Dear Markus,
in case you ran into the Float8GetDatum undefined symbol issue (it just
happened to me), please make sure that you are actually building the
cartridge against the PostgreSQL 11 headers.
You may check this in the CMake output; for example, in my case it has
to be:
postgres: /usr/pgsql-11/include;/usr/pgsql-11/include/server
and to obtain this I had to define in my cmake command line:
-DPostgreSQL_ROOT=/usr/pgsql-11 \
-DPostgreSQL_INCLUDE_DIR=/usr/pgsql-11/include \
-DPostgreSQL_TYPE_INCLUDE_DIR=/usr/pgsql-11/include/server \
-DPostgreSQL_LIBRARY_DIR=/usr/pgsql-11/lib \
in addition to the usual
-DRDK_BUILD_PGSQL=ON \
-DRDK_PGSQL_STATIC=ON \
to avoid that FindPostgreSQL.cmake finds the headers of the system
CentOS 7 PostgreSQL in /usr/include rather than the PostgreSQL headers
in /usr/pgsql-11/include.
HTH, cheers,
p.
On 05/04/2019 17:42, Markus Sitzmann wrote:
Hi Greg,
my Chembience RDKit image build with version 2019.03-b1b went fine
(well, I just pull it with conda; in case someone is interested it is
available with tag 0.2.10-beta-1 at Dockerhub).
For the Postgres extension (which I still compile myself during the
Docker build against Postgress), your python 3 enforcement uncovered
some dark corners of my build process, but that is fixed. However,
compiling 2019.03-b1b against Postgres 11 fails during compilation (am
I too cheeky?).
Markus
On Wed, Apr 3, 2019 at 11:38 AM Greg Landrum <greg.land...@gmail.com
<mailto:greg.land...@gmail.com>> wrote:
Dear all,
The beta of the 2019.03 RDKit release has been tagged in github:
https://github.com/rdkit/rdkit/releases/tag/Release_2019_03_1b1
There are a couple more bug fixes and maybe one more feature
expected before the actual release, but I wanted to go ahead and
get the beta out there.
I've done conda builds for Python 3.6 and 3.7 for Windows, Mac,
and Linux. These all use the beta label so that they do not
install by default; you'll need to run "conda install" as follows:
conda install -c rdkit/label/beta rdkit
Be sure to confirm that it's installing the right version when you
are prompted (if there's no build available, it will pick the
current production release instead).
The relevant section of the release notes is below, or you can see
a nicely formatted version here:
https://github.com/rdkit/rdkit/releases/tag/Release_2019_03_1b1
As usual, if you have time to try out the new release I would love
feedback. If nothing major comes up, I plan to do the actual
release early next week.
Best,
-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, 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, 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)
- 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)
## 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)
- 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)
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