Francois,
I'm assuming you are meaning to install those packages on the debian
system prior to installing the RDKit-2018.03.1.dev1-Linux-*.deb files.
Unfortunately that didn't help.
Tim
On 27/11/2017 23:50, Francois BERENGER wrote:
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
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