Thanks for that feedback; when I am back in the office this weekend I will take a look at the Mac conda install and see if we can fix this with some specified dependencies
On Wed, 10 Apr 2019 at 01:20, Drew Gibson <drew.gibso...@googlemail.com> wrote: > Hi, > > I'm using the 2019-03.1 conda build of the new version of rdkit-postgresql > on macOS Mohave 10.14.4. > > just FYI, I got the following error when trying to create the cartridge > extension in a postgresql chembl_25 instance in the conda build - > > chembl_25=# create extension if not exists rdkit; > ERROR: could not load library > "/Users/drew/anaconda3/envs/rdkit-psql-2019/lib/rdkit.so": > dlopen(/Users/drew/anaconda3/envs/rdkit-psql-2019/lib/rdkit.so, 10): > Library not loaded: @rpath/libboost_system.dylib > Referenced from: /Users/drew/anaconda3/envs/rdkit-psql-2019/lib/rdkit.so > Reason: image not found > > I couldn't see "libboost_system.dylib" in my conda environment /lib > directory, so I installed anaconda boost and it fixed the problem - (from > within the conda environment) > > conda install -c anaconda boost > > chembl_25=# create extension if not exists rdkit; > CREATE EXTENSION > chembl_25=# > > I then followed the other commands in the rdkit docs to create some > fingerprints and build the similarity search index - all seems to be > working ok. > > Cheers, Drew > > > > > > On Tue, 9 Apr 2019 at 04:42, Greg Landrum <greg.land...@gmail.com> wrote: > >> Dear all, >> >> I'm pleased to announce that the next version of the RDKit - 2019.03 - is >> released. The release notes are below. >> >> The release files are on the github release page: >> https://github.com/rdkit/rdkit/releases/tag/Release_2019_03_1 >> >> Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit). >> The available conda binaries for this release are: >> Linux 64bit: python 3.6, 3.7 >> Mac OS 64bit: python 3.6, 3.7 >> Windows 64bit: python 3.6, 3.7 >> >> I believe that conda-forge will also switch to the new version in the >> near future. >> >> Please note that the RDKit no longer supports Python 2.7. More details on >> this here: >> >> https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08354.html >> >> I plan to put conda builds of the PostgreSQL cartridge up in the near >> future. >> >> The online version of the documentation at rdkit.org ( >> http://rdkit.org/docs/index.html) has been updated. >> >> Some things that will be finished over the next couple of days: >> - The conda build scripts will be updated to reflect the new version >> - The homebrew script >> >> Thanks to everyone who submitted code, bug reports, and suggestions for >> this release! >> >> Please let me know if you find any problems with the release or have >> suggestions for the next one, which is scheduled for October 2019. >> >> Best Regards, >> -greg >> >> # Release_2019.03.1 >> (Changes relative to Release_2018.09.1) >> >> ## REALLY IMPORTANT ANNOUNCEMENT >> - As of this realease (2019.03.1) the RDKit no longer supports Python 2. >> Please >> read this rdkit-discuss post to learn what your options are if you need >> to >> keep using Python 2: >> >> https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08354.html >> >> ## Backwards incompatible changes >> - The fix for github #2245 means that the default behavior of the >> MaxMinPicker >> is now truly random. If you would like to reproduce the previous >> behavior, >> provide a seed value of 42. >> - The uncharging method in the MolStandardizer now attempts to generate >> canonical results for a given molecule. This may result in different >> output >> for some molecules. >> >> ## Highlights: >> - There's now a Japanese translation of large parts of the RDKit >> documentation >> - SGroup data can now be read from and written to Mol/SDF files >> - The enhanced stereo handling has been improved: the information is now >> accessible from Python, EnumerateStereoisomers takes advantage of it, >> and it >> can be read from and written to CXSmiles >> >> ## Acknowledgements: >> Michael Banck, Francois Berenger, Thomas Blaschke, Brian Cole, Andrew >> Dalke, >> Bakary N'tji Diallo, Guillaume Godin, Anne Hersey, Jan Holst Jensen, >> Sunhwan Jo, >> Brian Kelley, Petr Kubat, Karl Leswing, Susan Leung, John Mayfield, Adam >> Moyer, >> Dan Nealschneider, Noel O'Boyle, Stephen Roughley, Takayuki Serizawa, >> Gianluca >> Sforna, Ricardo Rodriguez Schmidt, Gianluca Sforna, Matt Swain, Paolo >> Tosco, >> Ricardo Vianello, 'John-Videogames', 'magattaca', 'msteijaert', >> 'paconius', >> 'sirbiscuit' >> >> ## Bug Fixes: >> - PgSQL: fix boolean definitions for Postgresql 11 >> (github pull #2129 from pkubatrh) >> - update