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.nealschnei...@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
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
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>>>>> Rdkit-discuss mailing list
>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>
>>>>
>>>> ------------------------------------------------------------------------------
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>>>>
>>>
>
>
> --
> 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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