Re: [Rdkit-discuss] cmake error building master

[Greg L. <gre...@gm...>]

I've been building with 1.65.1 and 1.63, but I don't think I've tried 1.64
at all.

I will take a look at the other problems tomorrow morning

On Thu, Apr 19, 2018 at 8:12 PM, Jason Biggs <jas...@gm...> wrote:

> Greg,
> I have boost version 1.64.  I found reference to this error on the web,
> always in reference to boost version 1.64.  But what I don't see is whether
> this is fixed in later or previous versions.
>
> I forgot to include the first error I get, actually during the cmake
> stage, when it tries to download the maeparser tarball.  Somehow the curl
> command isn't downloading the file with the right name.  I get this error
>
> - Found Threads: TRUE
> -- Boost version: 1.64.0
> -- Found the following Boost libraries:
> --   serialization
> == Using strict rotor definition
> Downloading https://codeload.github.com/schrodinger/maeparser/tar.gz/
> 83368293dcc0eb07562dadfb7728b8d18d23a6cb...
>   % Total    % Received % Xferd  Average Speed   Time    Time     Time
> Current
>                                  Dload  Upload   Total   Spent    Left
> Speed
> 100 24984  100 24984    0     0  73460      0 --:--:-- --:--:-- --:--:--
> 274k
> CMake Error at Code/cmake/Modules/RDKitUtils.cmake:198 (MESSAGE):
>   The md5 checksum for
>   base/rdkit/External/CoordGen/master.tar.gz
>   is incorrect; expected: 32c0c3b315bba49fbf4c41a07aa58528, found:
>   d41d8cd98f00b204e9800998ecf8427e
> Call Stack (most recent call first):
>   External/CoordGen/CMakeLists.txt:9 (downloadAndCheckMD5)
>
>
>
> If I go to the Coordgen directory after getting this error, I see the
> following
>
> drwxr-xr-x 3 jasonb users 4.0K Apr 19 13:06 .
> drwxr-xr-x 7 jasonb users 4.0K Apr 19 13:05 ..
> -rw-r--r-- 1 jasonb users  25K Apr 19 13:06 83368293dcc0eb07562dadfb7728b8
> d18d23a6cb
> -rw-r--r-- 1 jasonb users 2.8K Apr 19 13:05 CMakeLists.txt
> -rw-r--r-- 1 jasonb users 5.6K Apr 19 13:05 CoordGen.h
> -rw-r--r-- 1 jasonb users    0 Apr 19 13:06 master.tar.gz
> -rw-r--r-- 1 jasonb users  12K Apr 19 13:05 test.cpp
> drwxr-xr-x 2 jasonb users 4.0K Apr 19 13:05 Wrap
>
>
> So the curl command downloaded the tarball as "
> 83368293dcc0eb07562dadfb7728b8d18d23a6cb", and created an empty file
> "master.tar.gz" which of course doesn't match the md5 sum.  I definitely
> don't know enough about cmake, or curl for that matter, to see why this is
> happening.  But if I manually download the maeparser, the coordgenlibs, and
> the rapidjson files and put them in External/ then it works fine.
>
> Thanks,
> Jason
>
>
>
> Jason Biggs
>
>
> On Thu, Apr 19, 2018 at 12:42 PM, Greg Landrum <gre...@gm...>
> wrote:
>
>> Which version of boost is that?
>>
>> On Thu, 19 Apr 2018 at 19:34, Jason Biggs <jas...@gm...> wrote:
>>
>>> Trying to build on Scientific Linux release 6.9, and I'm getting boost
>>> serialization errors, both on the recent release branch and on master
>>>
>>>
>>> In file included from base/Boost/include/boost/numer
>>>> ic/ublas/vector.hpp:21:0,
>>>>                  from base/Boost/include/boost/numer
>>>> ic/ublas/matrix.hpp:18,
>>>>                  from base/rdkit/Code/GraphMol/Subst
>>>> ruct/ullmann.hpp:41,
>>>>                  from base/rdkit/Code/GraphMol/Subst
>>>> ruct/SubstructMatch.cpp:29:
>>>> base/Boost/include/boost/numeric/ublas/storage.hpp: In member function
>>>> ‘void boost::numeric::ublas::unbounded_array<T,
>>>> ALLOC>::serialize(Archive&, unsigned int)’:
>>>> base/Boost/include/boost/numeric/ublas/storage.hpp:299:18: error:
>>>> ‘make_array’ is not a member of ‘boost::serialization’
>>>>              ar & serialization::make_array(data_, s);
>>>>                   ^~~~~~~~~~~~~
>>>> base/Boost/include/boost/numeric/ublas/storage.hpp: In member function
>>>> ‘void boost::numeric::ublas::bounded_array<T, N,
>>>> ALLOC>::serialize(Archive&, unsigned int)’:
>>>> base/Boost/include/boost/numeric/ublas/storage.hpp:494:18: error:
>>>> ‘make_array’ is not a member of ‘boost::serialization’
>>>>              ar & serialization::make_array(data_, s);
>>>
>>>
>>>
>>> If I add
>>>
>>> #include <boost/serialization/array_wrapper.hpp>
>>>
>>>
>>> to the SubstructMatch.cpp file, as instructed here
>>> https://stackoverflow.com/q/44534516/4712538, then compilation
>>> continues fine.
>>>
>>>
>>> Jason
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>>> _________________________________________
>>> Rdkit-discuss mailing list
>>> Rdk...@li...
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>
>