Re: [Rdkit-discuss] library name change?

2016-08-19 Thread Gianluca Sforna
On Fri, Aug 19, 2016 at 1:52 PM, Greg Landrum wrote: > Nice suggestion. It seems logical to me, though I would probably go with > RDKit instead of RD as the prefix. > It's not a small change for people who are using the C++ libs without cmake > (I wouldn't change the names of the cmake projects,

Re: [Rdkit-discuss] library name change?

2016-08-19 Thread Gianluca Sforna
On Fri, Aug 19, 2016 at 3:23 PM, Greg Landrum wrote: > > That sounds like an argument for doing it sooner rather than later... > Yeah, but really I don't think we are in a hurry here, so I'd consider the timeline outlined by Brian pretty sensible. -- Gianluca Sforna htt

[Rdkit-discuss] RDKit official packages from Fedora repos

2016-08-26 Thread Gianluca Sforna
/rdkit/ -- Gianluca Sforna http://plus.google.com/+gianlucasforna - http://twitter.com/giallu Tinker Garage - http://tinkergarage.it -- ___ Rdkit-discuss mailing list Rdkit

Re: [Rdkit-discuss] junit version problems

2016-08-26 Thread Gianluca Sforna
w if it works? Open up Code/JavaWrappers/gmwrapper/CMakelists.txt and change the line 13 from: find_jar(JUNIT_JAR junit PATHS ${RDKit_JavaLibDir}) to find_jar(JUNIT_JAR junit PATHS ${RDKit_JavaLibDir} VERSIONS 4) According to cmake documentation, that should force a version match and use the correc

Re: [Rdkit-discuss] compiling with the RDKit with cairo on Fedora

2016-11-02 Thread Gianluca Sforna
>MolDraw2DSVG.h >MolDraw2Dwx.h >MolDraw2DUtils.h > ) > > needs added: DEST GraphMol/MolDraw2D > > (the current git master has the same) I could not find this change, so I went ahead and created the patch. Testing it in a new build right now. -- Gianluca Sf

Re: [Rdkit-discuss] compiling with the RDKit with cairo on Fedora

2016-11-04 Thread Gianluca Sforna
updated to 2016.03.5, I regularly miss those minor release (are they announced somewhere?) let me know if it works for you G. -- Gianluca Sforna http://plus.google.com/+gianlucasforna - http://twitter.com/giallu Tinker Garage

[Rdkit-discuss] Coot heading to Fedora

2016-11-18 Thread Gianluca Sforna
://bugzilla.redhat.com/show_bug.cgi?id=1359402 -- Gianluca Sforna http://plus.google.com/+gianlucasforna - http://twitter.com/giallu Tinker Garage - http://tinkergarage.it

Re: [Rdkit-discuss] Hankering after faster builds

2016-12-02 Thread Gianluca Sforna
On Fri, Dec 2, 2016 at 6:29 PM, Tim Dudgeon wrote: > But since I've been working with the Release_2016_09_2 release my Docker > image builds on Docker Hub [1] are timing out as they sometimes exceed > the 2 hour limit. If I try at a quiet time I can sometimes get them to > complete, but I suppose

Re: [Rdkit-discuss] Cannot import rdBase after installed rdkit by source in a non-administrator linux cluster

2017-03-29 Thread Gianluca Sforna
ion phase period on March 31; I do hope your admins have an upgrade path for your cluster because it will stop receiving security updates very soon now. https://access.redhat.com/support/policy/updates/errata -- Gianluca Sforna http://plus.google.com/+gianlucasforna - http://twitter.com/giallu Tink

Re: [Rdkit-discuss] RDKit on armv7h

2017-06-02 Thread Gianluca Sforna
On Thu, Jun 1, 2017 at 12:03 AM, Samo Turk wrote: > Thanks! It seems to work, but it's still compiling. Rockchip CPU in my > Chromebook is not very fast.. > How did it turn out? According to my Fedora builds, compiling is fine but tests are going to fail :) -- Gianluc

[Rdkit-discuss] RPM maintenance status

2017-11-24 Thread Gianluca Sforna
coprs/giallu/rdkit/ x86_64 only for Fedora 26, Fedora 27 and RHEL/CentOS 7 Hope that helps Gianluca -- Gianluca Sforna http://plus.google.com/+gianlucasforna - http://twitter.com/giallu Tinker Garage - http://tinkergara

