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
>>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>>
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>>>>>>> http://sdm.link/slashdot
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>>
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>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>
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