fingerprint tutorial notebook >> (github pull #2130 from greglandrum) >> - Fix typo in RecapHierarchyNode destructor >> (github pull #2137 from iwatobipen) >> - SMARTS roundtrip failure >> (github issue #2142 from mcs07) >> - Error thrown in rdMolStandardize.ChargeParent >> (github issue #2144 from paconius) >> - SMILES parsing inconsistency based on input order >> (github issue #2148 from coleb) >> - MolDraw2D: line width not in python wrapper >> (github issue #2149 from greglandrum) >> - Missing Python API Documentation >> (github issue #2158 from greglandrum) >> - PgSQL: mol_to_svg() changes input molecule. >> (github issue #2174 from janholstjensen) >> - Remove Unicode From AcidBasePair Name >> (github pull #2185 from lilleswing) >> - Inconsistent treatment of `[as]` in SMILES and SMARTS >> (github issue #2197 from greglandrum) >> - RGroupDecomposition fixes, keep userLabels more robust >> onlyMatchAtRGroups >> (github pull #2202 from bp-kelley) >> - Fix TautomerTransform in operator= >> (github pull #2203 from bp-kelley) >> - testEnumeration hangs/takes where long on 32bit architectures >> (github issue #2209 from mbanck) >> - Silencing some Python 3 warning messages >> (github pull #2223 from coleb) >> - removeHs shouldn't remove atom lists >> (github issue #2224 from rvianello) >> - failure round-tripping mol block with Q atom >> (github issue #2225 from rvianello) >> - problem round-tripping mol files that include bond topology info >> (github issue #2229 from rvianello) >> - aromatic main-group atoms written to SMARTS incorrectly >> (github issue #2237 from greglandrum) >> - findPotentialStereoBonds() stopping too early >> (github issue #2244 from greglandrum) >> - MinMax Diversity picker seeding shows deterministic / non-random >> behaviour >> (github issue #2245 from sroughley) >> - Fix to serialize binary strings >> (github pull #2264 from bp-kelley) >> - Recognize N in three-membered rings as potentially chiral >> (github issue #2268 from greglandrum) >> - Failure when parsing mol block with M PXA >> (github issue #2277 from greglandrum) >> - query-query matching failing for atoms constructed from SMARTS >> (github issue #2299 from greglandrum) >> - SMILES parsing fails for dative ring closures >> (github issue #2303 from greglandrum) >> - Missing Dict.h overload: std::string Dict::getVal<std::string> >> (github issue #2308 from greglandrum) >> - fix a problem with the random pickers test >> (github pull #2310 from greglandrum) >> - Some tests still failing on less common platforms. >> (github issue #2311 from giallu) >> - AddHs() using 3D coordinates with 2D conformations >> (github pull #2328 from greglandrum) >> - change to make the SWIG builds work on windows >> (github pull #2340 from greglandrum) >> - uncharger behaves differently on molecules constructed from mol >> blocks and SMILES >> (github issue #2346 from greglandrum) >> - Memory Error When Writing ToBinary With "AllProps" >> (github issue #2352 from atom-moyer) >> - Seg fault on init if RDBASE is not set >> (github issue #2368 from greglandrum) >> - PandasTools.FrameToGridImage() fails with SVG output >> (github issue #2380 from greglandrum) >> - ClusterMols.GetDistanceMatrix throws a type error in Python 3 >> (github issue #2387 from John-Videogames) >> - Uncharging logic reversed: protonate non-acids first >> (github issue #2392 from Anne Hersey) >> >> ## New Features and Enhancements: >> - Allow access to Enhanced Stereochemistry information from Python >> (github issue #2108 from d-b-w) >> - Adopt EnumerateStereoisomers to use extended stereo >> (github issue #2109 from greglandrum) >> - Enable ctest -T memcheck >> (github pull #2113 from ricrogz) >> - Support for parsing/writing SGroups in SD Mol files >> (github pull #2138 from ricrogz) >> - Rename the #define _DEBUG to MMPA_DEBUG in mmpa.cpp >> (github pull #2140 from baoilleach) >> - MolDraw2D: line width should be controlled by MolDrawOptions >> (github issue #2151 from greglandrum) >> - Some refactoring of the distance geometry code >> (github pull #2153 from greglandrum) >> - Less warnings >> (github pull #2155 from UnixJunkie) >> - ShapeTverskyIndex python function >> (github pull #2156 from susanhleung) >> - Skip compound if smiles conversion fails >> (github pull #2168 from msteijaert) >> - Fix #2176: InChI functions should return NULL on un-InChI-able input >> molecules. >> (github pull #2177 from janholstjensen) >> - Update installation instructions for Linux >> (github pull #2181 from sirbiscuit) >> - Update CMake rules to find external coorgen & maeparser libs >> (github pull #2184 from ricrogz) >> - Update to use the travis Xenial