Re: [Rdkit-discuss] RPM distros

2017-12-01 Thread Gianluca Sforna
pm > RDKit-2018.03.1.dev1-Linux-Python.rpm > RDKit-2018.03.1.dev1-Linux-Runtime.rpm Sorry guys, I got back on the list mid-thread so I really need to ask: is there a reason why you are trying to use cpack to build RPMs, instead of the standard rpmbuild tools? -- Gianluca Sforna http://p

Re: [Rdkit-discuss] Support for newer conda versions

2017-12-05 Thread Gianluca Sforna
it/ HTH Gianluca -- Gianluca Sforna http://plus.google.com/+gianlucasforna - http://twitter.com/giallu Tinker Garage - http://tinkergarage.it -- Check out the vibrant tech community on one of the world's most engagi

[Rdkit-discuss] 2019.03.1 Compile failure

2019-04-12 Thread Gianluca Sforna
y I don't have time now to track it down, so any help is appreciated. Regards Gianluca -- Gianluca Sforna ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Adding molecules to pandas dataframe

2019-07-25 Thread Gianluca Sforna
docs and examples I found around always assume you have a SMILES string to start with. Any pointers? -- Gianluca Sforna ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Adding molecules to pandas dataframe

2019-07-26 Thread Gianluca Sforna
ting: > https://gist.github.com/greglandrum/914ae66fd2f97addbbd472ae726567b1 > > -greg > > > On Thu, Jul 25, 2019 at 4:45 PM Gianluca Sforna wrote: >> >> Hi all, >> is it possible to manually add molecules to a pandas dataframe? I am >> reading a bunch of mol2 files, adding some properti

Re: [Rdkit-discuss] MolDrawing.registerCanvas('agg') missing in SVN

2011-06-14 Thread Gianluca Sforna
having a black variant enough? that would imply just swapping the background color with the default bond color -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- EditLiv

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q2 2011 Release Available

2011-07-07 Thread Gianluca Sforna
hat means python bindings are basically unusable right now unless you also activate Inchi support. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- All of

Re: [Rdkit-discuss] label properties on 2D depiction

2011-07-12 Thread Gianluca Sforna
ype of highlighting (changing the backbone color is not always suitable). Can't sign off any timing though, it mostly depend about whether I'll need those at work Cheers G. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://tw

Re: [Rdkit-discuss] Problem when building RDKit 2011_09 on CentOs (ouch!)

2011-11-24 Thread Gianluca Sforna
ed with -fPIC (that's why you get the same error, compiling rdkit with or witout -fPIC does not affect libpython). I think the easiest solution would be to use the dynamic library libpython2.7.so instead, which I hope is included in the ROCKS distribution. -- Gia

Re: [Rdkit-discuss] Problem when building RDKit 2011_09 on CentOs (ouch!)

2011-11-24 Thread Gianluca Sforna
e to move away from 2.4 Hope that helps G. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- All the data continuously generated in your IT infrastructure contains a

Re: [Rdkit-discuss] Building the RDKit on CentOS 5.7

2011-12-19 Thread Gianluca Sforna
more spare time to bring it on. * Is python 2.7 really required? I know 2.4 is getting pretty old but if we can manage to keep it supported it would be very nice. Alternatively, EPEL ships a python26 package that I would use rather than compiling from sources. -- Gianluca Sforna http://morefedo

Re: [Rdkit-discuss] [Rdkit-devel] 2012.03 (Q1 2012) RDKit release

2012-04-13 Thread Gianluca Sforna
exit /usr/lib64/libSmilesParse.so.1.2012.03.1 exit@GLIBC_2.2.5 rdkit.x86_64: W: shared-lib-calls-exit /usr/lib64/libSLNParse.so.1.2012.03.1 exit@GLIBC_2.2.5 Cheers G. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu --

Re: [Rdkit-discuss] [Rdkit-devel] 2012.03 (Q1 2012) RDKit release

2012-04-16 Thread Gianluca Sforna
On Sat, Apr 14, 2012 at 6:29 AM, Greg Landrum wrote: > On Fri, Apr 13, 2012 at 9:03 PM, Gianluca Sforna wrote: >> >> Apparently, the tarball filename grew a ".src" suffix. If this new >> naming scheme is going to stick I can adapt the package, otherwise I'd &

Re: [Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.

