无法在MonetDB.R中建立与本地数据库的连接

Question

The title summarizes my problem, I think. I'd appreciate any pointers anybody might have on what else I could try. I've pasted the console output with comments in bold below. Theinstalled version of MonetDB.R is the latest from R-forge (0.8.5).

fabians@wap27:~$ R

[...]

> library(MonetDB.R)   
Loading required package: DBI
Loading required package: digest

Attaching package: ‘MonetDB.R’

The following objects are masked from ‘package:stats’:

    sd, var

The following objects are masked from ‘package:base’:

    sample, tabulate

> sessionInfo()
R version 3.0.2 (2013-09-25)
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] MonetDB.R_0.8.5 digest_0.6.3    DBI_0.2-7      
> 
> # as @ https://github.com/ajdamico/usgsd/tree/master/MonetDB:
> batfile <- monetdb.server.setup(
+         database.directory = "~/monetdb",
+         monetdb.program.path = "/usr",
+         dbname = "test",
+         dbport = 50000L)
/home/fabians/monetdb did not exist.  now it does

seems to have worked...

>
> batfile <- "/home/fabians/monetdb/test.sh"

> system(paste("cat ", batfile))
#!/bin/sh
/usr/bin/mserver5 --set prefix=/usr --set exec_prefix=/usr --dbpath /home/fabians/monetdb/test --set mapi_port=50000 --daemon yes > /dev/null &
echo $! > /home/fabians/monetdb/mserver5.started.from.R.pid

Can anybody tell me whether that shell script looks like it's supposed to?

> system(paste("ls ~/monetdb"))
test  test.sh

OK, so an (empty) 'test'-directory was created along with the .sh

> monetpid <- monetdb.server.start(batfile)
Read 1 item
> system(paste("ls ~/monetdb/test"))
00e3bc31-ca59-43e6-ace8-a96aac37bddd  bat  box

Now after starting the monetdb server the test directory contains the data base info, I guess?

> dbname <- "test"
> dbport <- 50000L
> monet.url <- paste0("monetdb://localhost/", dbname)
> db <- dbConnect( MonetDB.R(), monet.url, 
+                  port=as.integer(dbport), timeout=as.integer(86400))
Error in .monetAuthenticate(socket, dbname, user, password) : 
  Authentication error: !monetdbd: no such database 'test', please create it first

What could be the reason that the test-directory is not found?

Slightly different command, as in the help for monetdb.server.start and also at https://github.com/ajdamico/usgsd/tree/master/MonetDB :

> monet.url <- paste0("monetdb://localhost:", dbport, "/", dbname)
> db <- dbConnect( MonetDB.R(), monet.url, wait = TRUE )
R: mapi.c:72: mapiConnect: Assertion `Rf_isInteger(port)' failed.
Aborted

This bug is supposed to have been fixed, see here ...

Answer 1

The reason for the error is that you have monetdbd still running on port 50000, which is why the mserver5 process spawned by monetdb.server.start cannot bind to it. So either choose a different port in monetdb.server.setup (eg 50001) or kill monetdbd before calling monetdb.server.start. Perhaps we could add a check to monetdb.server.setup to make sure no process is listening on the specified port...