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sivarajankumar / zinba

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buffer overflow when running zinba #15

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
1) What operating system are you using?
ubuntu 11.04
2) What error message was displayed?
Overwriting previously existing directory ./result_zinba/mid_none/_files/

--------BEGIN BUILDING WINDOW DATA-------- 2012-03-06 10:51:36 

Importing reads from file mid.bed 
    Filetype is bed 
    Extension is 200 
    Importing bed formatted reads
*** buffer overflow detected ***: /usr/local/lib64/R/bin/exec/R terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7fa467ecd1d7]
/lib/x86_64-linux-gnu/libc.so.6(+0xfd0f0)[0x7fa467ecc0f0]
/home/teavee/R/x86_64-unknown-linux-gnu-library/2.14/zinba/libs/zinba.so(_ZN6imp
ort9importBedEPKcii+0x20a)[0x7fa465b6536a]
/home/teavee/R/x86_64-unknown-linux-gnu-library/2.14/zinba/libs/zinba.so(_ZN8cal
cCovs15importRawSignalEPKciS1_iS1_+0x2c4)[0x7fa465b24484]
/home/teavee/R/x86_64-unknown-linux-gnu-library/2.14/zinba/libs/zinba.so(buildWi
ndows+0x16b)[0x7fa465b1d89b]
/usr/local/lib64/R/bin/exec/R[0x546519]
/usr/local/lib64/R/bin/exec/R(Rf_eval+0x65c)[0x573dac]
/usr/local/lib64/R/bin/exec/R[0x576840]
/usr/local/lib64/R/bin/exec/R(Rf_eval+0x4d9)[0x573c29]
/usr/local/lib64/R/bin/exec/R[0x5769ae]
/usr/local/lib64/R/bin/exec/R(Rf_eval+0x4d9)[0x573c29]
/usr/local/lib64/R/bin/exec/R(Rf_applyClosure+0x30f)[0x577b9f]
/usr/local/lib64/R/bin/exec/R(Rf_eval+0x3cf)[0x573b1f]
/usr/local/lib64/R/bin/exec/R[0x5769ae]
/usr/local/lib64/R/bin/exec/R(Rf_eval+0x4d9)[0x573c29]
======= Memory map: ========
00400000-006eb000 r-xp 00000000 08:05 9443181                            
/usr/local/lib64/R/bin/exec/R
008ea000-008eb000 r--p 002ea000 08:05 9443181                            
/usr/local/lib64/R/bin/exec/R
008eb000-008fa000 rw-p 002eb000 08:05 9443181                            
/usr/local/lib64/R/bin/exec/R
008fa000-0097b000 rw-p 00000000 00:00 0 
00cfd000-023e1000 rw-p 00000000 00:00 0                                  [heap]
7fa465380000-7fa4653ad000 rw-p 00000000 00:00 0 
7fa4653ad000-7fa4653b0000 r-xp 00000000 08:05 268024                     
/home/teavee/R/x86_64-unknown-linux-gnu-library/2.14/multicore/libs/multicore.so
7fa4653b0000-7fa4655af000 ---p 00003000 08:05 268024                     
/home/teavee/R/x86_64-unknown-linux-gnu-library/2.14/multicore/libs/multicore.so
7fa4655af000-7fa4655b0000 r--p 00002000 08:05 268024                     
/home/teavee/R/x86_64-unknown-linux-gnu-library/2.14/multicore/libs/multicore.so
7fa4655b0000-7fa4655b1000 rw-p 00003000 08:05 268024                     
/home/teavee/R/x86_64-unknown-linux-gnu-library/2.14/multicore/libs/multicore.so
7fa4655b1000-7fa4655c6000 r-xp 00000000 08:05 8916644                    
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fa4655c6000-7fa4657c5000 ---p 00015000 08:05 8916644                    
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fa4657c5000-7fa4657c6000 r--p 00014000 08:05 8916644                    
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fa4657c6000-7fa4657c7000 rw-p 00015000 08:05 8916644                    
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fa4657c7000-7fa4658af000 r-xp 00000000 08:05 3154109                    
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.14
7fa4658af000-7fa465aae000 ---p 000e8000 08:05 3154109                    
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.14
7fa465aae000-7fa465ab6000 r--p 000e7000 08:05 3154109                    
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.14
7fa465ab6000-7fa465ab8000 rw-p 000ef000 08:05 3154109                    
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.14
7fa465ab8000-7fa465acd000 rw-p 00000000 00:00 0 
7fa465acd000-7fa465bde000 r-xp 00000000 08:05 266982                     
/home/teavee/R/x86_64-unknown-linux-gnu-library/2.14/zinba/libs/zinba.so
7fa465bde000-7fa465ddd000 ---p 00111000 08:05 266982                     
/home/teavee/R/x86_64-unknown-linux-gnu-library/2.14/zinba/libs/zinba.so
7fa465ddd000-7fa465dde000 r--p 00110000 08:05 266982                     
/home/teavee/R/x86_64-unknown-linux-gnu-library/2.14/zinba/libs/zinba.so
7fa465dde000-7fa465dfd000 rw-p 00111000 08:05 266982                     
/home/teavee/R/x86_64-unknown-linux-gnu-library/2.14/zinba/libs/zinba.so
7fa465dfd000-7fa465e13000 rw-p 00000000 00:00 0 
7fa465e13000-7fa465e7f000 r-xp 00000000 08:05 10223866                   
/usr/local/lib64/R/library/stats/libs/stats.so
7fa465e7f000-7fa46607e000 ---p 0006c000 08:05 10223866                   
/usr/local/lib64/R/library/stats/libs/stats.so
7fa46607e000-7fa466080000 r--p 0006b000 08:05 10223866                   
/usr/local/lib64/R/library/stats/libs/stats.so
7fa466080000-7fa466082000 rw-p 0006d000 08:05 10223866                   
/usr/local/lib64/R/library/stats/libs/stats.so
7fa466082000-7fa4661ed000 rw-p 00000000 00:00 0 
7fa4661ed000-7fa46621b000 r-xp 00000000 08:05 10224079                   
/usr/local/lib64/R/library/grDevices/libs/grDevices.so
7fa46621b000-7fa46641b000 ---p 0002e000 08:05 10224079                   
/usr/local/lib64/R/library/grDevices/libs/grDevices.so
7fa46641b000-7fa46641c000 r--p 0002e000 08:05 10224079                   
/usr/local/lib64/R/library/grDevices/libs/grDevices.so
7fa46641c000-7fa46641d000 rw-p 0002f000 08:05 10224079                   
/usr/local/lib64/R/library/grDevices/libs/grDevices.so
7fa46641d000-7fa466673000 rw-p 00000000 00:00 0 
7fa466673000-7fa466675000 r-xp 00000000 08:05 3542173                    
/usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7fa466675000-7fa466874000 ---p 00002000 08:05 3542173                    
/usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7fa466874000-7fa466875000 r--p 00001000 08:05 3542173                    
/usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7fa466875000-7fa466876000 rw-p 00002000 08:05 3542173                    
/usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7fa466876000-7fa46697a000 rw-p 00000000 00:00 0 
7fa46697a000-7fa466981000 r-xp 00000000 08:05 10223714                   
/usr/local/lib64/R/library/methods/libs/methods.so
7fa466981000-7fa466b80000 ---p 00007000 08:05 10223714                   
/usr/local/lib64/R/library/methods/libs/methods.so
7fa466b80000-7fa466b81000 r--p 00006000 08:05 10223714                   
/usr/local/lib64/R/library/methods/libs/methods.so
7fa466b81000-7fa466b82000 rw-p 00007000 08:05 10223714                   
/usr/local/lib64/R/library/methods/libs/methods.so
7fa466b82000-7fa466c15000 rw-p 00000000 00:00 0 
7fa466c15000-7fa466c21000 r-xp 00000000 08:05 8916662                    
/lib/x86_64-linux-gnu/libnss_files-2.13.so
7fa466c21000-7fa466e20000 ---p 0000c000 08:05 8916662                    
/lib/x86_64-linux-gnu/libnss_files-2.13.so
7fa466e20000-7fa466e21000 r--p 0000b000 08:Aborted