environment >> (github pull #2200 from greglandrum) >> - Do not allow PandasTools to overwrite pandas settings >> (github pull #2206 from sirbiscuit) >> - re-enable (and update) the file parser tests >> (github pull #2208 from greglandrum) >> - Added documentation files written in Japanese into Book directory >> (github pull #2210 from magattaca) >> - Add C++ convenience function for drawing ROMols >> (github issue #2220 from greglandrum) >> - Change boost int types to std types >> (github pull #2233 from bp-kelley) >> - Added exports for SGroup functions >> (github pull #2242 from ricrogz) >> - Use coordMap when starting embedding from random coords >> (github issue #2246 from greglandrum) >> - Improve interactivity of output SVG >> (github pull #2253 from greglandrum) >> - Add options for substructure searching >> (github pull #2254 from greglandrum) >> - keep extra information about bonds from Mol files >> (github pull #2260 from greglandrum) >> - Allow converting mol blocks directly to InChI >> (github pull #2262 from greglandrum) >> - Patch/pains updates >> (github pull #2272 from johnmay) >> - add warning for 2D conformations flagged as 3D >> (github pull #2273 from greglandrum) >> - Store extra CXSMILES data as a property >> (github pull #2281 from ricrogz) >> - Parse enhanced stereo information from CXSMILES >> (github pull #2282 from ricrogz) >> - Robustify parsing of CTABs and SGROUPs >> (github pull #2283 from greglandrum) >> - Write enhanced stereo to cxsmiles >> (github pull #2290 from greglandrum) >> - Allow custom type-handlers in the RDProps interface >> (github pull #2293 from bp-kelley) >> - Add serialization to SubstructLibrary >> (github pull #2295 from bp-kelley) >> - support reading/writing atom props from SD files >> (github pull #2297 from greglandrum) >> - Add test for issue #2285, fix molbundle test >> (github pull #2301 from bp-kelley) >> - Update maeparser & coordgen libraries >> (github pull #2302 from ricrogz) >> - Mem errors clean up >> (github pull #2305 from ricrogz) >> - Add definition of MolFragmentToCXSmiles >> (github pull #2307 from greglandrum) >> - Doc update >> (github pull #2312 from greglandrum) >> - Adds gzstream stream, exposes to swig >> (github pull #2314 from bp-kelley) >> - Remove a bunch of Python2-related warts >> (github pull #2315 from greglandrum) >> - some much-needed optimization work on the new property lists >> (github pull #2317 from greglandrum) >> - Build warnings revisited >> (github pull #2318 from ricrogz) >> - change bogus "3D" to "2D" in a test file >> (github pull #2319 from greglandrum) >> - Allow copying atoms in Python >> (github pull #2322 from d-b-w) >> - fixes an r-group symmetrization problem >> (github pull #2324 from greglandrum) >> - simple docstring fix >> (github pull #2326 from sunhwan) >> - allow using system's catch2 for tests >> (github pull #2327 from giallu) >> - Python wrap DetectAtomStereoChemistry from MolFileStereochem.h >> (github issue #2329 from d-b-w) >> - switch to using cmake to handle the C++ spec >> (github pull #2334 from greglandrum) >> - WIP: optional integration with YAeHMOP >> (github pull #2335 from greglandrum) >> - Exposes substructlibrary to swig >> (github pull #2337 from bp-kelley) >> - Add a skip_all_if_match option to the FragmentRemover >> (github pull #2338 from greglandrum) >> - Dev/general csharp fixes >> (github pull #2341 from bp-kelley) >> - Add a read-only Python wrapper for SGroups >> (github pull #2343 from greglandrum) >> - Expose RGroupDecomposition to SWIG >> (github pull #2345 from greglandrum) >> - update debian build script to python3 >> (github pull #2350 from UnixJunkie) >> - add GetStereoIsomerCount() function to EnumerateStereoisomers >> (github pull #2354 from greglandrum) >> - Update coordgenlibs to v1.2.2 >> (github pull #2355 from ricrogz) >> - Small fixes to get DLLs to build on Windows >> (github pull #2356 from ptosco) >> - Boost deprecation warning >> (github pull #2357 from d-b-w) >> - Removes an extra debugging cerr statment >> (github pull #2360 from d-b-w) >> - Preserve enhanced stereo in reactions >> (github pull #2366 from d-b-w) >> - improvements to the Uncharge functionality >> (github pull #2374 from greglandrum) >> - Add ExplicitBitVect prop and query >> (github pull #2384 from bp-kelley) >> - Allow components of the MolStandardize code to be initialized from >> streams >> (github pull #2385 from greglandrum) >> >> _______________________________________________ >> Rdkit-announce mailing list >> rdkit-annou...@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-announce >> >
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