master.tar.gz is empty.
kaushik@kuta:/data/kaushik/src/rdkit-Release_2018_03_2/External/CoordGen$
du -sh *
4.0K CMakeLists.txt
8.0K CoordGen.h
16K Wrap
0 master.tar.gz
12K test.cpp
On Thu, Jun 28, 2018 at 4:39 PM, Dan Nealschneider <
dan.nealschnei...@schrodinger.com> wrote:
> Oh, good point (that the version is pinned). I guess that I saw an md5
> mismatch which I addressed by submitting https://github.com/rdkit/
> rdkit/pull/1904. That case caused a md5sum mismatch because the reference
> md5sum was being compared to a different library. It would be interesting
> to know which library is stored in /data/kaushik/src/rdkit-
> Release_2018_03_2/External/CoordGen/master.tar.gz (Is it actually
> maeparser, or is it coordgen?).
>
>
> - dan nealschneider
>
> (né wandschneider)
>
> Senior Developer
> Schr*ö*dinger, Inc
> Portland, OR
>
>
>
>
> On Thu, Jun 28, 2018 at 1:13 PM Kaushik Lakkaraju <kaus...@silcsbio.com>
> wrote:
>
>> Thanks for helping out Greg and Dan.
>>
>> @Greg, rdkit version 2018_03_2.
>>
>> -Kaushik
>>
>>
>> On Thu, Jun 28, 2018 at 3:53 PM, Greg Landrum <greg.land...@gmail.com>
>> wrote:
>>
>>>
>>>
>>> On Thu, Jun 28, 2018 at 12:52 PM Greg Landrum <greg.land...@gmail.com>
>>> wrote:
>>>
>>>> I don't think that should be a problem. The versions should already be
>>>> pinned to a particular commit of both libraries in this case:
>>>> https://github.com/rdkit/rdkit/blob/Release_2018_03_2/
>>>> External/CoordGen/CMakeLists.txt
>>>>
>>>> I'm somewhat confused that you're seeing md5 errors at all since the
>>>> 2018.03.2 version of the code doesn't have md5s for this package.
>>>>
>>>
>>> Sorry, mis-spoke here. The coordgen download isn't checking an md5 but
>>> the maeparser download is.
>>>
>>> I'm not at all sure where the problem is coming from though.
>>>
>>> -greg
>>>
>>>
>>>
>>>
>>>> @Kaushik: which version of the RDKit source are you using?
>>>>
>>>> -greg
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Jun 28, 2018 at 12:46 PM Dan Nealschneider <dan.nealschneider@
>>>> schrodinger.com> wrote:
>>>>
>>>>> I've noticed this as well, I think it's because maeparser has been
>>>>> updated since it was pinned within RDKit. You can work around this by
>>>>> downloading the mae[arser manually to External outside the make process.
>>>>> This may also be required for coordgen. I'll also submit a PR to either
>>>>> ignore the md5sum for these packages for now (this is what is done for
>>>>> other fast moving packages) or to get the correct tagged version of these
>>>>> libraries.
>>>>>
>>>>> - dan nealschneider
>>>>>
>>>>> (né wandschneider)
>>>>>
>>>>> Senior Developer
>>>>> Schr*ö*dinger, Inc
>>>>> Portland, OR
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Jun 25, 2018 at 2:19 PM Kaushik Lakkaraju <
>>>>> kaus...@silcsbio.com> wrote:
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I am trying to install rdkit from source on Ubuntu 14.04 using the
>>>>>> following commands. I have a previously compiled 2016 version on the same
>>>>>> machine, so my paths for boost, python etc are already set.
>>>>>>
>>>>>> The following is my sequence of steps:
>>>>>>
>>>>>> 1) wget https://github.com/rdkit/rdkit/archive/Release_2018_03_
>>>>>> 2.tar.gz
>>>>>>
>>>>>> 2) tar -xvzf Release_2018_03_2.tar.gz
>>>>>>
>>>>>> 3) cd rdkit-Release_2018_03_2
>>>>>>
>>>>>> 4) mkdir build
>>>>>>
>>>>>> 5) cd build
>>>>>>
>>>>>> 6) cmake .. -DCMAKE_INSTALL_PREFIX=/data/kaushik/apps/rdkit-2018
>>>>>>
>>>>>> Upon doing so, I bump into configuration errors :
>>>>>>
>>>>>> -- Boost version: 1.59.0
>>>>>>
>>>>>> -- Found the following Boost libraries:
>>>>>>
>>>>>> -- python
>>>>>>
>>>>>> PYTHON Py_ENABLE_SHARED: 1
>>>>>>
>>>>>> PYTHON USING LINK LINE: -pthread -shared -Wl,-O1
>>>>>> -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro
>>>>>> -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes
>>>>>> -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4
>>>>>> -Wformat
>>>>>> -Werror=format-security
>>>>>>
>>>>>> -- 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: 1.59.0
>>>>>>
>>>>>> -- Found the following Boost libraries:
>>>>>>
>>>>>> -- serialization
>>>>>>
>>>>>> == Using strict rotor definition
>>>>>>
>>>>>> Downloading https://codeload.github.com/schrodinger/maeparser/tar.gz/
>>>>>> 83368293dcc0eb07562dadfb7728b8d18d23a6cb...
>>>>>>
>>>>>> CMake Error at Code/cmake/Modules/RDKitUtils.cmake:194 (MESSAGE):
>>>>>>
>>>>>> The md5 checksum for
>>>>>>
>>>>>> /data/kaushik/src/rdkit-Release_2018_03_2/External/
>>>>>> CoordGen/master.tar.gz
>>>>>>
>>>>>> is incorrect; expected: 32c0c3b315bba49fbf4c41a07aa58528, found:
>>>>>>
>>>>>> d41d8cd98f00b204e9800998ecf8427e
>>>>>>
>>>>>> Call Stack (most recent call first):
>>>>>>
>>>>>> External/CoordGen/CMakeLists.txt:9 (downloadAndCheckMD5)
>>>>>>
>>>>>>
>>>>>>
>>>>>> -- Configuring incomplete, errors occurred!
>>>>>>
>>>>>>
>>>>>> Have others seen this problem? Could somebody please help with
>>>>>> proceeding forward with installation?
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Kaushik
>>>>>>
>>>>>> ------------------------------------------------------------
>>>>>> ------------------
>>>>>> 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
>>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
>>>>> 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
>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>
>>>>
>>
>>
>> --
>> Sirish Kaushik Lakkaraju, Ph.D.,
>> Director, Product Development
>> SilcsBio, LLC
>> 8 Market Place, Suite 300
>> <https://maps.google.com/?q=8+Market+Place,+Suite+300%C2%A0+Baltimore,+MD+21202&entry=gmail&source=g>
>> Baltimore, MD 21202
>> <https://maps.google.com/?q=8+Market+Place,+Suite+300%C2%A0+Baltimore,+MD+21202&entry=gmail&source=g>
>> (979) 587-3245
>> www.silcsbio.com
>>
>
--
Sirish Kaushik Lakkaraju, Ph.D.,
Director, Product Development
SilcsBio, LLC
8 Market Place, Suite 300
Baltimore, MD 21202
(979) 587-3245
www.silcsbio.com
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