2012-04-25 Thread Gianluca Sforna
to dig details now, but IIRC there are two different cartridges, one for 8.x and another one for 9.x. Just to be sure, I'd double check you are installing the right one in there. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/g

Re: [Rdkit-discuss] MolBlock for a fragment

2012-05-24 Thread Gianluca Sforna
ut giving your data to Accelrys site) is not covering this in much details, but from what I've gathered the use of bond types > 3 is reserved to substructure queries - you can use ctabs to make searches, much like SMARTS - so I would not expect programs (inclusing RDkit) to load it as a

Re: [Rdkit-discuss] Largest Common Substructure

2012-05-25 Thread Gianluca Sforna
ism techniques, is > there some out-of-the-box functionality for this? > Does anyone have some pointers on this subject? Maybe you missed this recent item? http://www.dalkescientific.com/writings/diary/archive/2012/05/12/mcs_background.html -- Gianluca Sforna http://morefedora.blogspot.com

Re: [Rdkit-discuss] [Rdkit-devel] 2012.06 (Q2 2012) RDKit release

2012-07-11 Thread Gianluca Sforna
etc) http://giallu.fedorapeople.org/rdkit/ They are all 64bit; 32 bit and F16 packages available upon request. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- Live Security Virtual

Re: [Rdkit-discuss] RDKIT installation issue on Centos 5.6

2012-07-19 Thread Gianluca Sforna
; 0. do *not* use gcc v4.1.x to build RDKit -- I am using v4.5.3. That is a > source of mishap and doom. As I noted earlier, the compiler should not be an issue anymore, just make sure you have gcc-4.1.2-49.el5 or newer. -- Gianluca Sforna http://morefedora.blogspot.com http:

Re: [Rdkit-discuss] (no subject)

2012-07-28 Thread Gianluca Sforna
how to modify the homebrew recipe so it has cairo/pycairo included in the build. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- Live Security Virtual Conference Exclusi

Re: [Rdkit-discuss] building rdkit under CentOS

2012-09-04 Thread Gianluca Sforna
on dance at each release. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- Live Security Virtual Conference Exclusive live event will cover all the ways today

Re: [Rdkit-discuss] [Rdkit-devel] RDKit on Github

2012-10-05 Thread Gianluca Sforna
On Fri, Oct 5, 2012 at 7:36 AM, Greg Landrum wrote: > I mentioned at the UGM that Gianluca Sforna has set up a mirror of the > RDKit subversion repository. > The repository is here: https://github.com/rdkit/rdkit > Thanks Greg, I really looked forward to join you for the UGM, but u

Re: [Rdkit-discuss] [Rdkit-devel] 2012.09 (Q3 2012) RDKit release

2012-10-21 Thread Gianluca Sforna
failing? Some expect a failure so I can't readily tell from the log which ones are problematic. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- Everyone hat

Re: [Rdkit-discuss] [Rdkit-devel] 2012.09 (Q3 2012) RDKit release

2012-10-22 Thread Gianluca Sforna
occurred on line 267 in file /builddir/build/BUILD/RDKit_2012_09_1/Code/GraphMol/Atom.cpp 76: Failed Expression: dp_mol 76: -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu --

Re: [Rdkit-discuss] better error messages (vol 3)

2012-11-08 Thread Gianluca Sforna
show atom indexes starting from 1. No one except RMS counts from 0 :) -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- Everyone hates slow websites. So do we. Make

Re: [Rdkit-discuss] RDKit_2012_09_1 build errors

2012-12-18 Thread Gianluca Sforna
ne reason why the 'package everything in proper RPM files' is always preferable, as RPM maintains its own DB of the installed files and it is able to remove all the old ones during upgrades. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu

Re: [Rdkit-discuss] [Rdkit-devel] Getting ready for the Q4 2012 release

2013-01-06 Thread Gianluca Sforna
e is still there. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and

Re: [Rdkit-discuss] Getting ready for the Q4 2012 release

2013-01-07 Thread Gianluca Sforna
nstances, I got a report of python crashing during those tests but I never got around determining what the cause could be. I will come back with the results of the new build. Thanks G. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q4 2012 release

2013-01-13 Thread Gianluca Sforna
ecode.com/files/RDKit_2012_12_1beta1.tgz > RPM packages builds correctly in Fedora 17/18. CentOS/RHEL 6 builds fails because postgres 9.1 or newer is now required. If this is the case also for the final release, I will disable the cartridge in the EL builds. Thanks for the notice G. -- Gia

