On May 6, 2014, at 8:19 PM, Thomas Lumley wrote: > The error message looks as if you need /bin on the end of the path: > it's looking for /usr/local/monetdb/mserver5 but the file is probably > /usr/local/monetdb/bin/mserver5 > > Personally, I start the server from the Terminal command line, per > http://www.monetdb.com/Documentation/monetdbd > > First time only > /usr/local/monetdb/bin/monetdbd create ~/my-dbfarm > > Subsequent times: > Before starting R > /usr/local/monetdb/bin/monetdbd start ~/my-dbfarm
Both of those commands run without error from the Terminal.app command line. When I execute one of the suggested commands in the Documentation page, I get: david-winsemiuss-mac-pro:~ davidwinsemius$ monetdbd get all ~/my-dbfarm -bash: monetdbd: command not found But if I give it a full path it succeeds: david-winsemiuss-mac-pro:~ davidwinsemius$ /usr/local/monetdb/bin/monetdbd get all ~/my-dbfarm property value hostname david-winsemiuss-mac-pro.local dbfarm /Users/davidwinsemius/my-dbfarm status monetdbd[22794] 1.7 (Jan2014-SP1) is serving this dbfarm mserver /usr/local/monetdb/bin/mserver5 logfile /Users/davidwinsemius/my-dbfarm/merovingian.log pidfile /Users/davidwinsemius/my-dbfarm/merovingian.pid sockdir /tmp port 50000 exittimeout 60 forward proxy discovery true discoveryttl 600 control no passphrase <unknown> mapisock /tmp/.s.monetdb.50000 controlsock /tmp/.s.merovingian.50000 So I think I may need to add /usr/local/monetdb/bin/ to my bash PATH. Adding it to my Sys.path may be needed as well because the help page example still fails: > library(MonetDB.R) Loading required package: DBI Loading required package: digest > conn <- dbConnect(MonetDB.R(), "monetdb://localhost/demo") Error in .monetAuthenticate(socket, dbname, user, password, language = language) : Authentication error: !monetdbd: no such database 'demo', please create it first > Sys.getenv()['PATH'] PATH "/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/X11R6/bin" I finally decide that was not needed after working through a bit more of the documentation going back and forth between the bash console and the R console: > conn <- dbConnect(MonetDB.R(), > "monetdb://david-winsemiuss-mac-pro.local/demo") Error in .monetAuthenticate(socket, dbname, user, password, language = language) : Authentication error: !monetdbd: no such database 'demo', please create it first So I tried creating it with: david-winsemiuss-mac-pro:~ davidwinsemius$ /usr/local/monetdb/bin/monetdb create demo created database in maintenance mode: demo > conn <- dbConnect(MonetDB.R(), > "monetdb://david-winsemiuss-mac-pro.local/demo") Error in .monetAuthenticate(socket, dbname, user, password, language = language) : Authentication error: !monetdbd: database 'demo' is under maintenance So I ran the next command from the MonetDB documentation: david-winsemiuss-mac-pro:~ davidwinsemius$ /usr/local/monetdb/bin/monetdb start demo starting database 'demo'... done Then the example code runs: > conn <- dbConnect(MonetDB.R(), > "monetdb://david-winsemiuss-mac-pro.local/demo") > dbListTables(conn) character(0) > data(iris) > dbWriteTable(conn, "iris", iris) [1] TRUE > dbGetQuery(conn, "SELECT COUNT(*) FROM iris;") L1 1 150 > d <- dbReadTable(conn, "iris") > str(d) 'data.frame': 150 obs. of 5 variables: $ sepal_length: num 5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ... $ sepal_width : num 3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ... $ petal_length: num 1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ... $ petal_width : num 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ... $ species : chr "setosa" "setosa" "setosa" "setosa" ... I still need to add the ../monetdb/bin location to my bash PATH, but I think I can figure than out Thank you for your assistance, Thomas. -- David > > After exiting R > /usr/local/monetdb/bin/monetdbd start ~/my-dbfarm > > > -thomas > > > > > On Wed, May 7, 2014 at 2:53 PM, David Winsemius <dwinsem...