crash on multiple queries to postgresql db [solved]

An off-list guess is, ironically, to NOT call dbDisconnect or gc().

The C code in the package registers a 'finalizer' that gets called when the
object is garbage collected. This is the same code that gets called by
dbDisconnect. Unfortunately, the code does not check to see if it's been
called already, so I think it's trying to double-close the db connection. By
removing dbDisconnect and gc(), the object gets garbage collected eventually
(when gc() is called, perhaps implicitly, after the function exits and there
are no longer any references to conn).

I think the other strategy is to remove dbDisconnect() and instead say
rm(conn); gc() so that the gc() is the only one that triggers the finalizer.

Martin

Dylan Beaudette wrote:

On Friday 09 January 2009, Joe Conway wrote:

Dylan Beaudette wrote:

Subsequent calls to:

conn <- dbConnect(PgSQL(), host="localhost", dbname="xxx", user="xxx")
query <- dbSendQuery(conn, query_text)
res <- dbGetResult(query)

are resulting in this:

*** glibc detected *** /usr/local/lib/R/bin/exec/R: realloc(): invalid

other attached packages:
[1] RdbiPgSQL_1.8.0 Rdbi_1.8.0      lattice_0.17-20

Any ideas?

Well, first off, since you are apparently using RdbiPgSQL from
bioconductor, you should probably try asking there.

But in any case, you might try the latest release from bioconductor:

http://www.bioconductor.org/packages/release/bioc/src/contrib/RdbiPgSQL_1.1
6.0.tar.gz

or else try the recently released PostgreSQL DBI package on CRAN:
http://cran.stat.ucla.edu/src/contrib/RPostgreSQL_0.1-3.tar.gz

HTH,

Joe

Thanks Joe. I have updated all of my R packages, along with my
Bioconductor packages... and I still get the odd behavior:

*** glibc detected *** /usr/local/lib/R/bin/exec/R: realloc(): invalid old
size: 0xb7dad1e0 ***
======= Backtrace: =========
/lib/i686/cmov/libc.so.6[0xb7cc3624]
/lib/i686/cmov/libc.so.6[0xb7cc71a1]
/lib/i686/cmov/libc.so.6(realloc+0x106)[0xb7cc7b46]
/usr/local/pgsql/lib/libpq.so.5[0xb7802166]
/usr/local/pgsql/lib/libpq.so.5[0xb780239c]
/usr/local/pgsql/lib/libpq.so.5[0xb77fbd31]
/usr/local/pgsql/lib/libpq.so.5(PQfinish+0x15)[0xb77fbe85]

/usr/local/lib/R/site-library/RdbiPgSQL/libs/RdbiPgSQL.so(PgSQLcloseConnection+0x38)
[0xb783bb98]

Again, here is my session info:

R version 2.8.0 (2008-10-20) i686-pc-linux-gnu
locale:

LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
 [8] base
other attached packages:
[1] RdbiPgSQL_1.16.0 Rdbi_1.16.0      lattice_0.17-20


Here is the code that appears to be causing the problems:

# load data from a PostGreSQL database, and return a dataframe
# this will get called whenever the parent function is called
# crashes after 3-5 subsequent calls
load_sensor_data <- function(query_text)
{

# conn becomes an object which contains the DB connection:
conn <- dbConnect(PgSQL(), host="localhost", dbname="SJER", user="dylan")

## pre-filter out possible bad data:
query <- dbSendQuery(conn, query_text)

# fetch data according to query:
res <- dbGetResult(query)
# convert characters to factors
res <- transform(res, probe_id = factor(probe_id))
res <- transform(res, pedon_id = factor(pedon_id))

# generate a new date-time object in the dataframe
res$date <- as.POSIXct(strptime(res$date_time, format="%a %b %e %H:%M:%S
%Y"))

# cleanup
dbDisconnect(conn)

# doesn't completely fix problem crashing
gc()

# return the resulting dataframe
return(res)
}


Thanks in advance,

Dylan

--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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