Re: [Rdkit-discuss] Beta of Q4 2012 release

2013-01-13 Thread Gianluca Sforna
.x, this will be there for the whole support lifecycle of the EL6, that is, until 2020. Given we are talking about a 3 years old product and there are no newer release (IIRC RHEL 7 is in beta right now), I doubt anyone on RHEL have a chance to use newer versions. I hope this counts as a valid argument

Re: [Rdkit-discuss] Beta of Q4 2012 release

2013-01-14 Thread Gianluca Sforna
e on that and notify you in case any 9.x appears in the repos > Gianluca: would I need to do a new beta release for your testing to work or > can you pull from svn? svn is fine for me -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/g

Re: [Rdkit-discuss] [Rdkit-devel] 2012.12 (Q4 2012) RDkit release

2013-01-22 Thread Gianluca Sforna
b them from: http://giallu.fedorapeople.org/rdkit-2012.12/ -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- Master Visual Studio, SharePoint, SQL, ASP.NET, C#

Re: [Rdkit-discuss] [Rdkit-devel] 2012.12 (Q4 2012) RDkit release

2013-01-22 Thread Gianluca Sforna
he rdkit.org namespace, I have surely nothing against :) -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, H

[Rdkit-discuss] Updated rpm packages

2013-02-07 Thread Gianluca Sforna
Hi all, I just updated the rdkit packages in my fedorapeople space: http://giallu.fedorapeople.org/rdkit-2012.12/ to include support for the inchi library. As usual, feel free to contact me for any question about these packages -- Gianluca Sforna http://morefedora.blogspot.com http

Re: [Rdkit-discuss] Coding convention/style?

2013-04-24 Thread Gianluca Sforna
rdkit@github master having commit access to SVN it would be possible to push commits from git to svn, but I have no such access and honestly I just hope we drop svn at some point and just use git :) -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/

Re: [Rdkit-discuss] [Rdkit-devel] 2013.03 (Q1 2013) RDkit release

2013-04-27 Thread Gianluca Sforna
2013.03/ I am sorry I did not find yet a reviewer for the package so it could go into the official repo. After this update I will try to lobby for it a little more. If you know any Fedora packager please ask him to have a look at https://bugzilla.redhat.com/show_bug.cgi?id=804125 Enjoy G. -- Gian

Re: [Rdkit-discuss] install RDKit on CentOS

2013-07-15 Thread Gianluca Sforna
On Sun, Jul 14, 2013 at 10:57 PM, Yingfeng Wang wrote: > I failed to install RDKit on CentOS. > Which version of centos? I have packages for version 6 (64 bit) ready to install with yum in http://giallu.fedorapeople.org/rdkit-2013.03/el6-x86_64/ -- Gianluca Sforna

Re: [Rdkit-discuss] 2013.06 (Q2 2013) RDKit release

2013-07-30 Thread Gianluca Sforna
ra 19 and RHEL6 at: http://giallu.fedorapeople.org/rdkit-2013.06/ as usual, feel free to report me any issue with those. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu

Re: [Rdkit-discuss] InChI support in Ubuntu repository version of rdkit?

2013-08-02 Thread Gianluca Sforna
On Fri, Aug 2, 2013 at 9:35 PM, Richard West wrote: > 1) Is there any hope of getting a version with InChI into the Ubuntu > repositories? You can probably report a bug against the package and let the maintainer rebuild it with inchi suppot. -- Gianluca Sforna http://morefedora.blogsp

Re: [Rdkit-discuss] Unable to build RDKit_2013_06_1 and Git version on Arch Linux

2013-08-17 Thread Gianluca Sforna
On Fri, Aug 16, 2013 at 8:30 PM, greg landrum wrote: > I definitely haven't tried it with bison 3.0 (and am kind of amazed that such > a version exists!) And then they mock Fedora for being too bleeding edge... :P -- Gianluca Sforna http://morefedora.blogspot.com http://ident

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-11 Thread Gianluca Sforna
On Thu, Sep 12, 2013 at 12:25 AM, Greg Landrum wrote: > Glad the problem is solved. And without disabling SELinux :) http://stopdisablingselinux.com/ -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/gia

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-12 Thread Gianluca Sforna
e software, so I tend to trust it more than many other things like, hard disks http://spritesmods.com/?art=hddhack :) -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -

Re: [Rdkit-discuss] docker.io - container for fully fledged rdkit installation on linux?

