Dear Greg,
I can again reproduce the Postgres 9.1 issue, this time in a brand new
64-bit VM.
Ubuntu 10.04.2 x86_64 server installed from scratch.
gnome-desktop-environment installed, VMware tools installed.
jhje@ubuntu-x64-build:~$ cat /etc/issue
Ubuntu 10.04.2 LTS \n \l
jhje@ubuntu-x64-build:~$ uname -a
Linux ubuntu-x64-build 2.6.32-28-server #55-Ubuntu SMP Mon Jan 10
23:57:16 UTC 2011 x86_64 GNU/Linux
jhje@ubuntu-x64-build:~$
Packages build-essential, bison, flex, boost libraries, numpy, cmake
installed.
RDKit_2012_03_1 builds (after the needed one-line patch to Wrap.h) and
all tests pass.
Installed OpenSCG postgresql 9.1.3 package (latest postgres for Ubuntu
10.04.2 is Pg 8.5, so not interesting).
Set "trust" authentication for local connections in pg_hba.conf so rdkit
postgres test suite can run without prompting for password.
postgres@ubuntu-x64-build:~$ createuser jhje
Shall the new role be a superuser? (y/n) y
postgres@ubuntu-x64-build:~$
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ .
/opt/postgres/9.1/pg91-openscg.env
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make
... builds with the usual 3-4 warnings ...
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ sudo su -
[sudo] password for jhje:
root@ubuntu-x64-build:~# cd /home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/
root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# .
/opt/postgres/9.1/pg91-openscg.env
root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# make
install
/bin/mkdir -p '/opt/postgres/9.1/lib/postgresql'
/bin/mkdir -p '/opt/postgres/9.1/share/postgresql/extension'
/bin/sh
/opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh
-c -m 755 rdkit.so '/opt/postgres/9.1/lib/postgresql/rdkit.so'
/bin/sh
/opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh
-c -m 644 ./rdkit.control '/opt/postgres/9.1/share/postgresql/extension/'
/bin/sh
/opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh
-c -m 644 ./rdkit--3.1.sql '/opt/postgres/9.1/share/postgresql/extension/'
root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit#
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make installcheck
/opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress
--inputdir=. --psqldir='/opt/postgres/9.1/bin'
--dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91
sfpgist slfpgist fps
(using postmaster on Unix socket, port 5432)
============== dropping database "contrib_regression" ==============
NOTICE: database "contrib_regression" does not exist, skipping
DROP DATABASE
============== creating database "contrib_regression" ==============
CREATE DATABASE
ALTER DATABASE
============== running regression test queries ==============
test rdkit-91 ... FAILED (test process exited with exit
code 2)
test props ... FAILED
test btree ... FAILED
test molgist ... FAILED
test bfpgist-91 ... FAILED
test sfpgist ... FAILED
test slfpgist ... FAILED
test fps ... FAILED
======================
8 of 8 tests failed.
======================
The differences that caused some tests to fail can be viewed in the
file "/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/regression.diffs". A
copy of the test summary that you see
above is saved in the file
"/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/regression.out".
make: *** [installcheck] Error 1
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ less
regression.diffs
[... ...]
--- 4,9 ----
--
SET client_min_messages = warning;
\set ECHO none
! FATAL: failed to initialize rdkit.dice_threshold to 0.5
! FATAL: failed to initialize rdkit.dice_threshold to 0.5
! connection to server was lost
OK, this time around it is the dice_threshold instead of the
tanimoto_threshold that cannot be initialized, but still...
Hmmm... 'less' is reporting a linking issue, but only when the postgres
environment has been loaded:
jhje@ubuntu-x64-build:~$ less
Missing filename ("less --help" for help)
jhje@ubuntu-x64-build:~$ . /opt/postgres/9.1/pg91-openscg.env
jhje@ubuntu-x64-build:~$ less
less: Symbol `ospeed' has different size in shared object, consider
re-linking
Missing filename ("less --help" for help)
jhje@ubuntu-x64-build:~$ echo $LD_LIBRARY_PATH
/opt/postgres/9.1/lib:
jhje@ubuntu-x64-build:~$
Could a library conflict be what causes rdkit to abort ?
Kind regards
-- Jan
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