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external name fits.listdir not bound (sys.listdir) Fatal error during initialization: #6794

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monetdb-team opened this issue Nov 30, 2020 · 0 comments

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@monetdb-team monetdb-team commented Nov 30, 2020

Date: 2019-12-02 08:30:47 +0100
From: wangkk
To: buildtools devs <>
Version: 11.35.3 (Nov2019)
CC: arnold.kuzniar, @PedroTadim, @yzchang

Last updated: 2020-02-16 22:42:03 +0100

Comment 27435

Date: 2019-12-02 08:30:47 +0100
From: wangkk

User-Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/78.0.3904.108 Safari/537.36
Build Identifier:

After I run
shell> monetdbd create /path/to/mydbfarm
shell> monetdbd start /path/to/mydbfarm
shell> monetdb create voc
shell> monetdb release voc
shell> mclient -u monetdb -d voc
It outputs the following:
monetdbd: internal error while starting mserver 'database 'voc' has crashed after starting, manual intervention needed, check monetdbd's logfile (merovingian.log) for details'

Reproducible: Always

Steps to Reproduce:

shell> monetdbd create /path/to/mydbfarm
shell> monetdbd start /path/to/mydbfarm
shell> monetdb create voc
shell> monetdb release voc
shell> mclient -u monetdb -d voc

Actual Results:

In logs:
external name fits.listdir not bound (sys.listdir) Fatal error during initialization:

Comment 27436

Date: 2019-12-02 08:31:14 +0100
From: wangkk

Created attachment 638
logs

Attached file: log.txt (text/plain, 6692 bytes)
Description: logs

Comment 27437

Date: 2019-12-02 09:09:48 +0100
From: @PedroTadim

Hello Wang,

On Nov2019 release, whenever a SQL function defined in MAL is called, the server tests if the MAL definition exists. At your setting, the server attempted to call the SQL procedure listdir from the FITS module, but the MAL definition was not found. Please confirm if the fits.mal script is at lib/monetdb5 directory, as well as the lib_fits.so native library. The latter must be set also on the linker path if not installed at a regular path: LD_LIBRARY_PATH

Comment 27439

Date: 2019-12-02 11:47:09 +0100
From: @yzchang

I can confirm this error. At least, our Debian installer is broken.

I installed MonetDB on a Ubuntu Bionis following the instructions here: https://www.monetdb.org/downloads/deb/

Then when I try to start a fresh database, I got:

$ mserver5 --dbpath=/tmp/test --set mapi_port=60000
MonetDB 5 server v11.35.3 (Nov2019)
...
loading sql script: 72_fits.sql
main thread:!ERROR:ParseException:SQLparser:3F000!CREATE PROCEDURE: external name fits.listdir not bound (sys.listdir)
ParseException:SQLparser:3F000!CREATE PROCEDURE: external name fits.listdir not bound (sys.listdir)Fatal error during initialization:
ParseException:SQLparser:3F000!CREATE PROCEDURE: external name fits.listdir not bound (sys.listdir)

Then, when I try to install the fits lib, I got another error:
$ sudo apt install libmonetdb5-server-cfitsio
...
Unpacking libmonetdb5-server-cfitsio (11.35.3) ...
dpkg: error processing archive /var/cache/apt/archives/libmonetdb5-server-cfitsio_11.35.3_amd64.deb (--unpack):
trying to overwrite '/usr/lib/x86_64-linux-gnu/monetdb5/createdb/72_fits.sql', which is also in package monetdb5-sql 11.35.3
E: Sub-process /usr/bin/dpkg returned an error code (1)

I can workaround this by deleting the file:
$ sudo rm /usr/lib/x86_64-linux-gnu/monetdb5/createdb/72_fits.sql
Now I can start a database

Comment 27440

Date: 2019-12-03 09:58:19 +0100
From: @sjoerdmullender

It seems the file /usr/lib/x86_64-linux-gnu/monetdb5/fits.mal has accidentally been included in the monetdb5-server package. Remove the file from you installation and things should work again.

Note, the file does need to be present if you als install the package libmonetdb5-server-cfitsio.

Comment 27441

Date: 2019-12-03 10:04:48 +0100
From: MonetDB Mercurial Repository <>

Changeset 302e85949ac8 made by Sjoerd Mullender sjoerd@acm.org in the MonetDB repo, refers to this bug.

For complete details, see https//devmonetdborg/hg/MonetDB?cmd=changeset;node=302e85949ac8

Changeset description:

Don't include fits.mal in monetdb5-server package.
This should fix bug #6794.

Comment 27468

Date: 2019-12-09 22:42:58 +0100
From: @sjoerdmullender

In addition to the file mentioned in comment 4, the file /usr/lib/x86_64-linux-gnu/monetdb5/createdb/72_fits.sql needs to be removed as well.

On Fedora systems, the file /usr/lib64/monetdb/createdb/72_fits.sql should be removed.

As in comment 4, don't remove these files if you've actually also installed the MonetDB cfitsio package (libmonetdb5-server-cfitsio on Debian/Ubuntu, MonetDB-cfitsio on Fedora).

Comment 27556

Date: 2020-02-16 22:42:03 +0100
From: @sjoerdmullender

*** Bug #6820 has been marked as a duplicate of this bug. ***

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