Re: [Rdkit-discuss] RPM distros

2017-11-27 Thread Francois BERENGER 
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 "", line 1, in 
>     File "/usr/lib/python2.7/dist-packages/rdkit/__init__.py", line
> 2, in
> 
>   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 "", line 1, in 
> 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 > > wrote:
>>
>>> OK, makes sense, but I'm building on a Debian system. So neither
>>> 'yum
>>> install

[Rdkit-discuss] suggestions for comprehensive searchable database of natural products

2017-11-27 Thread James T. Metz via Rdkit-discuss 
RDkit Discussion Group,


My apologies in advance if my request is not appropriate for this 
discussion group.



Given a small molecule that might have some resemblance to natural 
products, 

can someone suggest a free, comprehensive, PYTHON/RDkit searchable database
of natural products that might be suitable for similarity and substructure 
searching.


I am aware of a few websites that permit searching on the website. If 
possible,
I would like to programmatically search by running a PYTHON/RDkit script on my
local machine and then return the structures of related molecules to my local 
script.


I would prefer not having to download and store a huge database.



Also, if possible, it would be important to return the organism(s) that 
creates

the natural product.  Pathway information would be also very, very helpful.


I greatly welcome comments and suggestions.



Thank you.



Regards,

Jim Metz

Northwestern University









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Re: [Rdkit-discuss] RPM distros

2017-11-27 Thread Tim Dudgeon 

I see exactly the same when I build with those cmake args.


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 "", line 1, in 
    File "/usr/lib/python2.7/dist-packages/rdkit/__init__.py", line 2, in

  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 "", line 1, in 
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 > 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

Re: [Rdkit-discuss] Stop bond highlights

2017-11-27 Thread Nicholas Firth 
Hi Greg,

That's perfect. Thank you!

Cheers,
Nick

On Fri, 24 Nov 2017, 16:40 Greg Landrum,  wrote:

> Hi Nick,
>
> When you import IPythonConsole it monkey patches the substructure function
> so that it saves info about the results when you do a substructure search
> on a molecule.
> The data member is called __sssAtoms, and if you delete that you should no
> longer get the coloring:
> Heres a bit of demo:
>
> In [1]: from rdkit import Chem
>
> In [2]: from rdkit.Chem.Draw import IPythonConsole
>
> In [3]: m = Chem.MolFromSmiles('CCOC')
>
> In [4]: m.GetSubstructMatch(Chem.MolFromSmiles('CO'))
> Out[4]: (1, 2)
>
> In [5]: m.__sssAtoms
> Out[5]: [1, 2]
>
> In [7]: del m.__sssAtoms
>
>
> You, of course, need to check that the data member is there.
>
> If you're unlikely to want to see highlighting at all, it's easier to just
> turn if off:
>
> In [12]: IPythonConsole.highlightSubstructs=False
>
> In [13]: m.GetSubstructMatch(Chem.MolFromSmiles('CO'))
> Out[13]: (1, 2)
>
> In [14]: m.__sssAtoms
> Out[14]: []
>
>
>
> I hope this helps,
> -greg
>
>
>
> On Thu, Nov 23, 2017 at 2:05 PM, Nicholas Firth 
> wrote:
>
>> Howdy RDKitters,
>>
>> Been a while since I used this list, so forgive me if my question is
>> silly.
>>
>> I'm seeing some weird behaviour from drawing molecules. I've got some
>> wrapper classes that I'm using to write some de novo design code, which
>> involves fragmenting molecules, and I've obviously been fairly lax with my
>> namespacing. Essentially when I fragment my molecule the first bond that is
>> cut is highlighted when I draw the original molecule but the rest of the
>> cuts aren't (because I reassign variables). There's an example of what I
>> mean here  (
>> https://i.imgur.com/kvb3YyG.png)
>>
>> I tried to ClearComputedProps on the molecule but it still highlights the
>> bond, does anyone know of a way to clear this from the molecule so that it
>> doesn't get drawn? I'm going to clear up my programming issues to stop this
>> particular artefact, but it would definitely be helpful to understand this
>> for the rest of my code.
>>
>> Cheers,
>> Nick
>>
>>
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! 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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Re: [Rdkit-discuss] RPM distros

2017-11-27 Thread Francois BERENGER 
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 "", line 1, in 
>>>    File "/usr/lib/python2.7/dist-packages/rdkit/__init__.py", line 2, in
>>> 
>>>  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 "", line 1, in 
>>> 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 > 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

Re: [Rdkit-discuss] RPM distros

2017-11-27 Thread Tim Dudgeon 

I did:

cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_INSTALL_INTREE=OFF 
-DCMAKE_INSTALL_PREFIX=/usr/ ..

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 "", line 1, in 
   File "/usr/lib/python2.7/dist-packages/rdkit/__init__.py", line 2, in

     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 "", line 1, in 
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 > 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: