Hi Tim and Francois,
To fix missing dependencies use "sudo apt install -f" and use "yum install
rdkit_package_file.rpm" to install package to have all the dependencies.
On Debian (based systems) I prefer to install standalone packages via gdebi
which does this automatically.
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-11-28 0:50 GMT+01:00 Francois BERENGER <beren...@bioreg.kyushu-u.ac.jp>
:
> On 11/28/2017 12:42 AM, Tim Dudgeon wrote:
> > I see exactly the same when I build with those cmake args.
>
> Maybe you are missing some of the dependencies.
> I don't think the packages we create have all the dependency information:
>
> fonts-freefont-ttf,
> libboost-python1.58.0,
> libboost-regex1.58.0,
> libboost-system1.58.0,
> libboost-thread1.58.0,
> libc6 (>= 2.14),
> libgcc1 (>= 1:4.1.1),
> libpython2.7 (>= 2.7),
> libstdc++6 (>= 5.2),
> python (<< 2.8),
> python (>= 2.7~)
>
> You should install the ones you are missing and test again.
>
> > On 27/11/2017 09:11, Francois BERENGER wrote:
> >> On 11/27/2017 06:01 PM, Tim Dudgeon wrote:
> >>> I did:
> >>>
> >>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_INSTALL_INTREE=OFF
> >>> -DCMAKE_INSTALL_PREFIX=/usr/ ..
> >> Try this instead, just for the cmake part:
> >>
> >> cmake -Wno-dev \
> >> -DRDK_INSTALL_INTREE=OFF \
> >> -DRDK_BUILD_INCHI_SUPPORT=ON \
> >> -DRDK_BUILD_AVALON_SUPPORT=ON \
> >> -DRDK_BUILD_PYTHON_WRAPPERS=ON \
> >> -DCMAKE_INSTALL_PREFIX=/usr \
> >> -DRDKit_VERSION=`date +%Y.%m` \
> >> ../
> >>
> >> then do the rest (cpack ...) and test again
> >> after an install of the freshly created package.
> >>
> >> I advise to wipe out any prior rdkit install from your machine
> >> before installing the new packages (so that we test what we intend to
> >> test).
> >>
> >> On a Debian-like:
> >> sudo apt-get remove $(dpkg -l | grep rdkit | awk '{print $2}')
> >>
> >>> cpack -G DEB
> >>> cpack -G RPM
> >>>
> >>>
> >>> On 27/11/2017 00:05, Francois BERENGER wrote:
> >>>> 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
> >>>
> >>> ------------------------------------------------------------
> ------------------
> >>>
> >>>
> >>> 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
> >
> >
> > ------------------------------------------------------------
> ------------------
> >
> > 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
>
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