3) What was the exact command you used that resulted in the error?
> library(zinba)
> zinba(
+   refinepeaks=1, 
+   seq='mid.bed',
+   input='none.bed',
+   filetype="bed",
+   
+   align='./result_zinba/ath1_ext200/',
+   numProc=4,                    
+   twoBit='../zinba/hg19.2bit',
+   outfile="./result_zinba/mid_none/",
+   extension=200,
+   
+   basecountfile='result_zinba/high.basecount',
+   broad=F,
+   printFullOut=1
+ )

4) Please copy and paste any additional screen output that resulted from
running the command
After reporting issue #14, I decided to update to the latest zinba and try 
again. First thing I noticed was that the latest zinba requires R.utils but it 
is not required when installing/testing? Anyways, here is the output from 
install is attached

Original issue reported on code.google.com by daiyi...@gmail.com on 6 Mar 2012 at 7:07

Attachments:

GoogleCodeExporter commented 8 years ago 
what version of zinba are you using?  This may be an error related to a recent 
release.  If you are not using version 2.01, try installing the it (located 
here http://zinba.googlecode.com/files/zinba_2.01.tar.gz ) and see if the 
problem is replicated.

Original comment by homer...@gmail.com on 6 Mar 2012 at 7:28

GoogleCodeExporter commented 8 years ago 
This is for zinba 2.02.01 i got a different error for zinba 2.01 (see issue #14)

Original comment by daiyi...@gmail.com on 6 Mar 2012 at 10:48

GoogleCodeExporter commented 8 years ago 
Are these instances the first time you are using zinba?  Were you able to use 
it on other data before without issue?  If not, then please email me a set of 
randomly selected reads from your dataset so I can determine what could be the 
source of the segfault.  I am currently working on a similar issue, so it would 
help to see if they are connected in some what.

Original comment by homer...@gmail.com on 7 Mar 2012 at 1:00

GoogleCodeExporter commented 8 years ago 
problem fixed after update to buildwindows import function in 2.02.03 
(releasing soon)

Original comment by homer...@gmail.com on 9 Mar 2012 at 4:08

GoogleCodeExporter commented 8 years ago

Original comment by homer...@gmail.com on 9 Mar 2012 at 4:08