Hello, What are the exact commands you used to configure and compile rdkit?
The script in there is my best attempt: https://github.com/rdkit/rdkit/pull/1655 Regards, F. On 11/25/2017 12:50 AM, Tim Dudgeon wrote: > I got round to testing the debs and rpms but without success. > > For the debs the following were built: > > RDKit-2018.03.1.dev1-Linux-Development.deb > RDKit-2018.03.1.dev1-Linux-Extras.deb > RDKit-2018.03.1.dev1-Linux-Python.deb > RDKit-2018.03.1.dev1-Linux-Runtime.deb > > On a clean Ubuntu Xenial system, with just python added (apt-get -y > install python) the packages installed fine: > > # dpkg -i *.deb > Selecting previously unselected package rdkit-development. > (Reading database ... 5666 files and directories currently installed.) > Preparing to unpack RDKit-2018.03.1.dev1-Linux-Development.deb ... > Unpacking rdkit-development (2018.03.1.dev1) ... > Selecting previously unselected package rdkit-extras. > Preparing to unpack RDKit-2018.03.1.dev1-Linux-Extras.deb ... > Unpacking rdkit-extras (2018.03.1.dev1) ... > Selecting previously unselected package rdkit-python. > Preparing to unpack RDKit-2018.03.1.dev1-Linux-Python.deb ... > Unpacking rdkit-python (2018.03.1.dev1) ... > Selecting previously unselected package rdkit-runtime. > Preparing to unpack RDKit-2018.03.1.dev1-Linux-Runtime.deb ... > Unpacking rdkit-runtime (2018.03.1.dev1) ... > Setting up rdkit-development (2018.03.1.dev1) ... > Setting up rdkit-extras (2018.03.1.dev1) ... > Setting up rdkit-python (2018.03.1.dev1) ... > Setting up rdkit-runtime (2018.03.1.dev1) ... > > There seem to be header files in /usr/include/rdkit and the RDKit > installation (.py and .so files) in /usr/lib/python2.7/dist-packages/rdkit > > But RDKit doesn't work from Python: > > # python > Python 2.7.12 (default, Nov 19 2016, 06:48:10) > [GCC 5.4.0 20160609] on linux2 > Type "help", "copyright", "credits" or "license" for more information. >>>> import rdkit > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File "/usr/lib/python2.7/dist-packages/rdkit/__init__.py", line 2, in > <module> > from .rdBase import rdkitVersion as __version__ > ImportError: libpython2.7.so.1.0: cannot open shared object file: No > such file or directory >>>> > > > For the rpms the story is similar. The same 4 files are built as rpms. > Installing them on a clean centos7 machine went fine and the files seem > to get installed to the same places. > But RDKit again couldn't be used from Python, but with a different error: > > # python > Python 2.7.5 (default, Aug 4 2017, 00:39:18) > [GCC 4.8.5 20150623 (Red Hat 4.8.5-16)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. >>>> import rdkit > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > ImportError: No module named rdkit >>>> > > > On 15/11/2017 20:18, David Hall wrote: >> apt install rpm >> >> should get you rpmbuild >> >> -David >> >> On Nov 15, 2017, at 2:59 PM, Tim Dudgeon <tdudgeon...@gmail.com >> <mailto:tdudgeon...@gmail.com>> wrote: >> >>> OK, makes sense, but I'm building on a Debian system. So neither 'yum >>> install rpm-build' nor 'apt-get install rpm-build' doesn't work. >>> >>> So (sorry for the stupid question) can DEBs only be built on a Debian >>> based system and RPMs om a Red Hat based system? >>> >>> >>> On 15/11/2017 19:31, Paolo Tosco wrote: >>>> >>>> Hi Tim, >>>> >>>> It looks like you are missing the rpmbuild binary on the machine >>>> where you are trying to build the RPM. >>>> Issuing a >>>> >>>> yum install rpm-build >>>> >>>> as root should get it installed. >>>> >>>> Cheers, >>>> p. >>>> >>>> On 11/15/17 19:00, Tim Dudgeon wrote: >>>>> >>>>> So this now seems to have been merged to master so I gave it a try: >>>>> >>>>> root@f083c3e3b6a1:/rdkit/build# cmake -DRDK_BUILD_INCHI_SUPPORT=ON >>>>> -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/usr/ .. >>>>> -- Could NOT find InChI in system locations (missing: >>>>> INCHI_LIBRARY INCHI_INCLUDE_DIR) >>>>> CUSTOM_INCHI_PATH = /rdkit/External/INCHI-API >>>>> -- Found InChI software locally >>>>> -- Boost version: 1.62.0 >>>>> -- Found the following Boost libraries: >>>>> -- python >>>>> Python Install directory /usr/lib/python2.7/dist-packages >>>>> -- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR >>>>> EIGEN3_VERSION_OK) (Required is at least version "2.91.0") >>>>> Eigen3 not found, disabling the Descriptors3D build. >>>>> -- Boost version: 1.62.0 >>>>> -- Found the following Boost libraries: >>>>> -- thread >>>>> -- system >>>>> -- chrono >>>>> -- date_time >>>>> -- atomic >>>>> -- Boost version: 1.62.0 >>>>> -- Found the following Boost libraries: >>>>> -- serialization >>>>> == Using strict rotor definition >>>>> == Updating Filters.cpp from pains