2013-09-23 Thread Gianluca Sforna
m/2013/09/19/dotcloud-pivots-and-wins-big-with-docker-the-cloud-service-now-part-of-red-hat-openshift/ As enthusiast openshift user I will probably try to get rdkit running there using docker -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.c

Re: [Rdkit-discuss] Pre-release version of the 2013_09_1 release available

2013-09-29 Thread Gianluca Sforna
be useful for > Windows users attending the UGM. Do anyone need RPMs for the UGM? I could kick a build or two, just let me know version/arch needed -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu

Re: [Rdkit-discuss] javascript html5 renderer

2013-10-04 Thread Gianluca Sforna
back the resulting artifact for output. I guess if you want to add it quickly the MolToJSON approach is the obvious choice. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- O

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q3 2013 release available

2013-10-24 Thread Gianluca Sforna
^ compilation terminated. Did I mess up something? -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- October Webinars: Code for Performance F

Re: [Rdkit-discuss] RDKit & Java/Swig & Boost

2014-01-12 Thread Gianluca Sforna
d, I recently rebuild rdkit in copr and you can find the resulting binary RPMs here: http://copr.fedoraproject.org/coprs/giallu/rdkit/ Regards Gianluca -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/gial

Re: [Rdkit-discuss] RDKit & Java/Swig & Boost

2014-01-14 Thread Gianluca Sforna
> I have the most recent version of RDKit built and everything has passed the > tests. Great! > Is there something else > in the environment I need to set up to get through the UnsatisfiedLinkError? Sorry, I can't help there as I don't use Java. I hope someone else can chime

[Rdkit-discuss] Substructure search test cases

2014-01-15 Thread Gianluca Sforna
Before I go digging the repository, can anyone tell me if the test suite includes stuff for the postgres cartridge? I am particularly interested in comparing results and performance with a custom solution I have here. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu

Re: [Rdkit-discuss] InChI roundtrip

2014-01-28 Thread Gianluca Sforna
orge.net/mailarchive/message.php?msg_id=30885294 -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- WatchGuard Dimension instantly turns raw network data into actionable s

Re: [Rdkit-discuss] rdkit RPM for CentOS 5.3 ?

2014-02-26 Thread Gianluca Sforna
server. For a start, you can make your life easier by adding the EPEL repository and pulling python26 package from there. IIRC the only real blocker that prevented me from building RDKit against CentOS5 + EPEL was flex -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/g

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2014 release available

2014-05-07 Thread Gianluca Sforna
_03_1beta1.tar.gz I checked this builds in Fedora, a scratch build: http://koji.fedoraproject.org/koji/taskinfo?taskID=6821330 You may be happy to know it also works for ARM :) -- Gianluca Sforna http://morefedora.blogspot.com http://plus.google.com/+gianlucasforna - http://twitter.com/gial

Re: [Rdkit-discuss] [Rdkit-devel] 2014.03 (Q1 2014) RDKit release

2014-05-12 Thread Gianluca Sforna
or Fedora/CentOS. If someone is interested I can try including them in my next build. -- Gianluca Sforna http://morefedora.blogspot.com http://plus.google.com/+gianlucasforna - http://twitter.com/giallu -- "Acceler

Re: [Rdkit-discuss] [Rdkit-devel] 2014.03 (Q1 2014) RDKit release

2014-05-26 Thread Gianluca Sforna
tically receive the update as soon as it finish building. -- Gianluca Sforna http://morefedora.blogspot.com http://plus.google.com/+gianlucasforna - http://twitter.com/giallu -- The best possible search technologies

Re: [Rdkit-discuss] [Rdkit-devel] 2014.03 (Q1 2014) RDKit release

2014-05-27 Thread Gianluca Sforna
On Tue, May 27, 2014 at 9:36 AM, GALLY Jose Manuel < jose.manuel.ga...@gmail.com> wrote: > Do you think you could fix this? > ​Yeah, I got it fixed. Thanks for noticing. -- Gianluca Sforna http://morefedora.blogspot.com http://plus.google.com/+gianlucasforna - http://twitte

