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,
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.
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/rdkit/
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Rdkit
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
>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.
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updated to 2016.03.5, I regularly miss those minor
release (are they announced somewhere?)
let me know if it works for you
G.
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://bugzilla.redhat.com/show_bug.cgi?id=1359402
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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
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
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Tink
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 :)
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coprs/giallu/rdkit/
x86_64 only for Fedora 26, Fedora 27 and RHEL/CentOS 7
Hope that helps
Gianluca
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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?
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it/
HTH
Gianluca
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y I don't have time now to track it down, so any help is
appreciated.
Regards
Gianluca
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docs and examples I found around always assume you have a
SMILES string to start with.
Any pointers?
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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
having a black variant enough?
that would imply just swapping the background color with the default bond color
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hat means python bindings are
basically unusable right now unless you also activate Inchi support.
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All of
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.
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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.
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e to move away from 2.4
Hope that helps
G.
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All the data continuously generated in your IT infrastructure
contains a
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.
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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.
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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
&
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.
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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
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
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etc)
http://giallu.fedorapeople.org/rdkit/
They are all 64bit; 32 bit and F16 packages available upon request.
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; 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.
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how to modify the homebrew recipe
so it has cairo/pycairo included in the build.
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Exclusi
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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
failing? Some expect a
failure so I can't readily tell from the log which ones are
problematic.
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occurred on line 267 in file
/builddir/build/BUILD/RDKit_2012_09_1/Code/GraphMol/Atom.cpp
76: Failed Expression: dp_mol
76:
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show atom indexes starting from 1.
No one except RMS counts from 0 :)
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Make
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.
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e is still there.
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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.
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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.
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.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
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
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b them from: http://giallu.fedorapeople.org/rdkit-2012.12/
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he rdkit.org namespace, I have surely nothing against :)
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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
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http
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 :)
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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.
--
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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/
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ra 19 and RHEL6 at:
http://giallu.fedorapeople.org/rdkit-2013.06/
as usual, feel free to report me any issue with those.
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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.
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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
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On Thu, Sep 12, 2013 at 12:25 AM, Greg Landrum wrote:
> Glad the problem is solved.
And without disabling SELinux :)
http://stopdisablingselinux.com/
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e software, so I tend to trust it more
than many other things like, hard disks
http://spritesmods.com/?art=hddhack
:)
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-
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
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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
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back the resulting artifact
for output.
I guess if you want to add it quickly the MolToJSON approach is the
obvious choice.
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O
^
compilation terminated.
Did I mess up something?
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F
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
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> 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
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.
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orge.net/mailarchive/message.php?msg_id=30885294
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WatchGuard Dimension instantly turns raw network data into actionable
s
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
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_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 :)
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or Fedora/CentOS. If someone is interested I can try including them
in my next build.
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"Acceler
tically receive the update as soon as it finish building.
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The best possible search technologies
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.
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. 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
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)
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-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/
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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.
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:
/builddir/build/BUILD/rdkit-Release_2015_03_1beta1/Code/JavaWrappers/gmwrapper/libGraphMolWrap.so:
undefined symbol: _ZTVN5RDKi
t9MolDraw2DE
Any idea?
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rpath,/builddir/build/BUILD/rdkit-Release_2015_03_1beta1/lib:
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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
#x27;t Limit Your Business. Reach for the Cloud.
>>>> GigeNET's Cloud Solutions provide you with the tools and support that
>>>> you need to offload your IT needs and focus on growing your business.
>>>> Configured For All Businesses. Start Your Cloud Today.
>
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_
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
atulations and all the
best for this new adventure!
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m after.
In this case, you probably want to install the librdkit-dev package
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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
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!
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Tinker Ga
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
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
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uild should be fine.
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ora 25) has
been patched, so it can be used to build rdkit.
https://bodhi.fedoraproject.org/updates/FEDORA-2016-fff5d70162
Regards
G.
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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.
--
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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:
>
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
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.
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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
h a system wide boost
and a local one, I compiled against system stuff.
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boost installation?
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Gianluca Sforna
http://morefedora.blogspot.com
http://www.linkedin.com/in/gianlucasforna
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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
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
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Gianluca Sforna
http://morefedora.blogspot.com
http://www.lin
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
module is likely different.
However, you could try applying the patch I proposed and report if
things improves
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Gianluca Sforna
http://morefedora.blogspot.com
http://www.linkedin.com/in/gianlucasforna
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Through
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
REQUIRED)
include_directories(${PYTHON_NUMPY_INCLUDE_PATH})
to let the build proceed as expected.
HTH
Gianluca
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Gianluca Sforna
http://morefedora.blogspot.com
http://www.linkedin.com/in/gianlucasforna
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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_
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.
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Gianluca Sforna
http://morefedora.blogspot.com
http://www.linkedin.com/in/gianlu
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.
-
/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
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Gianluca Sforna
http://more
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