[Rdkit-discuss] ctest of new build - testGrid
Dear RDKitters, when running ctest on a new build, I run into an issue when it comes to testGrid - this step takes ages and does not stop... Of course, I checked the mail archive and found out some related problems: * --output-on-failure does not give any additional information Simply executing testGrid from Code/Geometry gives: *** Testing Grid - testUniformGrid1 - testUniformGrid2 - testUniformGridPickling Some other tests (prior to the testGrid part) do fail, which should be related to an LD_LIBRARY_PATH / PYTHONPATH setting, according to: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01332.html http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg02269.html But I guess that it makes sense to first solve the testGrid issue, or are the topics related to each other? Cheers Thanks, Paul This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.
Hi, I am having problems install the Postgres cartridge in Postgres 9.1 on Linux Mint 12 (which is based on Ubuntu 11.10). RDKit 2012_03_1 builds without any issues and all tests pass. The PgSQL cartridge builds fine too, and installs fine as seen below. jhje@linux-dev-x86 ~/RDKit_2012_03_1/Code/PgSQL/rdkit $ sudo make install /bin/mkdir -p '/usr/lib/postgresql/9.1/lib' /bin/mkdir -p '/usr/share/postgresql/9.1/extension' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 755 rdkit.so '/usr/lib/postgresql/9.1/lib/rdkit.so' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit.control '/usr/share/postgresql/9.1/extension/' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit--3.1.sql '/usr/share/postgresql/9.1/extension/' jhje@linux-dev-x86 ~/RDKit_2012_03_1/Code/PgSQL/rdkit $ However, the make installcheck step fails. In the regression.diffs I see: [... tons of lines ...] --- 4,9 -- SET client_min_messages = warning; \set ECHO none ! FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 ! FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 ! connection to server was lost The same thing happens when I try to enable the 'rdkit' extension directly. postgres@linux-dev-x86 ~ $ psql psql (9.1.3) Type help for help. postgres=# create extension rdkit; FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 The connection to the server was lost. Attempting reset: Succeeded. postgres=# /var/log/postgresql/postgres-9.1-main-log doesn't tell me anything extra: 2012-04-24 18:23:32 CEST LOG: invalid value for parameter rdkit.tanimoto_threshold: 0.5 2012-04-24 18:23:32 CEST STATEMENT: create extension rdkit; 2012-04-24 18:23:32 CEST FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 2012-04-24 18:23:32 CEST STATEMENT: create extension rdkit; Being in Denmark, I suspected regional settings, but apparently it is not the issue (?): postgres=# select 7.0/3; ?column? 2. (1 row) postgres=# \q The decimal separator used in Postgres is a period, not a comma as I feared. Any help appreciated :-). Cheers -- Jan Holst Jensen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.
Dear Jan, On Tue, Apr 24, 2012 at 6:55 PM, Jan Holst Jensen j...@biochemfusion.com wrote: Hi, I am having problems install the Postgres cartridge in Postgres 9.1 on Linux Mint 12 (which is based on Ubuntu 11.10). RDKit 2012_03_1 builds without any issues and all tests pass. good so far. The PgSQL cartridge builds fine too, and installs fine as seen below. jhje@linux-dev-x86 ~/RDKit_2012_03_1/Code/PgSQL/rdkit $ sudo make install /bin/mkdir -p '/usr/lib/postgresql/9.1/lib' /bin/mkdir -p '/usr/share/postgresql/9.1/extension' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 755 rdkit.so '/usr/lib/postgresql/9.1/lib/rdkit.so' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit.control '/usr/share/postgresql/9.1/extension/' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit--3.1.sql '/usr/share/postgresql/9.1/extension/' jhje@linux-dev-x86 ~/RDKit_2012_03_1/Code/PgSQL/rdkit $ That also looks ok The same thing happens when I try to enable the 'rdkit' extension directly. postgres@linux-dev-x86 ~ $ psql psql (9.1.3) Type help for help. postgres=# create extension rdkit; FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 The connection to the server was lost. Attempting reset: Succeeded. postgres=# This is an error message that's been reported before, but we never really did find a root cause. I will start from scratch on my VM with Ubuntu 11.10 and take careful notes as I'm doing the installation, then post those on the wiki. I don't have time to do it this morning, but I'll try and get to it tonight or tomorrow a.m. Best, -greg -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