Re: [Rdkit-discuss] installation problem

2014-06-06 Thread Gianluca Sforna
. If you > set RDK_BUILD_SWIG_WRAPPERS to OFF in your cmake command line, the java > wrapper will be disabled. Is there a reason why we don't just use SWIG for all wrappers, including python? I guess it would help exposing build or runtime issues with swig and probably also reduce build dependencie

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q3 2014 release now up

2014-10-29 Thread Gianluca Sforna
uild updated RPMs. Not critical, but this tag misses the "Release_" prefix so my download script broke :) Other than that, it builds correctly on Fedora 20 and 21 (64bit) -- Gianluca Sforna http://morefedora.blogspot.com http://plus.google.com/+gianlucasf

Re: [Rdkit-discuss] [Rdkit-devel] 2014.09 (Q3 2014) RDKit Release

2014-10-30 Thread Gianluca Sforna
-bit Windows binaries for > Java. binary RPMs for Fedora 20, 21 and RHEL/Centos 6, 7 are available from: https://copr.fedoraproject.org/coprs/giallu/rdkit/ -- Gianluca Sforna http://morefedora.blogspot.com http://plus.google.com

Re: [Rdkit-discuss] Inchi support with binary package Windows

2015-01-13 Thread Gianluca Sforna
s you have to actually compile the sources with the support activated, so if the Windows package was not compiled with inchi I guess there is no way to use it. -- Gianluca Sforna http://morefedora.blogspot.com http://plus.google.com/+gianlucasforna - htt

[Rdkit-discuss] Java wrappers

2015-04-26 Thread Gianluca Sforna
: /builddir/build/BUILD/rdkit-Release_2015_03_1beta1/Code/JavaWrappers/gmwrapper/libGraphMolWrap.so: undefined symbol: _ZTVN5RDKi t9MolDraw2DE Any idea? -- Gianluca Sforna http://morefedora.blogspot.com http://plus.google.com/+gianlucasforna - http://twitter.com/giallu

Re: [Rdkit-discuss] Java wrappers

2015-04-27 Thread Gianluca Sforna
rpath,/builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib: -- Gianluca Sforna http://morefedora.blogspot.com http://plus.google.com/+gianlucasforna - http://twitter.com/giallu -- One dashboard for servers and appli

Re: [Rdkit-discuss] Java wrappers

2015-04-29 Thread Gianluca Sforna
7fa53b8e) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x7fa53b6c9000) libc.so.6 => /lib64/libc.so.6 (0x7fa53b30b000) /lib64/ld-linux-x86-64.so.2 (0x7fa54039d000) However, I found that if you run java with the -cp option (as we do in tests) then the CLASSPATH env variable is ignored. I

Re: [Rdkit-discuss] new parallel execution features in the 2015.03 RDKit release

2015-07-06 Thread Gianluca Sforna
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Re: [Rdkit-discuss] 2015.09 (Q3 2015) RDKit Release

2015-11-18 Thread Gianluca Sforna
On Wed, Nov 18, 2015 at 3:24 AM, Greg Landrum wrote: > > Gianluca's binary RPMs for Fedora 20, 21 and RHEL/Centos 6, 7 will be > available from > this repository: > https://copr.fedoraproject.org/coprs/giallu/rdkit/ 2015_09_1 is already there for Fedora 21, 22 and 23, I'm rebuilding now for 2015_

Re: [Rdkit-discuss] RDKit Linux install error

2015-11-28 Thread Gianluca Sforna
l-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple > OSs. > http://pubads.g.doubleclick.net/gamp

Re: [Rdkit-discuss] [off topic] What comes next

2015-12-09 Thread Gianluca Sforna
atulations and all the best for this new adventure! -- Gianluca Sforna http://morefedora.blogspot.com http://plus.google.com/+gianlucasforna - http://twitter.com/giallu -- ___

Re: [Rdkit-discuss] Latest version

2015-12-10 Thread Gianluca Sforna
m after. In this case, you probably want to install the librdkit-dev package -- Gianluca Sforna http://morefedora.blogspot.com http://plus.google.com/+gianlucasforna

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

2016-04-11 Thread Gianluca Sforna
On Thu, Apr 7, 2016 at 6:24 AM, Greg Landrum wrote: > I have tagged a beta of the next RDKit release here: > https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1b1 Tried to rebuild the RPMs but got this right on cmake: -- Found INCHI: /usr/lib64/libinchi.so CMake Error at External/INCH

