build fails on CentOS 6.4

[SyBernot]

The following tests FAILED: 6 - testFPB (ILLEGAL) 10 - pyFPB (ILLEGAL)

Digging through the entire build log I see no obvious errors. Any thoughts on how to proceed?

[SyBernot]

5/105 Test #6: testFPB .........................._Exception: Illegal 0.31 sec 9/105 Test #10: pyFPB ............................_Exception: Illegal 0.30 sec

I tried running testFPB directly and got (my-rdkit-env) [root@xxx conda-rdkit]# /root/anaconda2/conda-bld/work/Code/DataStructs/testFPB [12:19:06] ----------------------- Testing FPBReader basics terminate called after throwing an instance of 'std::logic_error' what(): basic_string::_S_construct NULL not valid Aborted

looking at the source it isn't making it out of test1FPBReaderBasics()

[SyBernot]

D'oh (user error) After exporting RDBASE and running testFPB I now get this

[14:22:53] ----------------------- Testing FPBReader basics [14:22:53] Finished [14:22:53] ----------------------- Testing Lazy FPBReader basics [14:22:53] Finished [14:22:53] ----------------------- Testing FPBReader tanimoto Illegal instruction

[rvianello]

I will try to reproduce the error but it would be relevant to know what revision of the RDKit you tried to build, and which branch of the conda-rdkit recipes you used. In case you tried to build the latest RDKit release using the recipes from the master branch, you might then also consider installing the same packages from the rdkit channel on anaconda.org (those packages are built in a centos6 container using the included Dockerfile).

Please note that higher privileges (root) are not required to run the build (or more generically, to use anaconda).

[SyBernot]

2016_03_2 version of rdkit using conda-rdkit conda install conda-build conda install patchelf git clone https://github.com/rdkit/conda-rdkit.git conda build boost conda build rdkit

I set up conda as per instructions on the rdkit page

we have an older version running from rpm but our devs are chasing a feature that's only in the latest release

I'll try your suggestion of conda install -c rdkit rdkit=2016.03.2 tomorrow and see if that buys me anything

[SyBernot]

Seems like we can close this, an install vai miniconda by the developer seems to have made him happy. I still think there is a build issue with CentOS 6.4 but as that's not the latest and greatest it's probably not an issue for most.