rdkit-devel Mailing List for RDKit (Page 4)
Open-Source Cheminformatics and Machine Learning
Brought to you by:
glandrum
Menu
▾
▴
rdkit-devel — Developers information and discussion.
You can subscribe to this list here.
| 2006 |
Jan
|
Feb
|
Mar
|
Apr
|
May
(24) |
Jun
(20) |
Jul
|
Aug
(2) |
Sep
(4) |
Oct
(39) |
Nov
(33) |
Dec
(8) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2007 |
Jan
(17) |
Feb
(13) |
Mar
(35) |
Apr
(10) |
May
(1) |
Jun
(2) |
Jul
(3) |
Aug
(4) |
Sep
(4) |
Oct
(7) |
Nov
(1) |
Dec
|
| 2008 |
Jan
(10) |
Feb
(2) |
Mar
(2) |
Apr
(10) |
May
(8) |
Jun
(2) |
Jul
(1) |
Aug
(1) |
Sep
(3) |
Oct
(1) |
Nov
|
Dec
|
| 2009 |
Jan
(2) |
Feb
(1) |
Mar
(1) |
Apr
(1) |
May
|
Jun
(1) |
Jul
(7) |
Aug
(2) |
Sep
(6) |
Oct
(12) |
Nov
|
Dec
|
| 2010 |
Jan
(1) |
Feb
|
Mar
|
Apr
(2) |
May
(4) |
Jun
(2) |
Jul
(17) |
Aug
(7) |
Sep
(20) |
Oct
(8) |
Nov
(1) |
Dec
(12) |
| 2011 |
Jan
(8) |
Feb
(15) |
Mar
(20) |
Apr
(5) |
May
(8) |
Jun
(2) |
Jul
(17) |
Aug
(8) |
Sep
(4) |
Oct
(15) |
Nov
|
Dec
(2) |
| 2012 |
Jan
(3) |
Feb
|
Mar
(23) |
Apr
(2) |
May
(2) |
Jun
(8) |
Jul
(7) |
Aug
(18) |
Sep
(8) |
Oct
(10) |
Nov
(2) |
Dec
(7) |
| 2013 |
Jan
(6) |
Feb
(3) |
Mar
|
Apr
(3) |
May
(1) |
Jun
(1) |
Jul
(1) |
Aug
(2) |
Sep
|
Oct
(5) |
Nov
|
Dec
|
| 2014 |
Jan
(1) |
Feb
|
Mar
|
Apr
|
May
(10) |
Jun
|
Jul
(2) |
Aug
|
Sep
|
Oct
(7) |
Nov
(1) |
Dec
(6) |
| 2015 |
Jan
(22) |
Feb
|
Mar
(2) |
Apr
(5) |
May
(10) |
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(3) |
Nov
(9) |
Dec
(3) |
| 2016 |
Jan
(2) |
Feb
(5) |
Mar
|
Apr
(31) |
May
(3) |
Jun
(2) |
Jul
|
Aug
|
Sep
|
Oct
(4) |
Nov
(10) |
Dec
(7) |
| 2017 |
Jan
|
Feb
(7) |
Mar
(3) |
Apr
(6) |
May
(4) |
Jun
(6) |
Jul
(5) |
Aug
(1) |
Sep
(7) |
Oct
(1) |
Nov
|
Dec
|
| 2018 |
Jan
|
Feb
|
Mar
(11) |
Apr
(13) |
May
(18) |
Jun
(1) |
Jul
|
Aug
|
Sep
|
Oct
(5) |
Nov
(3) |
Dec
|
| 2019 |
Jan
|
Feb
|
Mar
|
Apr
(10) |
May
(4) |
Jun
|
Jul
|
Aug
|
Sep
|
Oct
(2) |
Nov
(1) |
Dec
(2) |
| 2020 |
Jan
(2) |
Feb
|
Mar
(5) |
Apr
(2) |
May
|
Jun
|
Jul
(4) |
Aug
|
Sep
|
Oct
(2) |
Nov
|
Dec
|
| 2021 |
Jan
|
Feb
|
Mar
(4) |
Apr
|
May
(1) |
Jun
|
Jul
(3) |
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: Greg L. <gre...@gm...> - 2018-04-05 10:56:42
|
This change has now been made. The RDKit master branch (the default one in github) has been moved to modern c++. The previous status of master is captured here: https://github.com/rdkit/rdkit/tree/legacy/master Hopefully this doesn't cause horrible problems for anyone with active forks, but I figure there are likely to be at least a few bumps. Hopefully they aren't too large. -greg On Thu, Apr 5, 2018 at 8:46 AM, Greg Landrum <gre...@gm...> wrote: > Thanks for raising this Markus. It had been on my list of things to look > into for a while and I had been kind of dreading it.[1] > > I did a bit of googling and experimentation and it looks like this > approach works well: > https://stackoverflow.com/questions/5956300/merging-two- > very-divergent-branches-using-git > Given that it also (at least to me) makes sense, I think that this is how > I'll proceed. > > -greg > [1] this is where I usually point to this xkcd: https://xkcd.com/1597/ > and make a joke about no longer being able to just walk over and ask Nadine > how to solve the problem. :-) > > On Wed, Apr 4, 2018 at 1:20 PM, Markus Sitzmann <mar...@gm... > > wrote: > >> Have you tried a merge (after branching the master to something like >> master-test-merge and then merge modern_cxx) ? How horrible does it look? >> It might be quiet okay. Or do you really have a lot of changes in the >> current master you don't have/want to have in modern_cxx and the future >> master. And well, it just was a concern by me that avoiding "early" horrors >> might cause bigger horrors later :-). Renaming the master in a GIT >> repository is something I wouldn't do easily - I would regard it more like >> a very, very last resort because if the master is renamed (or replaced by >> another branch), any branch in any remote repository by anybody who ever >> branched from master (including the RDKit github repository) becomes >> potentially (very likely) invalid by this step. Only if this is a small >> concern, I would do it (I doubt it is in case of RDKit). >> >> Markus >> >> On Wed, Apr 4, 2018 at 11:56 AM, Greg Landrum <gre...