@comcast.net> > wrote: >> Dear Hannes or anybody; >> >> I did not find any pages (despite searching) for the installation process of >> MonetDB on a Mac. I'm currently running MacOS 10.7.5 and R 3.1.0 Patched >> (2014-04-21 r65431) -- "Spring Dance". There is a source package for MonetDB >> at: >> >> https://www.monetdb.org/downloads/MacOSX/Jan2014-SP1/MonetDB-11.17.13-x86_64-Darwin-9-bin.tar.bz2 >> >> It's home page has direction for installation on Linux and PC but makes no >> mention of Macs. Downloading that file resulted in a couple of automatic >> steps and the creation in my ~/Download/ directory of a hierarchy of >> usr2/local/monetdb >> >> Reading the MacOS R-FAQ in "For R.app you may need to add e.g. >> /usr/local/bin and it is usually most convenient to use command-line R." >> Reasoning that the files in monetdb should actually go into usr/local/ I >> dragged them to that location with Finder.app, and authenticated when >> requested. >> >> (This process failed and I am now looking for instruction on properly >> installing on a Mac. Is this page going to lead me on the path of >> righteousness? >> >> https://developer.apple.com/library/mac/documentation/porting/conceptual/portingunix/compiling/compiling.html >> >> My reading of Mac-SIG leads me to believe that using MacPorts will not be a >> stable strategy for interaction with R. >> >> -- >> David. >> >> ========= failed efforts recorded below ================== >> >> I installed MonetDB.R from R.app using the Package installation dialog with >> "install dependencies" checked. >> >> library(MonetDB.R) # succeeded without complaint and reported: >> >> Loading required package: DBI >> Loading required package: digest >> >> help(package="MonetDB.r") # Trying the Example code in monetdb.server.setup >> >>> startscript <- monetdb.server.setup("/tmp/database","/usr/local/monetdb/", >>> "db1", 50001) >>> pid <- monetdb.server.start(startscript) >> /private/tmp/database/db1.sh: line 2: /usr/local/monetdb/mserver5: No such >> file or directory >> Read 1 item >>> monetdb.server.stop(pid) >> /bin/sh: line 0: kill: (22661) - No such process >>> conn <- dbConnect(MonetDB.R(), "monetdb://localhost:50001/db1") >> Error in .local(drv, ...) : Could not connect to localhost:50001 >> >> >> Then tried the code on the help page for 'MonetDB.R-package' >> >>> conn <- dbConnect(MonetDB.R(), "monetdb://localhost/demo") >> Error in .local(drv, ...) : Could not connect to localhost:50000 >>> dbListTables(conn) >> Error in is(object, Cl) : >> error in evaluating the argument 'conn' in selecting a method for function >> 'dbListTables': Error: object 'conn' not found >>> data(iris) >>> dbWriteTable(conn, "iris", iris) >> Error in is(object, Cl) : >> error in evaluating the argument 'conn' in selecting a method for function >> 'dbWriteTable': Error: object 'conn' not found >>> dbGetQuery(conn, "SELECT COUNT(*) FROM iris;") >> Error in dbGetQuery(conn, "SELECT COUNT(*) FROM iris;") : >> error in evaluating the argument 'conn' in selecting a method for function >> 'dbGetQuery': Error: object 'conn' not found >>> d <- dbReadTable(conn, "iris") >> Error in is(object, Cl) : >> error in evaluating the argument 'conn' in selecting a method for function >> 'dbReadTable': Error: object 'conn' not found >> >> So obviously there is something about this client server setup that I have >> not done properly or understood how to access. I've been through the R-FAQ >> many times and still do not understand the issues surrounding the use of >> homebrew and MacPorts. It's something to do with binary files in the right >> places and I fear this is another instance of such failure. >> >> (I'm also unable to scroll the Mac-FAQ to see the end of the file when the >> window is wider than about 60 characters.) >> -- >> David Winsemius >> Alameda, CA, USA >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > > -- > Thomas Lumley > Professor of Biostatistics > University of Auckland David Winsemius Alameda, CA, USA _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac