Closed ptosco closed 4 years ago
I have had a look at the build failure. Not sure what I can do to fix it - the meta.yaml
file has no version specifications in it. The build works fine on my laptop.
@ptosco : this fails for me on windows with a link error. It's not able to find Boost::iostreams.lib
@greglandrum I wonder if this depends on the Boost version. The build works for me using Boost 1.70:
-- The C compiler identification is MSVC 19.16.27034.0
-- The CXX compiler identification is MSVC 19.16.27034.0
-- Check for working C compiler: C:/Program Files (x86)/Microsoft Visual Studio/2017/Professional/VC/Tools/MSVC/14.16.27023/bin/Hostx64/x64/cl.exe
-- Check for working C compiler: C:/Program Files (x86)/Microsoft Visual Studio/2017/Professional/VC/Tools/MSVC/14.16.27023/bin/Hostx64/x64/cl.exe -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: C:/Program Files (x86)/Microsoft Visual Studio/2017/Professional/VC/Tools/MSVC/14.16.27023/bin/Hostx64/x64/cl.exe
-- Check for working CXX compiler: C:/Program Files (x86)/Microsoft Visual Studio/2017/Professional/VC/Tools/MSVC/14.16.27023/bin/Hostx64/x64/cl.exe -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Enabling RDK_INSTALL_STATIC_LIBS because RDK_PGSQL_STATIC is set.
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Catch not found in C:/a3/conda-bld/rdkit-postgresql_1578325985532/work/External/catch/catch
Downloading https://github.com/catchorg/Catch2/archive/v2.1.2.tar.gz...
CATCH: C:/a3/conda-bld/rdkit-postgresql_1578325985532/work/External/catch/catch/single_include
-- Could NOT find InChI in system locations (missing: INCHI_INCLUDE_DIR)
Downloading http://www.inchi-trust.org/download/105/INCHI-1-SRC.zip...
-- Found Boost 1.70.0 at C:/a3/Library/lib/cmake/Boost-1.70.0
-- Requested configuration: QUIET REQUIRED
-- Found boost_headers 1.70.0 at C:/a3/Library/lib/cmake/boost_headers-1.70.0
-- Boost 1.56.0 found.
-- Found Eigen3: C:/a3/conda-bld/rdkit-postgresql_1578325985532/_h_env/Library/include (Required is at least version "2.91.0")
-- Looking for pthread.h
-- Looking for pthread.h - not found
-- Found Threads: TRUE
-- Found PostgreSQL: C:/a3/conda-bld/rdkit-postgresql_1578325985532/_h_env/Library/lib/libpq.lib (found version "10.5")
== Using strict rotor definition
Downloading http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar...
-- Found Boost 1.70.0 at C:/a3/Library/lib/cmake/Boost-1.70.0
-- Requested configuration: QUIET REQUIRED COMPONENTS system;iostreams
-- Found boost_system 1.70.0 at C:/a3/Library/lib/cmake/boost_system-1.70.0
-- libboost_system.lib
-- Adding boost_system dependencies: headers
-- Found boost_iostreams 1.70.0 at C:/a3/Library/lib/cmake/boost_iostreams-1.70.0
-- libboost_iostreams.lib
-- Adding boost_iostreams dependencies: headers
-- Boost 1.56.0 found.
-- Found Boost components:
system;iostreams
-- Found Boost 1.70.0 at C:/a3/Library/lib/cmake/Boost-1.70.0
-- Requested configuration: QUIET COMPONENTS zlib
-- Boost 1.58.0 found.
-- Found Boost components:
zlib
-- maeparser include dir set as 'maeparser_INCLUDE_DIRS-NOTFOUND'
-- maeparser libraries set as 'C:/a3/Library/lib/maeparser.lib'
-- Could NOT find maeparser (missing: maeparser_INCLUDE_DIRS)
Downloading https://github.com/schrodinger/maeparser/archive/v1.2.2.tar.gz...
-- coordgen include dir set as coordgen_INCLUDE_DIRS-NOTFOUND
-- coordgen libraries set as 'C:/a3/Library/lib/coordgen.lib'
-- coordgen templates file set as 'coordgen_TEMPLATE_FILE-NOTFOUND'
-- Could NOT find coordgen (missing: coordgen_INCLUDE_DIRS coordgen_TEMPLATE_FILE)
Downloading https://github.com/schrodinger/coordgenlibs/archive/v1.3.2.tar.gz...
Downloading https://github.com/rareylab/RingDecomposerLib/archive/v1.1.3_rdkit.tar.gz...
-- Found Boost 1.70.0 at C:/a3/Library/lib/cmake/Boost-1.70.0
-- Requested configuration: QUIET REQUIRED COMPONENTS system;iostreams
-- Found boost_system 1.70.0 at C:/a3/Library/lib/cmake/boost_system-1.70.0
-- libboost_system.lib
-- Adding boost_system dependencies: headers
-- Found boost_iostreams 1.70.0 at C:/a3/Library/lib/cmake/boost_iostreams-1.70.0
-- libboost_iostreams.lib
-- Adding boost_iostreams dependencies: headers
-- Boost 1.56.0 found.
-- Found Boost components:
system;iostreams
-- Found Boost 1.70.0 at C:/a3/Library/lib/cmake/Boost-1.70.0
-- Requested configuration: QUIET COMPONENTS zlib
-- Boost 1.58.0 found.
