Maciek
The 'cpack -G RPM' command does not seem to create a rdkit_package_file.rpm.
The ones that are created are:
RDKit-2018.03.1.dev1-Linux-Development.rpm
RDKit-2018.03.1.dev1-Linux-Extras.rpm
RDKit-2018.03.1.dev1-Linux-Python.rpm
RDKit-2018.03.1.dev1-Linux-Runtime.rpm
Tim
On 28/11/2017 08:48, Maciek Wójcikowski wrote:
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 <mailto:mac...@wojcikowski.pl>
2017-11-28 0:50 GMT+01:00 Francois BERENGER
<beren...@bioreg.kyushu-u.ac.jp <mailto: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
<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>
>>>>>> <mailto: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/
<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
<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
<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
<mailto:Rdkit-discuss@lists.sourceforge.net>
>>>>>>>>>>>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
<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
<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
<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>
>>>>>>> <mailto:Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>>
>>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
<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
<mailto:Rdkit-discuss@lists.sourceforge.net>
>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
<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
<mailto:Rdkit-discuss@lists.sourceforge.net>
>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
<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
<mailto:Rdkit-discuss@lists.sourceforge.net>
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
<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
<mailto:Rdkit-discuss@lists.sourceforge.net>
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
<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
<mailto:Rdkit-discuss@lists.sourceforge.net>
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<https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
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