* using log directory ‘/data/gannet/ripley/R/packages/tests-clang-ASAN/glycanr.Rcheck’
* using R Under development (unstable) (2025-01-09 r87552)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 19.1.6
    flang-new version 19.1.6
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘glycanr/DESCRIPTION’ ... OK
* this is package ‘glycanr’ version ‘0.4.0’
* package encoding: UTF-8
* 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 ‘glycanr’ can be installed ... [29s/37s] 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 ... [28s/33s] ERROR
Running examples in ‘glycanr-Ex.R’ failed
The error most likely occurred in:

> ### Name: quantilenorm
> ### Title: Quantile Normalization of glycan data
> ### Aliases: quantilenorm
> 
> ### ** Examples
> 
> data(mpiu)
> if(requireNamespace("preprocessCore", quietly=TRUE)){
+   mpiun <- quantilenorm(mpiu)
+   head(mpiun)
+ 
+   # transpose (change) subjects and measurements
+   mpiunt <- quantilenorm(mpiu, transpose=TRUE)
+   head(mpiunt)
+ }
=================================================================
==3058658==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x510000120038 at pc 0x7f0bb4c1338e bp 0x7f0bb813dc30 sp 0x7f0bb813dc28
READ of size 8 at 0x510000120038 thread T2
    #0 0x7f0bb4c1338d in determine_target /tmp/RtmpsJDYnS/R.INSTALL3d03fb7c9e2b97/preprocessCore/src/qnorm.c:1841:21
    #1 0x7f0bb4c1357f in determine_target_group /tmp/RtmpsJDYnS/R.INSTALL3d03fb7c9e2b97/preprocessCore/src/qnorm.c:1894:3
    #2 0x5559e1d85da6 in asan_thread_start(void*) /data/gannet/ripley/Sources/LLVM/19/latest/compiler-rt/lib/asan/asan_interceptors.cpp:239:28
    #3 0x7f0bcce8cdcc in start_thread (/lib64/libc.so.6+0x8cdcc) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #4 0x7f0bccf1262f in __GI___clone3 (/lib64/libc.so.6+0x11262f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)

0x510000120038 is located 8 bytes before 192-byte region [0x510000120040,0x510000120100)
allocated by thread T2 here:
    #0 0x5559e1d883d9 in calloc /data/gannet/ripley/Sources/LLVM/19/latest/compiler-rt/lib/asan/asan_malloc_linux.cpp:75:3
    #1 0x5559e20e7104 in R_chk_calloc /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:3545:9
    #2 0x7f0bb4c12930 in determine_target /tmp/RtmpsJDYnS/R.INSTALL3d03fb7c9e2b97/preprocessCore/src/qnorm.c:1796:22
    #3 0x7f0bb4c1357f in determine_target_group /tmp/RtmpsJDYnS/R.INSTALL3d03fb7c9e2b97/preprocessCore/src/qnorm.c:1894:3
    #4 0x5559e1d85da6 in asan_thread_start(void*) /data/gannet/ripley/Sources/LLVM/19/latest/compiler-rt/lib/asan/asan_interceptors.cpp:239:28

Thread T2 created by T0 here:
    #0 0x5559e1d6dc7f in pthread_create /data/gannet/ripley/Sources/LLVM/19/latest/compiler-rt/lib/asan/asan_interceptors.cpp:250:3
    #1 0x7f0bb4c13b15 in qnorm_c_determine_target_l /tmp/RtmpsJDYnS/R.INSTALL3d03fb7c9e2b97/preprocessCore/src/qnorm.c:1995:18
    #2 0x7f0bb4c14b1e in qnorm_c_determine_target /tmp/RtmpsJDYnS/R.INSTALL3d03fb7c9e2b97/preprocessCore/src/qnorm.c:2073:12
    #3 0x7f0bb4c14b1e in qnorm_c_handleNA /tmp/RtmpsJDYnS/R.INSTALL3d03fb7c9e2b97/preprocessCore/src/qnorm.c:2182:3
    #4 0x7f0bb4c14b1e in R_qnorm_c_handleNA /tmp/RtmpsJDYnS/R.INSTALL3d03fb7c9e2b97/preprocessCore/src/qnorm.c:2223:3
    #5 0x5559e1f3e5f5 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757:11
    #6 0x5559e1f4a509 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437:11
    #7 0x5559e1ff4b4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122:14
    #8 0x5559e1fe6f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16
    #9 0x5559e1fe546a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8
    #10 0x5559e202ef3c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22
    #11 0x5559e202e101 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16
    #12 0x5559e1fe5eb9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16
    #13 0x5559e1fe5eb9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12
    #14 0x5559e20409d0 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3571:8
    #15 0x5559e1fe59b3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12
    #16 0x5559e203db09 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3000:10
    #17 0x5559e1fe59b3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12
    #18 0x5559e1fe59b3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12
    #19 0x5559e20bc66a in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265:2
    #20 0x5559e20beda0 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11
    #21 0x5559e20beda0 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1219:5
    #22 0x5559e20bee32 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1226:5
    #23 0x5559e1dcb12c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5
    #24 0x7f0bcce2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)

SUMMARY: AddressSanitizer: heap-buffer-overflow /tmp/RtmpsJDYnS/R.INSTALL3d03fb7c9e2b97/preprocessCore/src/qnorm.c:1841:21 in determine_target
Shadow bytes around the buggy address:
  0x51000011fd80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x51000011fe00: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x51000011fe80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x51000011ff00: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x51000011ff80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
=>0x510000120000: fa fa fa fa fa fa fa[fa]00 00 00 00 00 00 00 00
  0x510000120080: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
  0x510000120100: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x510000120180: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x510000120200: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa
  0x510000120280: 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
==3058658==ABORTING
* checking tests ... OK
  Running ‘testthat.R’
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [94s/107s] OK
* DONE
Status: 1 ERROR