-- Found Boost components:
zlib
-- Found Boost 1.70.0 at C:/a3/Library/lib/cmake/Boost-1.70.0
-- Requested configuration: QUIET REQUIRED COMPONENTS system;iostreams
-- Found boost_system 1.70.0 at C:/a3/Library/lib/cmake/boost_system-1.70.0
-- libboost_system.lib
-- Adding boost_system dependencies: headers
-- Found boost_iostreams 1.70.0 at C:/a3/Library/lib/cmake/boost_iostreams-1.70.0
-- libboost_iostreams.lib
-- Adding boost_iostreams dependencies: headers
-- Boost 1.56.0 found.
-- Found Boost components:
system;iostreams
-- Found Boost 1.70.0 at C:/a3/Library/lib/cmake/Boost-1.70.0
-- Requested configuration: QUIET COMPONENTS zlib
-- Boost 1.56.0 found.
-- Found Boost components:
zlib
== Making EnumerateLibrary without boost Serialization support
== Making FilterCatalog without boost Serialization support
-- Found PythonInterp: C:/a3/conda-bld/rdkit-postgresql_1578325985532/_build_env/python.exe (found version "3.7.5")
== Updating Filters.cpp from pains file
== Done updating pains files
== Making SubstructLibrary without boost Serialization support
Downloading https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz...
-- Found Boost 1.70.0 at C:/a3/Library/lib/cmake/Boost-1.70.0
-- Requested configuration: QUIET REQUIRED COMPONENTS iostreams
-- Found boost_iostreams 1.70.0 at C:/a3/Library/lib/cmake/boost_iostreams-1.70.0
-- boost_iostreams.lib
-- Adding boost_iostreams dependencies: headers
-- Boost 1.56.0 found.
-- Found Boost components:
iostreams
postgres: C:/a3/conda-bld/rdkit-postgresql_1578325985532/_h_env/Library/include;C:/a3/conda-bld/rdkit-postgresql_1578325985532/_h_env/Library/include/server
=====================================================================
After building, check
C:/a3/conda-bld/rdkit-postgresql_1578325985532/work/build/Code/PgSQL/rdkit/pgsql_install.bat
for correctness of installation paths. If everything is OK, gain
administrator privileges, stop the PostgreSQL service, run
C:/a3/conda-bld/rdkit-postgresql_1578325985532/work/build/Code/PgSQL/rdkit/pgsql_install.bat
to install the PostgreSQL RDKit cartridge, then start again
the PostgreSQL service
=====================================================================
and passes all tests:
test 1
Start 1: testPgSQL
1: Test command: %SRC_DIR%\build\Code\PgSQL\rdkit\pgsql_regress.bat
1: Test timeout computed to be: 10000000
1:
1: (%BUILD_PREFIX%) CLINK CLINK %SRC_DIR%\build\Code\PgSQL\rdkit>cd "%SRC_DIR%\build\Code\PgSQL\rdkit\"
1:
1: (%BUILD_PREFIX%) CLINK CLINK %SRC_DIR%\build\Code\PgSQL\rdkit>"C:\a3\CONDA-~2\RD87FB~1\_h_env\Library\lib\..\bin\pg_regress.exe" --inputdir=sql --bindir="C:/a3/CONDA-~2/RD87FB~1/_h_env/Library/lib/../bin" rdkit-91 props btree molgist bfpgist-91 sfpgist slfpgist fps reaction avalon inchi
1: (using postmaster on localhost, port 54321)
1: ============== dropping database "regression" ==============
1: NOTICE: database "regression" does not exist, skipping
1: DROP DATABASE
1: ============== creating database "regression" ==============
1: CREATE DATABASE
1: ALTER DATABASE
1: ============== running regression test queries ==============
1: test rdkit-91 ... ok
1: test props ... ok
1: test btree ... ok
1: test molgist ... ok
1: test bfpgist-91 ... ok
1: test sfpgist ... ok
1: test slfpgist ... ok
1: test fps ... ok
1: test reaction ... ok
1: test avalon ... ok
1: test inchi ... ok
1:
1: ======================
1: All 11 tests passed.
1: ======================
1:
1/1 Test #1: testPgSQL ........................ Passed 12.90 sec
100% tests passed, 0 tests failed out of 1
Total Test time (real) = 12.91 sec
What Boost version are you using?
@greglandrum Could you please send me the output of
conda list | grep boost
boost 1.70.0 py37h79cbd7a_1 conda-forge
boost-cpp 1.70.0 h6a4c333_2 conda-forge
Thanks.
@ptosco I'm pretty sure that whatever happens during a conda-build should not be influenced by what I have locally installed. The build process is supposed to create its own conda env and use that.
@greglandrum I agree, but if you look at my cmake
log above you will see that CMake somehow found the "global" Boost located in C:/a3/Library/lib/cmake
:
-- Found Boost 1.70.0 at C:/a3/Library/lib/cmake/Boost-1.70.0
I will figure out how I can avoid that.
Yeah, I saw that. It’s still wrong :-)
@greglandrum I have verified that the rdkit-postgresql
Windows build was failing also for me on a fresh, clean miniconda
installation.
Now the build works for me, but still fails on Travis.
Could you please check if now it works for you on your Windows machine? Thanks a lot!
@ptosco : yep, that did it. Thanks!
Currently the
conda
build of the PostgreSQL cartridge is broken on Windows. This PR allows building the PostgreSQL cartridge on WIndows.