Re: [Rdkit-devel] More build fun with RHEL 6

[Gianluca Sforna]

On Fri, Apr 15, 2016 at 1:36 PM, Greg Landrum  wrote:
> Would you be comfortable with me doing the release based on the current
> state of the code (once that PR is merged, of course)?

Yes, I guess we're good to go.
As soon as we have the final tarball I will build RHEL 7 and Fedora
RPMs at the usual COPR location, then will have a look at software
collections.



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Re: [Rdkit-devel] More build fun with RHEL 6

[Greg Landrum]

On Fri, Apr 15, 2016 at 1:18 PM, Gianluca Sforna  wrote:

> On Fri, Apr 15, 2016 at 11:20 AM, Greg Landrum 
> wrote:
> > The problem here is that the rdkit doesn't really support Python 2.6
> > anymore. I don't remember at the moment which pieces we used, but there
> are
> > 2.7+ bits in there
>
> Then I guess the Software Collections approach mentioned by Riccardo
> is best, so I can pick up an updated dep.
>

That would be excellent if it's possible


> By the way, the build succeeded except for the cartridge, apparently
> the makefile is broken for older versions (8.x);


Correct, support for 8.x was removed with the 2015_09 release.

Would you be comfortable with me doing the release based on the current
state of the code (once that PR is merged, of course)?

-greg
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Re: [Rdkit-devel] More build fun with RHEL 6

[Gianluca Sforna]

On Fri, Apr 15, 2016 at 11:20 AM, Greg Landrum  wrote:
> The problem here is that the rdkit doesn't really support Python 2.6
> anymore. I don't remember at the moment which pieces we used, but there are
> 2.7+ bits in there

Then I guess the Software Collections approach mentioned by Riccardo
is best, so I can pick up an updated dep.

By the way, the build succeeded except for the cartridge, apparently
the makefile is broken for older versions (8.x);

-- 
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Re: [Rdkit-devel] More build fun with RHEL 6

[Gianluca Sforna]

On Fri, Apr 15, 2016 at 9:04 AM, Riccardo Vianello
 wrote:
> Hi all,
>
> Maybe the centos6 rpms could be build with a dependency from the software
> collections repository
> (https://wiki.centos.org/AdditionalResources/Repositories/SCL)? Gianluca, do
> you know if this could be a viable solution?

Yes, provided I rebuild the RDKit RPM itself as a software collection,
so it can depend on other collections.

I will have a look at that

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Re: [Rdkit-devel] More build fun with RHEL 6

[Greg Landrum]

On Friday, 15 April 2016, Gianluca Sforna  wrote:

> On Fri, Apr 15, 2016 at 4:41 AM, Greg Landrum  > wrote:
> > Now that I have a Centos6 box available, I'm realizing that it has python
> > 2.6
> > Are you also installing Python 2.7 on those machines when you build the
> > RDKit?
>
> No, there are a few methods for getting 2.7 as RPMs, but the deafult
> build sticks to what Red Hat provides in the repo.
>
>

The problem here is that the rdkit doesn't really support Python 2.6
anymore. I don't remember at the moment which pieces we used, but there are
2.7+ bits in there

-greg
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Re: [Rdkit-devel] More build fun with RHEL 6

[Gianluca Sforna]

On Fri, Apr 15, 2016 at 8:39 AM, Greg Landrum  wrote:
> This PR: https://github.com/rdkit/rdkit/pull/864
> has a version that builds a python wrapper for me on Centos6 with python2.7
> installed manually.

I'll check it out



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Re: [Rdkit-devel] More build fun with RHEL 6

[Gianluca Sforna]

On Fri, Apr 15, 2016 at 4:41 AM, Greg Landrum  wrote:
> Now that I have a Centos6 box available, I'm realizing that it has python
> 2.6
> Are you also installing Python 2.7 on those machines when you build the
> RDKit?

No, there are a few methods for getting 2.7 as RPMs, but the deafult
build sticks to what Red Hat provides in the repo.

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Re: [Rdkit-devel] More build fun with RHEL 6

[Riccardo Vianello]

Hi all,

Maybe the centos6 rpms could be build with a dependency from the software
collections repository (
https://wiki.centos.org/AdditionalResources/Repositories/SCL)? Gianluca, do
you know if this could be a viable solution?

Best,
Riccardo
​
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Re: [Rdkit-devel] More build fun with RHEL 6

[Greg Landrum]

This PR: https://github.com/rdkit/rdkit/pull/864
has a version that builds a python wrapper for me on Centos6 with python2.7
installed manually.

FWIW, I've attached the bootstrap.sh that I used to configure the vagrant
box (clearly still a work in progress: it doesn't bring in the requirements
for the java wrappers or postgreSQL yet).

-greg


On Fri, Apr 15, 2016 at 4:41 AM, Greg Landrum 
wrote:

> Now that I have a Centos6 box available, I'm realizing that it has python
> 2.6
> Are you also installing Python 2.7 on those machines when you build the
> RDKit?
>
> On Thu, Apr 14, 2016 at 12:18 PM, Gianluca Sforna 
> wrote:
>
>> For the records, Build with RHEL/CentOS 7 succeded, this leaves us
>> with only one platform where it fails; if we think the older boost
>> version cannot be supported, I can just stick to an older release for
>> EL6
>>
>> On Thu, Apr 14, 2016 at 11:47 AM, Gianluca Sforna 
>> wrote:
>> > On Thu, Apr 14, 2016 at 11:37 AM, Greg Landrum 
>> wrote:
>> >> Which version of boost are you using?
>> >
>> > RPMs are built against the packages in the repositories (stock+updates).
>> >
>> > Right now it means 1.41.0 for RHEL6, 1.53 for RHEL 7 (building now,
>> > will let you know how it goes)
>>
>>
>>
>> --
>> Gianluca Sforna
>>
>> http://plus.google.com/+gianlucasforna - http://twitter.com/giallu
>> Tinker Garage - http://tinkergarage.it
>>
>
>


bootstrap.sh
Description: Bourne shell script
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Re: [Rdkit-devel] More build fun with RHEL 6

[Greg Landrum]

Now that I have a Centos6 box available, I'm realizing that it has python
2.6
Are you also installing Python 2.7 on those machines when you build the
RDKit?

On Thu, Apr 14, 2016 at 12:18 PM, Gianluca Sforna  wrote:

> For the records, Build with RHEL/CentOS 7 succeded, this leaves us
> with only one platform where it fails; if we think the older boost
> version cannot be supported, I can just stick to an older release for
> EL6
>
> On Thu, Apr 14, 2016 at 11:47 AM, Gianluca Sforna 
> wrote:
> > On Thu, Apr 14, 2016 at 11:37 AM, Greg Landrum 
> wrote:
> >> Which version of boost are you using?
> >
> > RPMs are built against the packages in the repositories (stock+updates).
> >
> > Right now it means 1.41.0 for RHEL6, 1.53 for RHEL 7 (building now,
> > will let you know how it goes)
>
>
>
> --
> Gianluca Sforna
>
> http://plus.google.com/+gianlucasforna - http://twitter.com/giallu
> Tinker Garage - http://tinkergarage.it
>
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Re: [Rdkit-devel] More build fun with RHEL 6

[Greg Landrum]

That'd be awesome.. thanks. :-)

On Thu, Apr 14, 2016 at 1:44 PM, Brian Kelley  wrote:

> The fix is buried here:
>
> https://github.com/rdkit/rdkit/pull/677/files
>
> It is in the BOOST_PYTHON_SUPPORT_SHARED_CONST
>
> The reason we didn't merge is was the problem with the exported defines,
> however I can tie it into the boost version in the FilterCatalog header
> file.  We had initially thought this only affected RHEL5 so it was a lower
> priority, I can have a PR by the end of the day (maybe even the Basel day :)
>
>
>
> On Thu, Apr 14, 2016 at 7:01 AM, Greg Landrum 
> wrote:
>
>> Under any circumstances: if we only support more recent versions we
>> should indicate that in the CMakeLists.txt, which claims to support back to
>> boost 1.39 with python2 and 1.45 with python3.
>>
>> I will take a look
>>
>> On Thu, Apr 14, 2016 at 12:58 PM, Brian Kelley 
>> wrote:
>>
>>> I think I have seen this before in FilterCatalog, I can try to patch it
>>> for boost 1.41 but I will say that version of boost is getting pretty long
>>> in the tooth.
>>>
>>> 
>>> Brian Kelley
>>>
>>> On Apr 14, 2016, at 6:43 AM, Greg Landrum 
>>> wrote:
>>>
>>> I'd like to have it work on EL6; that's still pretty common.
>>> I will make some time to investigate either this evening or tomorrow.
>>>
>>> Thanks for narrowing it down so much.
>>> -greg
>>>
>>>
>>> On Thu, Apr 14, 2016 at 12:18 PM, Gianluca Sforna 
>>> wrote:
>>>
 For the records, Build with RHEL/CentOS 7 succeded, this leaves us
 with only one platform where it fails; if we think the older boost
 version cannot be supported, I can just stick to an older release for
 EL6