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

2016-04-12 Thread Gianluca Sforna
On Mon, Apr 11, 2016 at 1:20 PM, Greg Landrum wrote: > This could be the issue fixed by this PR from Matt Swain: > https://github.com/rdkit/rdkit/pull/856 Yeah, that's it. Thanks! -- Gianluca Sforna http://plus.google.com/+gianlucasforna - http://twitter.com/giallu Tinker Ga

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

2016-04-12 Thread Gianluca Sforna
On Tue, Apr 12, 2016 at 11:51 AM, Gianluca Sforna wrote: > On Mon, Apr 11, 2016 at 1:20 PM, Greg Landrum wrote: >> This could be the issue fixed by this PR from Matt Swain: >> https://github.com/rdkit/rdkit/pull/856 > > Yeah, that's it. Thanks! But no joy still

Re: [Rdkit-discuss] Boost 1.61 and the RDKit work together.

2016-06-01 Thread Gianluca Sforna
ting the code with v1.61 of boost > and everything works fine. So we still need to skip 1.60? I think that's what Fedora 24 is shipping -- Gianluca Sforna http://plus.google.com/+gianlucasforna - http://twitter.com/giallu Tinker Garag

Re: [Rdkit-discuss] PgSQL / cartridge installation problem

2016-07-28 Thread Gianluca Sforna
uild should be fine. -- Gianluca Sforna http://plus.google.com/+gianlucasforna - http://twitter.com/giallu Tinker Garage - http://tinkergarage.it -- ___ Rdkit-discuss mailing

Re: [Rdkit-discuss] FYI: problems with boost 1.60 and the RDKit

2016-08-04 Thread Gianluca Sforna
ora 25) has been patched, so it can be used to build rdkit. https://bodhi.fedoraproject.org/updates/FEDORA-2016-fff5d70162 Regards G. -- Gianluca Sforna http://plus.google.com/+gianlucasforna - http://twitter.com/giallu Tinker Garage - http://tink

[Rdkit-discuss] PGSQL build with cmake and system inchi

2016-08-05 Thread Gianluca Sforna
CMakeFile is hardcoding the "Inchi" name as library to search for Maybe it should be using the "FindInchi" macro and avoid putting the explicit name there? Not sure how to patch it. -- Gianluca Sforna http://plus.google.com/+gianlucasforna - http://twitter.com/giallu

Re: [Rdkit-discuss] PGSQL build with cmake and system inchi

2016-08-06 Thread Gianluca Sforna
Thanks for the patch Paolo. Is test 97 new? It seems it wants to use the Postgres server and fails, I am afraid it is not easy to have it working at build time. On Fri, Aug 5, 2016 at 11:45 AM, Gianluca Sforna wrote: > Anyone ever tested this combo? > > I am currently getting: >

Re: [Rdkit-discuss] PGSQL build with cmake and system inchi

2016-08-08 Thread Gianluca Sforna
On Mon, Aug 8, 2016 at 11:20 AM, Greg Landrum wrote: > As Paolo points out, this really just integrates the cartridge tests into > the rest of the test suite. Ok, so basically I was not seeing this before because I was not running it with the old style build > > @Gianluca: If you need to be able

Re: [Rdkit-discuss] Please help test the new build system

2010-01-17 Thread Gianluca Sforna
On Sun, Jan 17, 2010 at 10:14 AM, Greg Landrum wrote: > I have successfully specified an alternate > boost directory using cmake v2.8.0, but I guess Fedora 12 comes with > v2.6. Yes, for the records it's 2.6.4. -- Gianluca Sforna http://morefedora.blogspot.com http://www.l

Re: [Rdkit-discuss] beta of Q4 2009 release up

2010-01-20 Thread Gianluca Sforna
N_INCLUDE_DIR}) +find_package(PythonLibs REQUIRED) +include_directories(${PYTHON_INCLUDE_PATH}) link_directories(${PYTHON_LIBRARIES}) + find_package(NumPy REQUIRED) include_directories(${PYTHON_NUMPY_INCLUDE_P

Re: [Rdkit-discuss] beta of Q4 2009 release up

2010-01-20 Thread Gianluca Sforna
h a system wide boost and a local one, I compiled against system stuff. -- Gianluca Sforna http://morefedora.blogspot.com http://www.linkedin.com/in/gianlucasforna -- Throughout its 18-year history, RSA Conference consis

