SHZ66 / zinba

Automatically exported from code.google.com/p/zinba
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Segfault running run.zinba #64

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago
1) What operating system are you using? Linux

2) What error message was displayed?

3) What was the exact command you used that resulted in the error?
run.zinba(seq=bed.file,outfile=out.file,filetype='bed',align=alignability.dir,nu
mProc=2,
          twoBit=twoBit.file,winSize=300,offset=75,extension=0,basecountfile=basealigncount.file,
          selectmodel=TRUE,selectchr='22',selecttype='dirty',selectcovs='align_perc',cleanup=TRUE)

4) Please copy and paste any additional screen output that resulted from
running the command

*** glibc detected *** /usr/lib64/R/bin/exec/R: free(): invalid next size 
(normal): 0x00000000024cac30 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3c3c276166]
/lib64/libc.so.6[0x3c3c278c93]
/usr/lib64/libstdc++.so.6(_ZNSt13basic_filebufIcSt11char_traitsIcEE26_M_destroy_
internal_bufferEv+0x1e)[0x3c40a6b8ae]
/usr/lib64/libstdc++.so.6(_ZNSt13basic_filebufIcSt11char_traitsIcEE5closeEv+0x64
)[0x3c40a6cb24]
/nethome/wliao/lib/R/zinba/libs/zinba.so(_ZN8calcCovs14processSignalsEiiiiSsPKcS
1_SsS1_iS1_+0xc0a)[0x7ff36e4553ea]
/nethome/wliao/lib/R/zinba/libs/zinba.so(buildWindows+0x332)[0x7ff36e44e9f2]
/usr/lib64/R/lib/libR.so[0x38910957f1]
/usr/lib64/R/lib/libR.so(Rf_eval+0x6f1)[0x38910c8fa1]
/usr/lib64/R/lib/libR.so[0x38910cbfd0]
/usr/lib64/R/lib/libR.so(Rf_eval+0x4ec)[0x38910c8d9c]
/usr/lib64/R/lib/libR.so[0x38910cc1c0]
/usr/lib64/R/lib/libR.so(Rf_eval+0x4ec)[0x38910c8d9c]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x371)[0x38910bb311]
/usr/lib64/R/lib/libR.so(Rf_eval+0x21d)[0x38910c8acd]
/usr/lib64/R/lib/libR.so[0x38910cc1c0]
/usr/lib64/R/lib/libR.so(Rf_eval+0x4ec)[0x38910c8d9c]
/usr/lib64/R/lib/libR.so(Rf_eval+0x4ec)[0x38910c8d9c]
/usr/lib64/R/lib/libR.so[0x38910cc1c0]
/usr/lib64/R/lib/libR.so(Rf_eval+0x4ec)[0x38910c8d9c]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x371)[0x38910bb311]
/usr/lib64/R/lib/libR.so(Rf_eval+0x21d)[0x38910c8acd]
/usr/lib64/R/lib/libR.so(Rf_ReplIteration+0x232)[0x38910ec8f2]
/usr/lib64/R/lib/libR.so[0x38910ecb79]
/usr/lib64/R/lib/libR.so(run_Rmainloop+0x44)[0x38910ed094]
/usr/lib64/R/bin/exec/R(main+0x1b)[0x40084b]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3c3c21ed1d]
/usr/lib64/R/bin/exec/R[0x400739]
======= Memory map: ========
00400000-00401000 r-xp 00000000 fd:01 2768024                            
/usr/lib64/R/bin/exec/R
00600000-00603000 rw-p 00000000 fd:01 2768024                            
/usr/lib64/R/bin/exec/R
009b9000-03c0f000 rw-p 00000000 00:00 0                                  [heap]
3890c00000-3890c0d000 r-xp 00000000 fd:01 2758497                        
/usr/lib64/libgomp.so.1.0.0
3890c0d000-3890e0c000 ---p 0000d000 fd:01 2758497                        
/usr/lib64/libgomp.so.1.0.0
3890e0c000-3890e0d000 rw-p 0000c000 fd:01 2758497                        
/usr/lib64/libgomp.so.1.0.0
3891000000-38912a5000 r-xp 00000000 fd:01 2756862                        
/usr/lib64/R/lib/libR.so
38912a5000-38914a5000 ---p 002a5000 fd:01 2756862                        
/usr/lib64/R/lib/libR.so
38914a5000-38914b5000 rw-p 002a5000 fd:01 2756862                        
/usr/lib64/R/lib/libR.so
38914b5000-38915a0000 rw-p 00000000 00:00 0
3891600000-3891788000 r-xp 00000000 fd:01 2754992                        
/usr/lib64/libicui18n.so.42.1
3891788000-3891988000 ---p 00188000 fd:01 2754992                        
/usr/lib64/libicui18n.so.42.1
3891988000-3891995000 rw-p 00188000 fd:01 2754992                        
/usr/lib64/libicui18n.so.42.1
3891995000-3891996000 rw-p 00000000 00:00 0
3891a00000-3891a2b000 r-xp 00000000 fd:01 2778278                        
/usr/lib64/R/lib/libRblas.so
3891a2b000-3891c2a000 ---p 0002b000 fd:01 2778278                        
/usr/lib64/R/lib/libRblas.so
3891c2a000-3891c2b000 rw-p 0002a000 fd:01 2778278                        
/usr/lib64/R/lib/libRblas.so
3894400000-389453f000 r-xp 00000000 fd:01 2779411                        
/usr/lib64/libicuuc.so.42.1
389453f000-389473f000 ---p 0013f000 fd:01 2779411                        
/usr/lib64/libicuuc.so.42.1
389473f000-3894750000 rw-p 0013f000 fd:01 2779411                        
/usr/lib64/libicuuc.so.42.1
3894750000-3894752000 rw-p 00000000 00:00 0
3c3ba00000-3c3ba20000 r-xp 00000000 fd:01 3023100                        
/lib64/ld-2.12.so
3c3bc1f000-3c3bc20000 r--p 0001f000 fd:01 3023100                        
/lib64/ld-2.12.so
3c3bc20000-3c3bc21000 rw-p 00020000 fd:01 3023100                        
/lib64/ld-2.12.so
3c3bc21000-3c3bc22000 rw-p 00000000 00:00 0
3c3be00000-3c3be83000 r-xp 00000000 fd:01 3023104                        
/lib64/libm-2.12.so
3c3be83000-3c3c082000 ---p 00083000 fd:01 3023104                        
/lib64/libm-2.12.so
3c3c082000-3c3c083000 r--p 00082000 fd:01 3023104                        
/lib64/libm-2.12.so
3c3c083000-3c3c084000 rw-p 00083000 fd:01 3023104                        
/lib64/libm-2.12.so
3c3c200000-3c3c38b000 r-xp 00000000 fd:01 3023101                        
/lib64/libc-2.12.so
3c3c38b000-3c3c58a000 ---p 0018b000 fd:01 3023101                        
/lib64/libc-2.12.so
3c3c58a000-3c3c58e000 r--p 0018a000 fd:01 3023101                        
/lib64/libc-2.12.so
3c3c58e000-3c3c58f000 rw-p 0018e000 fd:01 3023101                        
/lib64/libc-2.12.so
3c3c58f000-3c3c594000 rw-p 00000000 00:00 0
3c3c600000-3c3c602000 r-xp 00000000 fd:01 3023103                        
/lib64/libdl-2.12.so
3c3c602000-3c3c802000 ---p 00002000 fd:01 3023103                        
/lib64/libdl-2.12.so
3c3c802000-3c3c803000 r--p 00002000 fd:01 3023103                        
/lib64/libdl-2.12.so
3c3c803000-3c3c804000 rw-p 00003000 fd:01 3023103                        
/lib64/libdl-2.12.so
3c3d600000-3c3d61d000 r-xp 00000000 fd:01 3023141                        
/lib64/libtinfo.so.5.7
3c3d61d000-3c3d81d000 ---p 0001d000 fd:01 3023141                        
/lib64/libtinfo.so.5.7
3c3d81d000-3c3d821000 rw-p 0001d000 fd:01 3023141                        
/lib64/libtinfo.so.5.7
3c3e400000-3c3e4f0000 r-xp 00000000 fd:01 2756604                        
/usr/lib64/libgfortran.so.3.0.0
3c3e4f0000-3c3e6ef000 ---p 000f0000 fd:01 2756604                        
/usr/lib64/libgfortran.so.3.0.0
3c3e6ef000-3c3e6f1000 rw-p 000ef000 fd:01 2756604                        
/usr/lib64/libgfortran.so.3.0.0
3c3e6f1000-3c3e6f2000 rw-p 00000000 00:00 0
3c3ee00000-3c3ee16000 r-xp 00000000 fd:01 3023105                        
/lib64/libgcc_s-4.4.7-20120601.so.1
3c3ee16000-3c3f015000 ---p 00016000 fd:01 3023105                        
/lib64/libgcc_s-4.4.7-20120601.so.1
3c3f015000-3c3f016000 rw-p 00015000 fd:01 3023105                        
/lib64/libgcc_s-4.4.7-20120601.so.1
3c40a00000-3c40ae8000 r-xp 00000000 fd:01 2769257                        
/usr/lib64/libstdc++.so.6.0.13
3c40ae8000-3c40ce8000 ---p 000e8000 fd:01 2769257                        
/usr/lib64/libstdc++.so.6.0.13
3c40ce8000-3c40cef000 r--p 000e8000 fd:01 2769257                        
/usr/lib64/libstdc++.so.6.0.13
3c40cef000-3c40cf1000 rw-p 000ef000 fd:01 2769257                        
/usr/lib64/libstdc++.so.6.0.13
3c40cf1000-3c40d06000 rw-p 00000000 00:00 0
3c41600000-3c4163a000 r-xp 00000000 fd:01 3023142                        
/lib64/libreadline.so.6.0
3c4163a000-3c4183a000 ---p 0003a000 fd:01 3023142                        
/lib64/libreadline.so.6.0[1]+  Killed                  R
Aborted (core dumped)

Original issue reported on code.google.com by will.l...@gmail.com on 12 Jun 2014 at 5:58