinlinedfuns.h:607 #3 0x7fdb5763ce8c in MatrixSubset /home/hornik/src/R/src/main/subset.c:330 #4 0x7fdb5763ce8c in do_subset_dflt /home/hornik/src/R/src/main/subset.c:892 #5 0x7fdb571e2c0c in bcEval_loop /home/hornik/src/R/src/main/eval.c:8269 #6 0x7fdb571d783f in bcEval /home/hornik/src/R/src/main/eval.c:7505 #7 0x7fdb57183992 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #8 0x7fdb5717d642 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #9 0x7fdb5718236a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #10 0x7fdb57184271 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #11 0x7fdb57184271 in Rf_eval /home/hornik/src/R/src/main/eval.c:1280 #12 0x7fdb571a2716 in do_set /home/hornik/src/R/src/main/eval.c:3571 #13 0x7fdb571848b3 in Rf_eval /home/hornik/src/R/src/main/eval.c:1232 #14 0x7fdb5731d5fc in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:265 #15 0x7fdb5731d5fc in R_ReplConsole /home/hornik/src/R/src/main/main.c:317 #16 0x7fdb5732ce33 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1219 #17 0x55d4fd44d0c9 in main /home/hornik/src/R/src/main/Rmain.c:29 #18 0x7fdb55633d67 in __libc_start_call_main ../sysdeps/nptl/libc_start_call_main.h:58 SUMMARY: AddressSanitizer: heap-buffer-overflow /home/hornik/tmp/scratch/Rtmp03Y2PN/R.INSTALL45416696b6de8/MassSpecWavelet/src/find_local_maximum.c:492 in localMaximumSlidingWindow Shadow bytes around the buggy address: 0x52e0001d3980: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52e0001d3a00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52e0001d3a80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52e0001d3b00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52e0001d3b80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x52e0001d3c00: 00 00 00 00 00 00 00 00 00 00[fa]fa fa fa fa fa 0x52e0001d3c80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52e0001d3d00: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52e0001d3d80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52e0001d3e00: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52e0001d3e80: 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 ==339618==ABORTING * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [11s/11s] 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 600x600 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 21949 bytes Input file size = 22831 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19770 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 19448 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 = 16942 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 16672 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 = 16672 Output IDAT size = 16672 bytes (5277 bytes decrease) Output file size = 16750 bytes (6081 bytes = 26.63% decrease) ================================================================= ==341327==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x52e00077fc50 at pc 0x7f2fdba88a3b bp 0x7ffd03cdea20 sp 0x7ffd03cdea18 READ of size 8 at 0x52e00077fc50 thread T0 #0 0x7f2fdba88a3a in localMaximumSlidingWindow /home/hornik/tmp/scratch/Rtmp03Y2PN/R.INSTALL45416696b6de8/MassSpecWavelet/src/find_local_maximum.c:492 #1 0x7f2fffe5d1ac in R_doDotCall /home/hornik/src/R/src/main/dotcode.c:757 #2 0x7f2fffffec96 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8672 #3 0x7f2ffffd783f in bcEval /home/hornik/src/R/src/main/eval.c:7505 #4 0x7f2ffff83992 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #5 0x7f2ffff7d642 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #6 0x7f2ffff8236a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #7 0x7f2ffff84271 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #8 0x7f2ffff84271 in Rf_eval /home/hornik/src/R/src/main/eval.c:1280 #9 0x7f2ffff9ad28 in applydefine /home/hornik/src/R/src/main/eval.c:3392 #10 0x7f2ffff848b3 in Rf_eval /home/hornik/src/R/src/main/eval.c:1232 #11 0x7f2ffffabd41 in do_eval /home/hornik/src/R/src/main/eval.c:3945 #12 0x7f2ffffeae20 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8122 #13 0x7f2ffffd783f in bcEval /home/hornik/src/R/src/main/eval.c:7505 #14 0x7f2ffff83992 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #15 0x7f30000495bb in forcePromise.part.0.lto_priv.0 /home/hornik/src/R/src/main/eval.c:976 #16 0x7f2ffff8567e in forcePromise /home/hornik/src/R/src/main/eval.c:956 #17 0x7f2ffff8567e in Rf_eval /home/hornik/src/R/src/main/eval.c:1187 #18 0x7f2ffffaf116 in do_withVisible /home/hornik/src/R/src/main/eval.c:3988 #19 0x7f30001a07da in do_internal /home/hornik/src/R/src/main/names.c:1410 #20 0x7f2ffffea609 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8142 #21 0x7f2ffffd783f in bcEval /home/hornik/src/R/src/main/eval.c:7505 #22 0x7f2ffff83992 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #23 0x7f30000495bb in forcePromise.part.0.lto_priv.0 /home/hornik/src/R/src/main/eval.c:976 #24 0x7f2ffff8567e in forcePromise /home/hornik/src/R/src/main/eval.c:956 #25 0x7f2ffff8567e in Rf_eval /home/hornik/src/R/src/main/eval.c:1187 #26 0x7f30000495bb in forcePromise.part.0.lto_priv.0 /home/hornik/src/R/src/main/eval.c:976 #27 0x7f2ffffba03f in forcePromise /home/hornik/src/R/src/main/eval.c:956 #28 0x7f2ffffba03f in getvar /home/hornik/src/R/src/main/eval.c:5839 #29 0x7f2ffffffd58 in bcEval_loop /home/hornik/src/R/src/main/eval.c:7852 #30 0x7f2ffffd783f in bcEval /home/hornik/src/R/src/main/eval.c:7505 #31 0x7f2ffff83992 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #32 0x7f2ffff7d642 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #33 0x7f2ffff8236a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #34 0x7f2ffff84271 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #35 0x7f2ffff84271 in Rf_eval /home/hornik/src/R/src/main/eval.c:1280 #36 0x7f2ffffabd41 in do_eval /home/hornik/src/R/src/main/eval.c:3945 #37 0x7f2ffffeae20 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8122 #38 0x7f2ffffd783f in bcEval /home/hornik/src/R/src/main/eval.c:7505 #39 0x7f2ffff83992 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #40 0x7f2ffff7d642 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #41 0x7f2ffff8236a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #42 0x7f2ffff84271 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #43 0x7f2ffff84271 in Rf_eval /home/hornik/src/R/src/main/eval.c:1280 #44 0x7f2ffff7d642 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #45 0x7f2ffff8236a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #46 0x7f2ffffeb2ca in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #47 0x7f2ffffeb2ca in bcEval_loop /home/hornik/src/R/src/main/eval.c:8093 #48 0x7f2ffffd783f in bcEval /home/hornik/src/R/src/main/eval.c:7505 #49 0x7f2ffff83992 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #50 0x7f2ffff7d642 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #51 0x7f2ffff8236a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #52 0x7f2ffff84271 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #53 0x7f2ffff84271 in Rf_eval /home/hornik/src/R/src/main/eval.c:1280 #54 0x7f300011d5fc in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:265 #55 0x7f300011d5fc in R_ReplConsole /home/hornik/src/R/src/main/main.c:317 #56 0x7f300012ce33 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1219 #57 0x55e35fc050c9 in main /home/hornik/src/R/src/main/Rmain.c:29 #58 0x7f2ffe433d67 in __libc_start_call_main ../sysdeps/nptl/libc_start_call_main.h:58 #59 0x7f2ffe433e24 in __libc_start_main_impl ../csu/libc-start.c:360 #60 0x55e35fc05110 in _start (/home/hornik/tmp/R-d-gcc-xtra/bin/exec/R+0x1110) (BuildId: c7fe195d896200455f7f0ce073f110b1c5100f12) 0x52e00077fc50 is located 0 bytes after 47184-byte region [0x52e000774400,0x52e00077fc50) allocated by thread T0 here: #0 0x7f3001af4c77 in malloc ../../../../src/libsanitizer/asan/asan_malloc_linux.cpp:69 #1 0x7f3000185e17 in Rf_allocVector3 /home/hornik/src/R/src/main/memory.c:2890 #2 0x7f300043ce8c in Rf_allocVector /home/hornik/src/R/src/include/Rinlinedfuns.h:607 #3 0x7f300043ce8c in MatrixSubset /home/hornik/src/R/src/main/subset.c:330 #4 0x7f300043ce8c in do_subset_dflt /home/hornik/src/R/src/main/subset.c:892 #5 0x7f2ffffe2c0c in bcEval_loop /home/hornik/src/R/src/main/eval.c:8269 #6 0x7f2ffffd783f in bcEval /home/hornik/src/R/src/main/eval.c:7505 #7 0x7f2ffff83992 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #8 0x7f2ffff7d642 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 #9 0x7f2ffff8236a in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306 #10 0x7f2ffff84271 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328 #11 0x7f2ffff84271 in Rf_eval /home/hornik/src/R/src/main/eval.c:1280 #12 0x7f2ffff9ad28 in applydefine /home/hornik/src/R/src/main/eval.c:3392 #13 0x7f2ffff848b3 in Rf_eval /home/hornik/src/R/src/main/eval.c:1232 #14 0x7f2ffffabd41 in do_eval /home/hornik/src/R/src/main/eval.c:3945 #15 0x7f2ffffeae20 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8122 #16 0x7f2ffffd783f in bcEval /home/hornik/src/R/src/main/eval.c:7505 #17 0x7f2ffff83992 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #18 0x7f30000495bb in forcePromise.part.0.lto_priv.0 /home/hornik/src/R/src/main/eval.c:976 #19 0x7f2ffff8567e in forcePromise /home/hornik/src/R/src/main/eval.c:956 #20 0x7f2ffff8567e in Rf_eval /home/hornik/src/R/src/main/eval.c:1187 #21 0x7f2ffffaf116 in do_withVisible /home/hornik/src/R/src/main/eval.c:3988 #22 0x7f30001a07da in do_internal /home/hornik/src/R/src/main/names.c:1410 #23 0x7f2ffffea609 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8142 #24 0x7f2ffffd783f in bcEval /home/hornik/src/R/src/main/eval.c:7505 #25 0x7f2ffff83992 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #26 0x7f30000495bb in forcePromise.part.0.lto_priv.0 /home/hornik/src/R/src/main/eval.c:976 #27 0x7f2ffff8567e in forcePromise /home/hornik/src/R/src/main/eval.c:956 #28 0x7f2ffff8567e in Rf_eval /home/hornik/src/R/src/main/eval.c:1187 #29 0x7f30000495bb in forcePromise.part.0.lto_priv.0 /home/hornik/src/R/src/main/eval.c:976 #30 0x7f2ffffba03f in forcePromise /home/hornik/src/R/src/main/eval.c:956 #31 0x7f2ffffba03f in getvar /home/hornik/src/R/src/main/eval.c:5839 #32 0x7f2ffffffd58 in bcEval_loop /home/hornik/src/R/src/main/eval.c:7852 #33 0x7f2ffffd783f in bcEval /home/hornik/src/R/src/main/eval.c:7505 #34 0x7f2ffff83992 in Rf_eval /home/hornik/src/R/src/main/eval.c:1167 #35 0x7f2ffff7d642 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393 SUMMARY: AddressSanitizer: heap-buffer-overflow /home/hornik/tmp/scratch/Rtmp03Y2PN/R.INSTALL45416696b6de8/MassSpecWavelet/src/find_local_maximum.c:492 in localMaximumSlidingWindow Shadow bytes around the buggy address: 0x52e00077f980: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52e00077fa00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52e00077fa80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52e00077fb00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52e00077fb80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x52e00077fc00: 00 00 00 00 00 00 00 00 00 00[fa]fa fa fa fa fa 0x52e00077fc80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52e00077fd00: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52e00077fd80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52e00077fe00: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52e00077fe80: 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 ==341327==ABORTING * checking PDF version of manual ... [5s/6s] 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: 2 ERRORs