On Wed, Jul 01, 2015 at 03:52:23PM +0100, Brian Hood wrote:

Hi Niels,

I didn't have R installed that is not fixed but i still see the same errors.

2015-07-01 14:45:13 MSG threatmonitor[3741]: # MonetDB 5 server v11.19.15 "Oct2014-SP4" 2015-07-01 14:45:13 MSG threatmonitor[3741]: # Serving database 'threatmonitor', using 2 threads 2015-07-01 14:45:13 MSG threatmonitor[3741]: # Compiled for x86_64-unknown-linux-gnu/64bit with 64bit OIDs dynamically linked 2015-07-01 14:45:13 MSG threatmonitor[3741]: # Found 7.411 GiB available main-memory. 2015-07-01 14:45:13 MSG threatmonitor[3741]: # Copyright (c) 1993-July 2008 CWI. 2015-07-01 14:45:13 MSG threatmonitor[3741]: # Copyright (c) August 2008-2015 MonetDB B.V., all rights reserved 2015-07-01 14:45:13 MSG threatmonitor[3741]: # Visit http:// www.monetdb.org/ for further information 2015-07-01 14:45:13 MSG threatmonitor[3741]: !TypeException:user.main [1412]:object code for command rapi.prelude missing 2015-07-01 14:45:13 MSG threatmonitor[3741]: !TypeException:user.main [1412]:'rapi.prelude' undefined in: _1412:void := rapi.prelude() 2015-07-01 14:45:13 MSG merovingian[9]: database 'threatmonitor' (3741) has exited with exit status 0 2015-07-01 14:45:13 MSG merovingian[9]: database 'threatmonitor' has shut down 2015-07-01 14:45:18 ERR merovingian[9]: client error: database 'threatmonitor' started up, but failed to open up a communication channel 2015-07-01 14:46:35 MSG merovingian[9]: caught SIGTERM, starting shutdown sequence 2015-07-01 14:46:38 MSG control[9]: control channel closed

The linking against R shared library looks good. You could check if the RAPIprelude function is in the library (ie if everything compiled correctly). Using nm and grep should something like nm lib_rapi.so |grep RAPIpre 0000000000009bdb T RAPIprelude

Niels

[root@dev-vnc-01 lib]# ldd /usr/lib64/monetdb5/lib_rapi.so linux-vdso.so.1 (0x00007fff843fe000) libmonetdb5.so.17 => /usr/lib/libmonetdb5.so.17 (0x00007fa313eb8000) libmapi.so.7 => /usr/lib/libmapi.so.7 (0x00007fa313c9f000) libuuid.so.1 => /usr/lib/libuuid.so.1 (0x00007fa313a9a000) libreadline.so.6 => /usr/lib/libreadline.so.6 (0x00007fa31384e000) libpcre.so.1 => /usr/lib/libpcre.so.1 (0x00007fa3135de000) libxml2.so.2 => /usr/lib/libxml2.so.2 (0x00007fa313279000) libbat.so.11 => /usr/lib/libbat.so.11 (0x00007fa312ba1000) libstream.so.6 => /usr/lib/libstream.so.6 (0x00007fa312993000) libssl.so.1.0.0 => /usr/lib/libssl.so.1.0.0 (0x00007fa312718000) libcrypto.so.1.0.0 => /usr/lib/libcrypto.so.1.0.0 (0x00007fa3122a0000) libcurl.so.4 => /usr/lib/libcurl.so.4 (0x00007fa31202c000) libz.so.1 => /usr/lib/libz.so.1 (0x00007fa311e16000) libbz2.so.1.0 => /usr/lib/libbz2.so.1.0 (0x00007fa311c05000) libR.so => /usr/lib/libR.so (0x00007fa311662000) liblzma.so.5 => /usr/lib/liblzma.so.5 (0x00007fa31143c000) librt.so.1 => /usr/lib/librt.so.1 (0x00007fa311233000) libdl.so.2 => /usr/lib/libdl.so.2 (0x00007fa31102f000) libm.so.6 => /usr/lib/libm.so.6 (0x00007fa310d2b000) libicuuc.so.55 => /usr/lib/libicuuc.so.55 (0x00007fa310997000) libicui18n.so.55 => /usr/lib/libicui18n.so.55 (0x00007fa310531000) libatomic_ops.so.1 => /usr/lib/libatomic_ops.so.1 (0x00007fa31032e000) libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007fa310110000) libc.so.6 => /usr/lib/libc.so.6 (0x00007fa30fd6e000) /usr/lib64/ld-linux-x86-64.so.2 (0x00007fa31456f000) libncursesw.so.5 => /usr/lib/libncursesw.so.5 (0x00007fa30fb08000) libidn.so.11 => /usr/lib/libidn.so.11 (0x00007fa30f8d4000) libssh2.so.1 => /usr/lib/libssh2.so.1 (0x00007fa30f6a9000) libgssapi_krb5.so.2 => /usr/lib/libgssapi_krb5.so.2 (0x00007fa30f45c000) libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0x00007fa30f177000) libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0x00007fa30ef43000) libcom_err.so.2 => /usr/lib/libcom_err.so.2 (0x00007fa30ed3f000) libRblas.so => /usr/lib/libRblas.so (0x00007fa30eb12000) libgomp.so.1 => /usr/lib/libgomp.so.1 (0x00007fa30e8ef000) libicudata.so.55 => /usr/lib/libicudata.so.55 (0x00007fa30ce39000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007fa30cab6000) libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007fa30c8a0000) libkrb5support.so.0 => /usr/lib/libkrb5support.so.0 (0x00007fa30c693000) libkeyutils.so.1 => /usr/lib/libkeyutils.so.1 (0x00007fa30c48e000) libresolv.so.2 => /usr/lib/libresolv.so.2 (0x00007fa30c277000)