 On Thu, Apr 14, 2016 at 11:47 AM, Gianluca Sforna 
 wrote:
 > On Thu, Apr 14, 2016 at 11:37 AM, Greg Landrum <
 greg.land...@gmail.com> wrote:
 >> Which version of boost are you using?
 >
 > RPMs are built against the packages in the repositories
 (stock+updates).
 >
 > Right now it means 1.41.0 for RHEL6, 1.53 for RHEL 7 (building now,
 > will let you know how it goes)



 --
 Gianluca Sforna

 http://plus.google.com/+gianlucasforna - http://twitter.com/giallu
 Tinker Garage - http://tinkergarage.it

>>>
>>>
>>> --
>>> Find and fix application performance issues faster with Applications
>>> Manager
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>>> tiers of
>>> your business applications. It resolves application problems quickly and
>>> reduces your MTTR. Get your free trial!
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>>>
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>>>
>>>
>>
>
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Re: [Rdkit-devel] More build fun with RHEL 6

[Brian Kelley]

The fix is buried here:

https://github.com/rdkit/rdkit/pull/677/files

It is in the BOOST_PYTHON_SUPPORT_SHARED_CONST

The reason we didn't merge is was the problem with the exported defines,
however I can tie it into the boost version in the FilterCatalog header
file.  We had initially thought this only affected RHEL5 so it was a lower
priority, I can have a PR by the end of the day (maybe even the Basel day :)



On Thu, Apr 14, 2016 at 7:01 AM, Greg Landrum 
wrote:

> Under any circumstances: if we only support more recent versions we should
> indicate that in the CMakeLists.txt, which claims to support back to boost
> 1.39 with python2 and 1.45 with python3.
>
> I will take a look
>
> On Thu, Apr 14, 2016 at 12:58 PM, Brian Kelley 
> wrote:
>
>> I think I have seen this before in FilterCatalog, I can try to patch it
>> for boost 1.41 but I will say that version of boost is getting pretty long
>> in the tooth.
>>
>> 
>> Brian Kelley
>>
>> On Apr 14, 2016, at 6:43 AM, Greg Landrum  wrote:
>>
>> I'd like to have it work on EL6; that's still pretty common.
>> I will make some time to investigate either this evening or tomorrow.
>>
>> Thanks for narrowing it down so much.
>> -greg
>>
>>
>> On Thu, Apr 14, 2016 at 12:18 PM, Gianluca Sforna 
>> wrote:
>>
>>> For the records, Build with RHEL/CentOS 7 succeded, this leaves us
>>> with only one platform where it fails; if we think the older boost
>>> version cannot be supported, I can just stick to an older release for
>>> EL6
>>>
>>> On Thu, Apr 14, 2016 at 11:47 AM, Gianluca Sforna 
>>> wrote:
>>> > On Thu, Apr 14, 2016 at 11:37 AM, Greg Landrum 
>>> wrote:
>>> >> Which version of boost are you using?
>>> >
>>> > RPMs are built against the packages in the repositories
>>> (stock+updates).
>>> >
>>> > Right now it means 1.41.0 for RHEL6, 1.53 for RHEL 7 (building now,
>>> > will let you know how it goes)
>>>
>>>
>>>
>>> --
>>> Gianluca Sforna
>>>
>>> http://plus.google.com/+gianlucasforna - http://twitter.com/giallu
>>> Tinker Garage - http://tinkergarage.it
>>>
>>
>>
>> --
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>> Manager
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>>
>>
>
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