In is(object, Cl) : error while fetching rows R - mysql

Question

I have a MySQL table I am attempting to access with R using RMySQL.
There are 1690004 rows that should be returned from
dbGetQuery(con, "SELECT * FROM tablename WHERE export_date ='2015-01-29'")
Unfortunately, I receive the following warning messages:
In is(object, Cl) : error while fetching row
In dbGetQuery(con, "SELECT * FROM tablename WHERE export_date ='2015-01-29'", : pending rows
And only receive ~400K rows.
If I break the query into several "fetches" using dbSendQuery, the warning messages start appearing after ~400K rows are received.
Any help would be appreciated.

Answer 1

So, it looks like it was due to a 60 second timeout imposed by my hosting provider (damn Arvixe!). I got around this by "paging/chunking" the output. Because my data has an auto-incrementing primary key, every row returned is in order, allowing me to take the next X rows after each iteration.
To get 1.6M rows I did the following:
library(RMySQL)
con <- MySQLConnect() # mysql connection function
day <- '2015-01-29' # date of interest
numofids <- 50000 # number of rows to include in each 'chunk'
count <- dbGetQuery(con, paste0("SELECT COUNT(*) as count FROM tablename WHERE export_date = '",day,"'"))$count # get the number of rows returned from the table.
dbDisconnect(con)
ns <- seq(1, count, numofids) # get sequence of rows to work over
tosave <- data.frame() # data frame to bind results to
# iterate through table to get data in 50k row chunks
for(nextseries in ns){ # for each row
print(nextseries) # print the row it's on
con <- MySQLConnect()
d1 <- dbGetQuery(con, paste0("SELECT * FROM tablename WHERE export_date = '",day,"' LIMIT ", nextseries,",",numofids)) # extract data in chunks of 50k rows
dbDisconnect(con)
# bind data to tosave dataframe. (the ifelse is avoid an error when it tries to rbind d1 to an empty dataframe on the first pass).
if(nrow(tosave)>0){
tosave <- rbind(tosave, d1)
}else{
tosave <- d1
}
}