Regards,

Brian Hood

On Wed, Jul 1, 2015 at 2:12 PM, Niels Nes wrote:

On Wed, Jul 01, 2015 at 02:06:47PM +0100, Brian Hood wrote: > Hi All, > > I seems when i look at the output i of the error log it seems there are > missing methods, i have seen this as a bug report from a while ago > online but i can't see the see the solution. > > Any ideas ? wild guess, you didn't install R?

Niels > > [root@dev-vnc-01 /]# monetdbd start /var/monetdb5/dbfarm > > [root@dev-vnc-01 /]#  > [root@dev-vnc-01 /]# monetdb status >     name       state   health                      remarks > threatmonitor  S  5d  100%  7s  mapi:monetdb://dev-vnc-01:50000/ > threatmonitor > [root@dev-vnc-01 /]# monetdb start threatmonitor > starting database 'threatmonitor'... FAILED > start: starting 'threatmonitor' failed: database 'threatmonitor' > started up, but failed to open up a communication channel > [root@dev-vnc-01 /]# pacman -Q monetdb > monetdb 11.19.15-1 > [root@dev-vnc-01 /]# monetdb -v > MonetDB Database Server Toolkit v1.1 (Oct2014-SP4) > [root@dev-vnc-01 /]# tail -70 /var/monetdb5/dbfarm/ merovingian.log  > 2015-06-25 23:31:58 MSG merovingian[293]: monitoring dbfarm /var/ > monetdb5/dbfarm > 2015-06-25 23:32:18 MSG merovingian[293]: accepting connections on TCP > socket 0.0.0.0:50000 > 2015-06-25 23:32:18 MSG merovingian[293]: accepting connections on UNIX > domain socket /tmp/.s.monetdb.50000 > 2015-06-25 23:32:38 MSG discovery[293]: listening for UDP messages on > 0.0.0.0:50000 > 2015-06-25 23:32:38 MSG control[293]: accepting connections on UNIX > domain socket /tmp/.s.merovingian.50000 > 2015-06-25 23:32:38 MSG discovery[293]: new neighbour dev-vnc-01 > (dev-vnc-01) > 2015-06-25 23:32:53 MSG control[293]: (local): created database > 'threatmonitor' > 2015-06-25 23:32:59 MSG control[293]: (local): served status list > 2015-06-25 23:32:59 MSG control[293]: (local): released database > 'threatmonitor' > 2015-06-25 23:32:59 MSG discovery[293]: new database mapi:monetdb:// > dev-vnc-01:50000/threatmonitor (ttl=660s) > 2015-06-25 23:33:08 MSG merovingian[293]: starting database > 'threatmonitor', up min/avg/max: 0s/0s/0s, crash average: 0.00 0.00 > 0.00 (0-0=0) > 2015-06-25 23:33:08 MSG merovingian[293]: sending process 304 (database > 'threatmonitor') the TERM signal > 2015-06-25 23:33:08 MSG threatmonitor[304]: arguments: /usr/bin/ > mserver5 --dbpath=/var/monetdb5/dbfarm/threatmonitor --set > merovingian_uri=mapi:monetdb://dev-vnc-01:50000/threatmonitor --set > mapi_open=false --set mapi_port=0 --set mapi_usock=/var/monetdb5/ dbfarm > /threatmonitor/.mapi.sock --set monet_vault_key=/var/monetdb5/ dbfarm/ > threatmonitor/.vaultkey --set gdk_nr_threads=2 --set max_clients= 64 > --set sql_optimizer=default_pipe --set monet_daemon=yes > 2015-06-25 23:33:08 MSG threatmonitor[304]: # MonetDB 5 server > v11.19.15 "Oct2014-SP4" > 2015-06-25 23:33:08 MSG threatmonitor[304]: # Serving database > 'threatmonitor', using 2 threads > 2015-06-25 23:33:08 MSG threatmonitor[304]: # Compiled for > x86_64-unknown-linux-gnu/64bit with 64bit OIDs dynamically linked > 2015-06-25 23:33:08 MSG threatmonitor[304]: # Found 7.411 GiB available > main-memory. > 2015-06-25 23:33:08 MSG threatmonitor[304]: # Copyright (c) 1993-July > 2008 CWI. > 2015-06-25 23:33:08 MSG threatmonitor[304]: # Copyright (c) August > 2008-2015 MonetDB B.V., all rights reserved > 2015-06-25 23:33:08 MSG threatmonitor[304]: # Visit http:// > www.monetdb.org/ for further information > 2015-06-25 23:33:08 MSG threatmonitor[304]: ! TypeException:user.main > [1412]:object code for command rapi.prelude missing > 2015-06-25 23:33:08 MSG threatmonitor[304]: ! TypeException:user.main > [1412]:'rapi.prelude' undefined in: _1412:void := rapi.prelude() > 2015-06-25 23:33:08 MSG merovingian[293]: database 'threatmonitor' > (304) has exited with exit status 0 > 2015-06-25 23:33:08 MSG merovingian[293]: database 'threatmonitor' has > shut down > 2015-06-25 23:33:08 ERR merovingian[293]: client error: database > 'threatmonitor' started up, but failed to open up a communication > channel > 2015-06-25 23:33:08 MSG merovingian[293]: starting database > 'threatmonitor', up min/avg/max: 0s/0s/0s, crash average: 0.00 0.00 > 0.00 (1-1=0) > 2015-06-25 23:33:09 MSG merovingian[293]: sending process 307 (database > 'threatmonitor') the TERM signal > 2015-06-25 23:33:09 MSG threatmonitor[307]: arguments: /usr/bin/ > mserver5 --dbpath=/var/monetdb5/dbfarm/threatmonitor --set > merovingian_uri=mapi:monetdb://dev-vnc-01:50000/threatmonitor --set > mapi_open=false --set mapi_port=0 --set mapi_usock=/var/monetdb5/ dbfarm > /threatmonitor/.mapi.sock --set monet_vault_key=/var/monetdb5/ dbfarm/ > threatmonitor/.vaultkey --set gdk_nr_threads=2 --set max_clients= 64 > --set sql_optimizer=default_pipe --set monet_daemon=yes > 2015-06-25 23:33:09 MSG threatmonitor[307]: # MonetDB 5 server > v11.19.15 "Oct2014-SP4" > 2015-06-25 23:33:09 MSG threatmonitor[307]: # Serving database > 'threatmonitor', using 2 threads > 2015-06-25 23:33:09 MSG threatmonitor[307]: # Compiled for > x86_64-unknown-linux-gnu/64bit with 64bit OIDs dynamically linked > 2015-06-25 23:33:09 MSG threatmonitor[307]: # Found 7.411 GiB available > main-memory. > 2015-06-25 23:33:09 MSG threatmonitor[307]: # Copyright (c) 1993-July > 2008 CWI. > 2015-06-25 23:33:09 MSG threatmonitor[307]: # Copyright (c) August > 2008-2015 MonetDB B.V., all rights reserved > 2015-06-25 23:33:09 MSG threatmonitor[307]: # Visit http:// > www.monetdb.org/ for further information > 2015-06-25 23:33:09 MSG threatmonitor[307]: ! TypeException:user.main > [1412]:object code for command rapi.prelude missing > 2015-06-25 23:33:09 MSG threatmonitor[307]: ! TypeException:user.main > [1412]:'rapi.prelude' undefined in: _1412:void := rapi.prelude() > 2015-06-25 23:33:09 MSG merovingian[293]: database 'threatmonitor' > (307) has exited with exit status 0 > 2015-06-25 23:33:09 MSG merovingian[293]: database 'threatmonitor' has > shut down > 2015-06-25 23:33:13 ERR merovingian[293]: client error: database > 'threatmonitor' started up, but failed to open up a communication > channel > 2015-06-26 00:08:20 MSG control[293]: (local): served status list > 2015-06-26 00:08:20 ERR control[293]: (local): received stop signal for > non running database: threatmonitor > 2015-06-26 00:08:29 MSG merovingian[293]: caught SIGTERM, starting > shutdown sequence > 2015-06-26 00:08:30 MSG control[293]: control channel closed > 2015-06-26 00:08:31 MSG merovingian[293]: Merovingian 1.7 stopped > 2015-07-01 12:57:10 MSG merovingian[9]: Merovingian 1.7 (Oct2014-SP4) > starting > 2015-07-01 12:57:10 MSG merovingian[9]: monitoring dbfarm /var/ monetdb5 > /dbfarm > 2015-07-01 12:57:30 MSG merovingian[9]: accepting connections