I am running an Rscipt which calculates economic parameters for around 1000 cities in a loop. The data is stored in MySQL which I am accessing using RMySQL and DBI packages.
However I keep getting segmentation fault errors. I have no idea why this happens. Most of the time the script works fine but all of a sudden it throws segmentation fault error. When I rerun the script it works fine again. From what I am able to gather its some kind of memory issue. I tried debugging it using valgrind, but I am not able to understand the output and remedial action which needs to be taken.
Here is the output from valgrind. I want to know what the output means and where the error is.
==5856== Invalid read of size 1
==5856== at 0x4F3CF17: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F3EF2B: Rf_cons (in /usr/lib/R/lib/libR.so)
==5856== by 0x4EDF18B: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4EDFF66: Rf_shallow_duplicate (in /usr/lib/R/lib/libR.so)
==5856== by 0x4EB9CBB: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F4276B: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F43D24: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F019FA: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F0CF6F: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F1249C: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F0D065: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F0D38F: ??? (in /usr/lib/R/lib/libR.so)
==5856== Address 0x122ca7f3 is 3 bytes inside a block of size 296 free'd
==5856== at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==5856== by 0x4F3D707: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F3EF2B: Rf_cons (in /usr/lib/R/lib/libR.so)
==5856== by 0x4E82027: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4E86414: Rf_namesgets (in /usr/lib/R/lib/libR.so)
==5856== by 0xCB18756: RS_DBI_createNamedList (RS-DBI.c:731)
==5856== by 0xCB1BB0B: RS_MySQL_resultSetInfo (RS-MySQL.c:1029)
==5856== by 0x4ECD51B: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F0D5A2: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F10955: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F0D38F: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F10BA1: ??? (in /usr/lib/R/lib/libR.so)
==5856==
==5856== Invalid read of size 8
==5856== at 0x4F3CF23: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F3EF2B: Rf_cons (in /usr/lib/R/lib/libR.so)
==5856== by 0x4EDF18B: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4EDFF66: Rf_shallow_duplicate (in /usr/lib/R/lib/libR.so)
==5856== by 0x4EB9CBB: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F4276B: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F43D24: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F019FA: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F0CF6F: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F1249C: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F0D065: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F0D38F: ??? (in /usr/lib/R/lib/libR.so)
==5856== Address 0x122ca808 is 24 bytes inside a block of size 296 free'd
==5856== at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==5856== by 0x4F3D707: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F3EF2B: Rf_cons (in /usr/lib/R/lib/libR.so)
==5856== by 0x4E82027: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4E86414: Rf_namesgets (in /usr/lib/R/lib/libR.so)
==5856== by 0xCB18756: RS_DBI_createNamedList (RS-DBI.c:731)
==5856== by 0xCB1BB0B: RS_MySQL_resultSetInfo (RS-MySQL.c:1029)
==5856== by 0x4ECD51B: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F0D5A2: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F10955: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F0D38F: ??? (in /usr/lib/R/lib/libR.so)
==5856== by 0x4F10BA1: ??? (in /usr/lib/R/lib/libR.so)
This is my session info when I started the run.
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pryr_0.1.2 gdata_2.17.0 lubridate_1.3.3 dplyr_0.2
[5] DataCombine_0.1.26 quantmod_0.4-0 Defaults_1.1-1 TTR_0.22-0
[9] xts_0.9-7 zoo_1.7-11 RMySQL_0.9-3 DBI_0.2-7
loaded via a namespace (and not attached):
[1] assertthat_0.1 codetools_0.2-8 data.table_1.9.2 digest_0.6.8
[5] grid_3.1.1 gtools_3.5.0 lattice_0.20-31 memoise_0.2.1
[9] parallel_3.1.1 plyr_1.8.1 Rcpp_0.11.2 reshape2_1.4
[13] stringr_0.6.2 tools_3.1.1
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