Re: [Rdkit-discuss] 2018_03_2 md5 checksum problems
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 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 > 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 >> 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 >>> wrote: On Thu, Jun 28, 2018 at 12:52 PM Greg Landrum 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 > 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 >> 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 >>> >>> >>>
Re: [Rdkit-discuss] 2018_03_2 md5 checksum problems
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 > 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 >> wrote: >> >>> >>> >>> On Thu, Jun 28, 2018 at 12:52 PM Greg Landrum >>> 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 >>> 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
Re: [Rdkit-discuss] 2018_03_2 md5 checksum problems
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 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 > wrote: > >> >> >> On Thu, Jun 28, 2018 at 12:52 PM Greg Landrum >> 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 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 >
Re: [Rdkit-discuss] 2018_03_2 md5 checksum problems
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 wrote: > > > On Thu, Jun 28, 2018 at 12:52 PM Greg Landrum > 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 > 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 >>> 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 -- Check out the vibrant tech community on one of the world's most engaging tech
Re: [Rdkit-discuss] 2018_03_2 md5 checksum problems
On Thu, Jun 28, 2018 at 12:52 PM Greg Landrum 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 >> 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 >> > -- 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
Re: [Rdkit-discuss] 2018_03_2 md5 checksum problems
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. @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 > 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 > -- 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
Re: [Rdkit-discuss] 2018_03_2 md5 checksum problems
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 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