file >>>>> == Done updating pains files >>>>> -- Boost version: 1.62.0 >>>>> -- Found the following Boost libraries: >>>>> -- regex >>>>> -- Configuring done >>>>> -- Generating done >>>>> -- Build files have been written to: /rdkit/build >>>>> >>>>> >>>>> root@f083c3e3b6a1:/rdkit/build# cpack -G DEB >>>>> CPack: Create package using DEB >>>>> CPack: Install projects >>>>> CPack: - Run preinstall target for: RDKit >>>>> CPack: - Install project: RDKit >>>>> CPack: - Install component: runtime >>>>> CPack: - Install component: base >>>>> CPack: - Install component: data >>>>> CPack: - Install component: docs >>>>> CPack: - Install component: dev >>>>> CPack: - Install component: python >>>>> CPack: - Install component: extras >>>>> CPack: Create package >>>>> CPack: - package: >>>>> /rdkit/build/RDKit-2018.03.1.dev1-Linux-Development.deb generated. >>>>> CPack: - package: >>>>> /rdkit/build/RDKit-2018.03.1.dev1-Linux-Extras.deb generated. >>>>> CPack: - package: >>>>> /rdkit/build/RDKit-2018.03.1.dev1-Linux-Python.deb generated. >>>>> CPack: - package: >>>>> /rdkit/build/RDKit-2018.03.1.dev1-Linux-Runtime.deb generated. >>>>> >>>>> >>>>> root@f083c3e3b6a1:/rdkit/build# cpack -G RPM >>>>> CPack: Create package using RPM >>>>> CPack: Install projects >>>>> CPack: - Run preinstall target for: RDKit >>>>> CPack: - Install project: RDKit >>>>> CPack: - Install component: runtime >>>>> CPack: - Install component: base >>>>> CPack: - Install component: data >>>>> CPack: - Install component: docs >>>>> CPack: - Install component: dev >>>>> CPack: - Install component: python >>>>> CPack: - Install component: extras >>>>> CPack: Create package >>>>> CMake Error at /usr/share/cmake-3.7/Modules/CPackRPM.cmake:1573 >>>>> (message): >>>>> RPM package requires rpmbuild executable >>>>> Call Stack (most recent call first): >>>>> /usr/share/cmake-3.7/Modules/CPackRPM.cmake:2442 >>>>> (cpack_rpm_generate_package) >>>>> >>>>> >>>>> CPack Error: Error while execution CPackRPM.cmake >>>>> CPack Error: Error while execution CPackRPM.cmake >>>>> CPack Error: Error while execution CPackRPM.cmake >>>>> CPack Error: Error while execution CPackRPM.cmake >>>>> CPack Error: Problem compressing the directory >>>>> CPack Error: Error when generating package: RDKit >>>>> >>>>> >>>>> So it looks like the building the debs works OK (I didn't test >>>>> them) but building rpms fails. >>>>> >>>>> I'm probably doing something stupid here as I'm not that familiar >>>>> with cmake and cpack. >>>>> >>>>> >>>>> On 10/11/2017 00:03, Francois BERENGER wrote: >>>>>> On 11/08/2017 08:47 PM, Tim Dudgeon wrote: >>>>>>> There is mention of RPM distributions of RDKit >>>>>>> (https://copr.fedorainfracloud.org/coprs/giallu/rdkit/). >>>>>>> >>>>>>> But on trying these: >>>>>>> >>>>>>> 1. the distro is based on the 2017_03_1 release >>>>>>> 2. it fails due to missing libinchi.so.1 dependency. >>>>>> >>>>>> In the bugtracker, there is an issue about the .deb: >>>>>> >>>>>> https://github.com/rdkit/rdkit/issues/911 >>>>>> >>>>>> and there is a pull request by Patrick Avery >>>>>> to fix them: >>>>>> >>>>>> https://github.com/rdkit/rdkit/pull/1580 >>>>>> >>>>>> Maybe you can read the pull request, replace DEB by RPM and see >>>>>> if that produces usable RPMs for your distro. >>>>>> >>>>>>> This is presumably no longer being maintained? >>>>>>> Anything that can be done to help with fixing this? >>>>>>> >>>>>>> Tim >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> >>>>>>> Check out the vibrant tech community on one of the world's most >>>>>>> engaging tech sites, Slashdot.org <http://Slashdot.org>! >>>>>>> http://sdm.link/slashdot >>>>>>> _______________________________________________ >>>>>>> Rdkit-discuss mailing list >>>>>>> Rdkit-discuss@lists.sourceforge.net >>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>>>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Check out the vibrant tech community on one of the world's most >>>>> engaging tech sites, Slashdot.org <http://Slashdot.org>! >>>>> http://sdm.link/slashdot >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rdkit-discuss mailing list >>>>> Rdkit-discuss@lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org <http://Slashdot.org>! >>>> http://sdm.link/slashdot >>>> >>>> >>>> _______________________________________________ >>>> Rdkit-discuss mailing list >>>> Rdkit-discuss@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org <http://Slashdot.org>! >>> http://sdm.link/slashdot >>> _______________________________________________ >>> Rdkit-discuss mailing list >>> Rdkit-discuss@lists.sourceforge.net >>> <mailto:Rdkit-discuss@lists.sourceforge.net> >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
