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rcconsult / rpostgresql

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Segmentation fault #41

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Not easily reproducible. Hard to determine pattern of occurrence
2.
3.

What is the expected output? What do you see instead?
Call to dbGetQuery sometimes (rarely) results in segmentation fault. Does not 
appear to be linked to a specific query, but traceback seems to lead to 
RPostgreSQL functions (see below)  

What version of the product are you using? On what operating system?
R 2.15.1, RPostgreSQL 0.3.2 DBI 0.2-5
Platform: x86_64-pc-linux-gnu (Ubuntu, 64-bit)

Please provide any additional information below.
Running a long script (several days to process), which processes and parses 
many XML files, and then inserts processed data into PostgreSQL database. 
Several hours (5-36) through the run, R crashes with a segmentation fault, 
memory not mapped. Restarting the script, which picks up at the file where it 
left off, the file is processed with no issues, so I believe it is not the 
specific queries / or file. The traceback is here:

 *** caught segfault ***
address 0x7f100000021a, cause 'memory not mapped'

Traceback:
 1: paste(sig, collapse = "#")
 2: .sigLabel(signature)
 3: .findMethodInTable(c(from, to), methods)
 4: .quickCoerceSelect(thisClass, Class, coerceFun, coerceMethods,     where)
 5: as(obj, "integer")
 6: isPostgresqlIdCurrent(obj)
 7: postgresqlResultInfo(dbObj, ...)
 8: dbGetInfo(res, "rowCount")
 9: dbGetInfo(res, "rowCount")
10: is(object, Cl)
11: is(object, Cl)
12: .valueClassTest(standardGeneric("dbGetRowCount"), "numeric",     
"dbGetRowCount")
13: dbGetRowCount(res)
14: postgresqlFetch(res, n, ...)
15: is(object, Cl)
16: is(object, Cl)
17: .valueClassTest(standardGeneric("fetch"), "data.frame", "fetch")
18: fetch(rs, n = -1)
19: postgresqlQuickSQL(conn, statement, ...)
20: dbGetQuery(connObj, queryStr)
21: dbGetQuery(connObj, queryStr)
22: gsmProcessSeasonFile(connObj, sourceDetails, sfile)
23: gsmProcessSeasons(connObj, sourceDetails)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

Original issue reported on code.google.com by david.ha...@rsimony.com on 2 Sep 2012 at 6:54

GoogleCodeExporter commented 9 years ago 
Assumeed to be the same as issue 42.
Will close because issue 42 was more detailed.

Original comment by tomoa...@kenroku.kanazawa-u.ac.jp on 25 Jun 2013 at 6:02