Hi, encountered this too. At least for me the problem was self-built cmake that did not automatically support https/ssl, which caused the empty downloads. The solution was to re-build cmake using the following instructions: https://github.com/ruslo/hunter/issues/328#issuecomment-198672048
Cheers, Juuso On Fri, Jun 29, 2018 at 12:28 AM Kaushik Lakkaraju <kaus...@silcsbio.com> wrote: > > 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 >> Schrödinger, 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 >>>>>> Schrödinger, 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 >>> Baltimore, MD 21202 >>> (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 > ------------------------------------------------------------------------------ > 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