@gm...> >> wrote: >> >>> >>> >>> On Wed, Apr 4, 2018 at 11:27 AM, Markus Sitzmann < >>> mar...@gm...> wrote: >>> >>>> Hi Greg, >>>> >>>> > Concretely what this means in github is that the current master >>>> branch will be renamed to legacy and the modern_cxx branch will be renamed >>>> to master. >>>> >>>> I hope you are not actually just renaming it - although I am not >>>> affected personally, that might be a call for trouble because it >>>> invalidates any remote repository of rdkit. >>>> >>> >>> If you have suggestions for how to do a large-delta change like that in >>> a non-horrible manner, I would love to hear them :-) >>> >>> -greg >>> >>> >> >> > |
|
From: Greg L. <gre...@gm...> - 2018-04-05 06:47:27
|
Thanks for raising this Markus. It had been on my list of things to look into for a while and I had been kind of dreading it.[1] I did a bit of googling and experimentation and it looks like this approach works well: https://stackoverflow.com/questions/5956300/merging-two-very-divergent-branches-using-git Given that it also (at least to me) makes sense, I think that this is how I'll proceed. -greg [1] this is where I usually point to this xkcd: https://xkcd.com/1597/ and make a joke about no longer being able to just walk over and ask Nadine how to solve the problem. :-) On Wed, Apr 4, 2018 at 1:20 PM, Markus Sitzmann <mar...@gm...> wrote: > Have you tried a merge (after branching the master to something like > master-test-merge and then merge modern_cxx) ? How horrible does it look? > It might be quiet okay. Or do you really have a lot of changes in the > current master you don't have/want to have in modern_cxx and the future > master. And well, it just was a concern by me that avoiding "early" horrors > might cause bigger horrors later :-). Renaming the master in a GIT > repository is something I wouldn't do easily - I would regard it more like > a very, very last resort because if the master is renamed (or replaced by > another branch), any branch in any remote repository by anybody who ever > branched from master (including the RDKit github repository) becomes > potentially (very likely) invalid by this step. Only if this is a small > concern, I would do it (I doubt it is in case of RDKit). > > Markus > > On Wed, Apr 4, 2018 at 11:56 AM, Greg Landrum <gre...@gm...> > wrote: > >> >> >> On Wed, Apr 4, 2018 at 11:27 AM, Markus Sitzmann < >> mar...@gm...> wrote: >> >>> Hi Greg, >>> >>> > Concretely what this means in github is that the current master >>> branch will be renamed to legacy and the modern_cxx branch will be renamed >>> to master. >>> >>> I hope you are not actually just renaming it - although I am not >>> affected personally, that might be a call for trouble because it >>> invalidates any remote repository of rdkit. >>> >> >> If you have suggestions for how to do a large-delta change like that in a >> non-horrible manner, I would love to hear them :-) >> >> -greg >> >> > > |
|
From: Greg L. <gre...@gm...> - 2018-04-04 09:56:55
|
On Wed, Apr 4, 2018 at 11:27 AM, Markus Sitzmann <mar...@gm...> wrote: > Hi Greg, > > > Concretely what this means in github is that the current master branch > will be renamed to legacy and the modern_cxx branch will be renamed to > master. > > I hope you are not actually just renaming it - although I am not affected > personally, that might be a call for trouble because it invalidates any > remote repository of rdkit. > If you have suggestions for how to do a large-delta change like that in a non-horrible manner, I would love to hear them :-) -greg |