on TCP > socket 0.0.0.0:50000 > 2015-07-01 12:57:30 MSG merovingian[9]: accepting connections on UNIX > domain socket /tmp/.s.monetdb.50000 > 2015-07-01 12:57:50 MSG discovery[9]: listening for UDP messages on > 0.0.0.0:50000 > 2015-07-01 12:57:50 MSG control[9]: accepting connections on UNIX > domain socket /tmp/.s.merovingian.50000 > 2015-07-01 12:57:50 MSG discovery[9]: new neighbour dev-vnc-01 > (dev-vnc-01) > 2015-07-01 12:57:50 MSG discovery[9]: new database mapi:monetdb:/ / > dev-vnc-01:50000/threatmonitor (ttl=660s) > 2015-07-01 12:57:54 MSG control[9]: (local): served status list > 2015-07-01 12:58:03 MSG control[9]: (local): served status list > 2015-07-01 12:58:03 MSG merovingian[9]: starting database > 'threatmonitor', up min/avg/max: 0s/7s/27s, crash average: 0.00 0.00 > 0.00 (10-10=0) > 2015-07-01 12:58:03 MSG merovingian[9]: sending process 15 (database > 'threatmonitor') the TERM signal > 2015-07-01 12:58:03 MSG threatmonitor[15]: arguments: /usr/bin/ mserver5 > --dbpath=/var/monetdb5/dbfarm/threatmonitor --set merovingian_uri = > mapi:monetdb://dev-vnc-01:50000/threatmonitor --set mapi_open= false > --set mapi_port=0 --set mapi_usock=/var/monetdb5/dbfarm/ threatmonitor > /.mapi.sock --set monet_vault_key=/var/monetdb5/dbfarm/ threatmonitor > /.vaultkey --set gdk_nr_threads=2 --set max_clients=64 --set > sql_optimizer=default_pipe --set monet_daemon=yes > 2015-07-01 12:58:03 MSG threatmonitor[15]: # MonetDB 5 server v11.19.15 > "Oct2014-SP4" > 2015-07-01 12:58:03 MSG threatmonitor[15]: # Serving database > 'threatmonitor', using 2 threads > 2015-07-01 12:58:03 MSG threatmonitor[15]: # Compiled for > x86_64-unknown-linux-gnu/64bit with 64bit OIDs dynamically linked > 2015-07-01 12:58:03 MSG threatmonitor[15]: # Found 7.411 GiB available > main-memory. > 2015-07-01 12:58:03 MSG threatmonitor[15]: # Copyright (c) 1993-July > 2008 CWI. > 2015-07-01 12:58:03 MSG threatmonitor[15]: # Copyright (c) August > 2008-2015 MonetDB B.V., all rights reserved > 2015-07-01 12:58:03 MSG threatmonitor[15]: # Visit http:// > www.monetdb.org/ for further information > 2015-07-01 12:58:03 MSG threatmonitor[15]: ! TypeException:user.main > [1412]:object code for command rapi.prelude missing > 2015-07-01 12:58:03 MSG threatmonitor[15]: ! TypeException:user.main > [1412]:'rapi.prelude' undefined in: _1412:void := rapi.prelude() > 2015-07-01 12:58:03 MSG merovingian[9]: database 'threatmonitor' (15) > has exited with exit status 0 > 2015-07-01 12:58:03 MSG merovingian[9]: database 'threatmonitor' has > shut down > 2015-07-01 12:58:03 ERR control[9]: (local): failed to fork mserver: > database 'threatmonitor' started up, but failed to open up a > communication channel > > Regards, > > Brian Hood

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-- Niels Nes, Manager ITF, Centrum Wiskunde & Informatica (CWI) Science Park 123, 1098 XG Amsterdam, The Netherlands room L3.14,  phone ++31 20 592-4098     sip:4098@sip.cwi.nl url: https://www.cwi.nl/people/niels    e-mail: Niels.Nes@cwi.nl

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_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- Niels Nes, Manager ITF, Centrum Wiskunde & Informatica (CWI) Science Park 123, 1098 XG Amsterdam, The Netherlands room L3.14, phone ++31 20 592-4098 sip:4098@sip.cwi.nl url: https://www.cwi.nl/people/niels e-mail: Niels.Nes@cwi.nl