Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

Hi Tim, the "traditional" method for building the PostgreSQL cartridge is still there - you can still build the PostgreSQL cartridge using the Makefile in Code/PgSQL/rdkit using the same procedure as in the previous versions. p. On 19/04/2016 19:21, Tim Dudgeon wrote: All, Paolo helped me

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

All, Paolo helped me off-list to resolve this (many thanks Paolo!). There were a number of things wrong, partly in what I was doing (cmake switches) and partly some problems in CMakeLists.txt that requires a patch until the PR that Paolo has submitted is merged. I'll spare you of all the

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

No, afraid that doesn't seem to help. The boost libs seem to be in /usr/lib/x86_64-linux-gnu but adding that directory to LD_LIBRARY_PATH doesn't fix the problem. In fact, for the plain rdkit image it works fine with just $RDBASE being on LD_LIBRARY_PATH. Tim On 18/04/2016 19:43, Paolo

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

Dear Tim, did you check that the Boost libraries you linked the RDKit against are in the postgres user LD_LIBRARY_PATH? You might need to login as root, then su postgres, and echo "export LD_LIBRARY_PATH=" > ~/.bashrc. Then, as root, restart the postgres service. That fixed the problem for

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

I spoke too soon! I'm still having problem with postgres cartridge. psql -c 'create extension rdkit' rdkitdb ERROR: could not load library "/usr/lib/postgresql/9.4/lib/rdkit.so": /usr/lib/postgresql/9.4/lib/rdkit.so: undefined symbol: _ZTIN5boost6detail16thread_data_baseE Is something else

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

Brian: thanks, adding libboost-system-dev libboost-thread-dev and libboost-serialization-dev solves the problem. Greg: confirmed, flex and bison are not needed. Many thanks. Tim On 17/04/2016 15:28, Greg Landrum wrote: On Sun, Apr 17, 2016 at 2:43 PM, Brian Kelley

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

On Sun, Apr 17, 2016 at 2:43 PM, Brian Kelley wrote: > Now that we made thread safe the default, you also need boost-system ( and > boost-serialization for FilterCatalog serialization) > > Here is the apt get we use to configure docker files. > > apt install -y wget flex

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

Now that we made thread safe the default, you also need boost-system ( and boost-serialization for FilterCatalog serialization) Here is the apt get we use to configure docker files. apt install -y wget flex bison build-essential python-numpy cmake python-dev sqlite3 libsqlite3-dev libboost-dev

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

I've hit the same issue. Any thoughts on what the underlying issue is (without reverting to using anaconda)? An example that illustrates this is here: https://github.com/InformaticsMatters/rdkit Tim On 20/11/2015 16:02, Greg Landrum wrote: Hi Huw, This is not directly responsive to your

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

Hi Greg, Many thanks. I’ll take a look. Huw > On 20 Nov 2015, at 16:02, Greg Landrum wrote: > > Hi Huw, > > This is not directly responsive to your question, but if you're working with > anaconda, it is probably easier to just build and install the RDKit using the >

[Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

Hi there, I’ve been building the Python RDKit modules direct from the GitHub repository recently on an Ubuntu 14.04 LTS VM (i.e. git clone https://github.com/rdkit/rdkit.git). I use the following aptitude packages for the build process: flex2.5.35-10.1ubuntu2 bison 2:3.0.2.dfsg-2

Re: [Rdkit-discuss] Ubuntu 14.04 LTS Build Post Commit 7478e3fd3bee0c20291c2b99776c40a0c7d8a955

Hi Huw, This is not directly responsive to your question, but if you're working with anaconda, it is probably easier to just build and install the RDKit using the conda-rdkit recipes here: https://github.com/rdkit/conda-rdkit The development branch there pulls from master. -greg On Fri, Nov