|
From: Maciek W. <ma...@wo...> - 2018-04-04 08:54:22
|
Hi Greg, I don't know if it is of any help, but we have fixed recent conda (linking against Python library) for OpenBabel by adding additional linker parameters for Mac in cmake config, see Matts patch here: https://github.com/openbabel/openbabel/pull/1807/files ---- Pozdrawiam, | Best regards, Maciek Wójcikowski ma...@wo... 2018-04-04 5:39 GMT+02:00 Greg Landrum <gre...@gm...>: > Dear all, > > As you may have noticed, the new release (2018.03) is late. > > This is not, as you might expect, connected to my previous email about the > backend code changes. It turned out to be much more difficult than > anticipated to straighten out the problems we were having with newer > versions of conda, particularly on the Mac, and we didn't want to do a > release until those were taken care of. > > It looks like we're almost there. Hopefully we will be able to do a beta > of the 2018.03 release by the end of the week. > > Best, > -greg > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Rdkit-devel mailing list > Rdk...@li... > https://lists.sourceforge.net/lists/listinfo/rdkit-devel > > |
|
From: Greg L. <gre...@gm...> - 2018-04-04 08:41:26
|
On Wed, Apr 4, 2018 at 10:30 AM, Maciek Wójcikowski <ma...@wo...> wrote: > > I don't know if it is of any help, but we have fixed recent conda (linking > against Python library) for OpenBabel by adding additional linker > parameters for Mac in cmake config, see Matts patch here: > https://github.com/openbabel/openbabel/pull/1807/files > Thanks for pointing that out. Matt has also done a similar PR against the RDKit (https://github.com/rdkit/rdkit/pull/1805), and that helps, but we've gotten some feedback that this isn't the best solution to the problem. There's another active PR where we're close to having an alternate fix (amusingly, the same number as the OB fix: https://github.com/rdkit/rdkit/pull/1807). I think we're very close. -greg > ---- > Pozdrawiam, | Best regards, > Maciek Wójcikowski > ma...@wo... > > 2018-04-04 5:39 GMT+02:00 Greg Landrum <gre...@gm...>: > >> Dear all, >> >> As you may have noticed, the new release (2018.03) is late. >> >> This is not, as you might expect, connected to my previous email about >> the backend code changes. It turned out to be much more difficult than >> anticipated to straighten out the problems we were having with newer >> versions of conda, particularly on the Mac, and we didn't want to do a >> release until those were taken care of. >> >> It looks like we're almost there. Hopefully we will be able to do a beta >> of the 2018.03 release by the end of the week. >> >> Best, >> -greg >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Rdkit-devel mailing list >> Rdk...@li... >> https://lists.sourceforge.net/lists/listinfo/rdkit-devel >> >> > |
|
From: Greg L. <gre...@gm...> - 2018-04-04 03:40:00
|
Dear all, As you may have noticed, the new release (2018.03) is late. This is not, as you might expect, connected to my previous email about the backend code changes. It turned out to be much more difficult than anticipated to straighten out the problems we were having with newer versions of conda, particularly on the Mac, and we didn't want to do a release until those were taken care of. It looks like we're almost there. Hopefully we will be able to do a beta of the 2018.03 release by the end of the week. Best, -greg |
|
From: Greg L. <gre...@gm...> - 2018-04-04 03:23:48
|