Re: [Rdkit-discuss] beta of Q4 2009 release up

2010-01-20 Thread Gianluca Sforna
s to your preferred boost installation? -- Gianluca Sforna http://morefedora.blogspot.com http://www.linkedin.com/in/gianlucasforna -- Throughout its 18-year history, RSA Conference consistently attracts the world's best

Re: [Rdkit-discuss] beta of Q4 2009 release up

2010-01-21 Thread Gianluca Sforna
On Thu, Jan 21, 2010 at 8:58 AM, Gianluca Sforna wrote: > On Wed, Jan 20, 2010 at 7:59 PM, Greg Landrum wrote: >> The reason for the hackery is to allow an alternate python >> installation to be used on systems that have more than one. This was >> the only way I could figu

Re: [Rdkit-discuss] beta of Q4 2009 release up

2010-01-21 Thread Gianluca Sforna
t; with the python versions. sorry for mixing up the two topics. For python, it seems you need to set PYTHON_INCLUDE_PATH and PYTHON_LIBRARY in order to use your own version -- Gianluca Sforna http://morefedora.blogspot.com http://www.lin

Re: [Rdkit-discuss] beta of Q4 2009 release up

2010-01-21 Thread Gianluca Sforna
On Thu, Jan 21, 2010 at 2:23 PM, Greg Landrum wrote: > On Thu, Jan 21, 2010 at 11:32 AM, Gianluca Sforna wrote: >> For python, it seems you need to set PYTHON_INCLUDE_PATH and >> PYTHON_LIBRARY in order to use your own version > > exactly, and that's what the "hac

Re: [Rdkit-discuss] beta of Q4 2009 release up

2010-01-21 Thread Gianluca Sforna
module is likely different. However, you could try applying the patch I proposed and report if things improves -- Gianluca Sforna http://morefedora.blogspot.com http://www.linkedin.com/in/gianlucasforna -- Through

Re: [Rdkit-discuss] beta of Q4 2009 release up

2010-01-21 Thread Gianluca Sforna
ens as expected against 2.4.6 > > I'm not currently at the machine where this problem arose, but I will > send an example tomorrow morning to show what I mean. While you are at that, please double check the PYTHON_LIBRARY vs PYTHON_LIBRARIES I mentioned above. Thanks for your patienc

[Rdkit-discuss] Q4_2009 do not build out of the box

2010-03-01 Thread Gianluca Sforna
REQUIRED) include_directories(${PYTHON_NUMPY_INCLUDE_PATH}) to let the build proceed as expected. HTH Gianluca -- Gianluca Sforna http://morefedora.blogspot.com http://www.linkedin.com/in/gianlucasforna -- Download Intel

Re: [Rdkit-discuss] Q4_2009 do not build out of the box

2010-03-04 Thread Gianluca Sforna
On Mon, Mar 1, 2010 at 9:26 PM, Greg Landrum wrote: > On Mon, Mar 1, 2010 at 11:24 AM, Gianluca Sforna wrote: >> Sorry for resurrecting this topic, but I just realized the Q4 2009 >> release tarball do not compile out of the box due to the previously >> discussed PYTHON_

Re: [Rdkit-discuss] Help wanted: packaging the RDKit

2010-07-02 Thread Gianluca Sforna
On Fri, Jul 2, 2010 at 10:31 AM, Greg Landrum wrote: > Do any of you have experience of this? I'm a Fedora package maintainer so I guess I can have a look at it. -- Gianluca Sforna http://morefedora.blogspot.com http://www.linkedin.com/in/gianlu

[Rdkit-discuss] RDKit packaging issues

2010-07-05 Thread Gianluca Sforna
standard paths, but I'd need to dig manuals and/or other projects to find out the correct spell to cast... I think I could uncover more packaging issues as I proceed, but I wanted to kick off some discussions on these points early so we move on quicker toward good linux packages. Cheers G. -

Re: [Rdkit-discuss] install problems on Centos 5.3

2010-07-26 Thread Gianluca Sforna
/decl.c:5067 > Please submit a full bug report, > with preprocessed source if appropriate. > See http://bugzilla.redhat.com/bugzilla> for instructions. This looks like a gcc bug I reported: https://bugzilla.redhat.com/show_bug.cgi?id=582682 -- Gianluca Sforna http://more

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