* using log directory ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/cghseg.Rcheck’ * using R Under development (unstable) (2020-02-13 r77800) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘cghseg/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cghseg’ version ‘1.0.5’ * 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 ‘cghseg’ can be installed ... [89s/202s] 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 compiled code ... OK * checking examples ... ERROR Running examples in ‘cghseg-Ex.R’ failed The error most likely occurred in: > ### Name: CGHresults-class > ### Title: Class "CGHresults" > ### Aliases: CGHresults-class [,CGHresults-method getbp,CGHresults-method > ### initialize,CGHresults-method getprobebias,CGHresults-method > ### getsegprofiles,CGHresults-method getlevels,CGHresults-method > ### getbgoutliers,CGHresults-method summary,CGHresults-method > ### Keywords: classes > > ### ** Examples > > set.seed(1) > simul = simulprofiles(M=5,n=100,k.mean=2,SNR=5,lambda=1) > CGHd = new("CGHdata",Y=simul$Y) [raw data: check] minimum number of positions per signal [raw data: check] number of records per position [raw data: format] changing dataframe to compact format (list) > CGHo = new("CGHoptions") > CGHr = multiseg(CGHd,CGHo) [getuniKmax] uniKmax initialized by pre-screening ================================================================= ==46542==ERROR: AddressSanitizer: alloc-dealloc-mismatch (operator new [] vs operator delete) on 0x6180000bcc80 #0 0x7f449d27f96f in operator delete(void*) (/lib64/libasan.so.5+0x11096f) #1 0x7f448b57dc18 in colibri_c(double*, int*, int*, double*, double*, int*, double*) /data/gannet/ripley/R/packages/tests-gcc-SAN/cghseg/src/colibri.cc:132 #2 0x58945f in do_dotCode /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1799 #3 0x61ced1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7054 #4 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #5 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853 #6 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779 #7 0x63c551 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7022 #8 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #9 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853 #10 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779 #11 0x63c551 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7022 #12 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #13 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853 #14 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779 #15 0x63c551 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7022 #16 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #17 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853 #18 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779 #19 0x678cdd in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1920 #20 0x44a6da in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:70 #21 0x714f9f in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1379 #22 0x62ccd1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7074 #23 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #24 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853 #25 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779 #26 0x63c551 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7022 #27 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #28 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853 #29 0x672806 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2029 #30 0x7f44905a7323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #31 0x721714 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #32 0x63b3b5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7011 #33 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #34 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853 #35 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779 #36 0x63c551 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7022 #37 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #38 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853 #39 0x672806 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2029 #40 0x7f44905a7323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #41 0x721714 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #42 0x63b3b5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7011 #43 0x669f8f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #44 0x66f385 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1853 #45 0x671aa4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1779 #46 0x66a3d8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811 #47 0x677d91 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2920 #48 0x66a8cc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #49 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #50 0x6e846d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200 #51 0x6e8b68 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314 #52 0x6e8cb4 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113 #53 0x419388 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #54 0x7f449bba3f42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #55 0x41bacd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41bacd) 0x6180000bcc80 is located 0 bytes inside of 800-byte region [0x6180000bcc80,0x6180000bcfa0) allocated by thread T0 here: #0 0x7f449d27ebd7 in operator new[](unsigned long) (/lib64/libasan.so.5+0x10fbd7) #1 0x7f448b57beed in colibri_c(double*, int*, int*, double*, double*, int*, double*) /data/gannet/ripley/R/packages/tests-gcc-SAN/cghseg/src/colibri.cc:61 #2 0x58945f in do_dotCode /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1799 SUMMARY: AddressSanitizer: alloc-dealloc-mismatch (/lib64/libasan.so.5+0x11096f) in operator delete(void*) ==46542==HINT: if you don't care about these errors you may set ASAN_OPTIONS=alloc_dealloc_mismatch=0 ==46542==ABORTING * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR