Memory usage keep growing until crash - r

Question

I'm running some scripts from R that gets info from some webs. The problems is that even though I clean the session with gc(), the memory keep growing until my session crashes.
Here is the script:
library(XML)
library(RJDBC)
library(RCurl)
procesarPublicaciones <- function(tabla){
log_file <<- file(log_path, open="a")
drv <<- JDBC("oracle.jdbc.OracleDriver", classPath="C:/jdbc/jre6/ojdbc6.jar"," ")
con <<- dbConnect(drv, "server_path", "user", "password")
query <- paste("SELECT * FROM",tabla,sep=' ')
bool <- tryCatch(
{
## Get a list of URLs from a DB
listUrl <- dbGetQuery(con, query)
if( nrow(listUrl) != 0) TRUE else FALSE
dbDisconnect(con)
}, error = function(e) return(FALSE)
)
if( bool ) {
file.create(data_file)
apply(listUrl,c(1),procesarHtml)
}else{
cat("\n",getTime(),"\t[ERROR]\t\t", file=log_file)
}
cat( "\n",getTime(),"\t[INFO]\t\t FINISH", file=log_file)
close(log_file)
}
procesarHtml <- function(pUrl){
headerGatherer <- basicHeaderGatherer()
html <- getURI(theUrl, headerfunction = headerGatherer$update, curl = curlHandle)
heatherValue <- headerGatherer$value()
if ( heatherValue["status"] == "200" ){
doc <- htmlParse(html)
tryCatch
(
{
## Here I get all the info that I need from the web and write it on a file.
## here is a simplification
info1 <- xpathSApply(doc, xPath.info1, xmlValue)
info2 <- xpathSApply(doc, xPath.info2, xmlValue)
data <- data.frame(col1 = info1, col2=info2)
write.table(data, file=data_file , sep=";", row.names=FALSE, col.names=FALSE, append=TRUE)
}, error= function(e)
{
## LOG ERROR
}
)
rm(info1, info2, data, doc)
}else{
## LOG INFO
}
rm(headerGatherer,html,heatherValue)
cat("\n",getTime(),"\t[INFO]\t\t memory used: ", memory.size()," MB", file=log_file)
gc()
cat("\n",getTime(),"\t[INFO]\t\t memory used after gc(): ", memory.size()," MB", file=log_file)
}
Even though I remove all internal variables with rm() and use gc(), memory keeps growing. It seems that all the html that I get from the web is kept in memory.
Here is my Session Info:
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows XP (build 2600) Service Pack 3
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RCurl_1.95-4.6 bitops_1.0-6 RJDBC_0.2-5 rJava_0.9-6 DBI_0.3.1
[6] XML_3.98-1.1
loaded via a namespace (and not attached):
[1] tools_3.2.0
--------------------EDIT 2015-06-08 --------------------
I'm still having the problem, but I found the same issue on other post, which is apparently resolved.
Serious Memory Leak When Iteratively Parsing XML Files

Answer 1

When using the XML package, you'll want to use free() to release the memory allocated by htmlParse() (or any of the other html parsing functions that allocate memory at the C level). I usually place a call to free(doc) as soon as I don't need the html doc any more.
So in your case, I would try placing free(doc) on its own line prior to rm(info1, info2, data, doc) in your function, like this:
free(doc)
rm(info1, info2, data, doc)
In fact the call to free() may be sufficient enough that you could remove the rm() call completely.

Answer 2

I had a related issue using htmlParse. Led to Windows crashing (out of memory) before my 10,000 iterataions completed.
Answer:
in addition to free/remove - do a garbage collect gc() (as suggested in Serious Memory Leak When Iteratively Parsing XML Files ) every n iterations