NOTE: If you don't work with the RDKit at the C++ level or build the code yourself from source, you probably don't need to read this email. TL;DR: When we do the beta for the 2018.03.1 release we're going to switch the C++ backend to use modern C++ (=C++11). For people who can't switch to use that code, we will continue to provide bug fixes for the 2017.09 release for at least another 6 months. -------------------------------------- # What's happening? As part of the upcoming 2018.03 release, we will start using modern C++ for the RDKit - this means C++11 at the moment, the goal is that you should be able to build the code with g++ v4.8. I've been talking about this for a while, blogged about it (https://medium.com/@greg.land rum_t5/the-rdkit-and-modern-c-48206b966218), and posted to the rdkit-devel list (https://sourceforge.net/p/rdkit/mailman/message/35811216/), now it's finally happening. Concretely what this means in github is that the current master branch will be renamed to legacy and the modern_cxx branch will be renamed to master. # Who does this affect? This should only affect people who need to build the RDKit C++ code themselves. If you use a binary version of the RDKit like the ones available inside of Anaconda Python or KNIME, this change should have no impact upon you. # What about people who can't use up-to-date compilers? We realize that some people on older operating systems will not be able to switch to start using a compiler that supports C++11. In order to continue to support this subset of developers, we will continue to apply bug fixes to the current Release_2017_09 branch and do occasional patch releases. Since this is intended for people who need to build the code themselves anyway, we won't do builds of these releases any more. We will keep doing these patch release at least until the 2018.09 release. Whether or not we continue past that date will depend on demand, so if you are using these releases please let us know. # Why are you doing this? There's a long, rambling answer to this, but I'm not going to give it here. :-) The simplest explanation is that we think that the core of the RDKit should be using a modern and (reasonably) up-to-date version of the language that it's written in. The developer experience is better and, happily, the code ends up being faster. |
|
From: TJ O'D. <tj...@ac...> - 2018-03-23 04:29:18
|
Greg- I tried the build using the last release rdkit-Release_2017_09_3.tar.gz and everything compiled fine! So, I'm out of the woods, but don't understand why it failed for the latest git clone. I'm satisfied for now, but if you'd like to pursue this and need any input from me, let me know. Thanks, TJ On Mon, Mar 19, 2018 at 7:21 AM, TJ O'Donnell <tj...@ac...> wrote: > Thanks for your attention to this. > Have a good ACS meeting and enjoy New Orleans! > > On Mon, Mar 19, 2018 at 7:04 AM, Greg Landrum <gre...@gm...> > wrote: > >> hmm, I'm stumped. >> I'm going to have to try to reproduce the problem on a linux box. >> Since I'm traveling this week (at the ACS in New Orleans), this may take >> a while. >> >> -greg >> >> >> On Mon, Mar 19, 2018 at 8:41 AM, TJ O'Donnell <tj...@ac...> wrote: >> >>> I grep'd with a slight mod to your suggestion and got these few lines. >>> There are many others with all lower case boost_thread and boost_serial >>> >>> tj@vmmint:~/RDKit/rdkit/build$ grep Boost_SERIAL CMakeCache.txt >>> Boost_SERIALIZATION_LIBRARY_DEBUG:FILEPATH=/usr/lib/x86_64-l >>> inux-gnu/libboost_serialization.so >>> Boost_SERIALIZATION_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_64 >>> -linux-gnu/libboost_serialization.so >>> //ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_DEBUG >>> Boost_SERIALIZATION_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 >>> //ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_RELEASE >>> Boost_SERIALIZATION_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 >>> >>> tj@vmmint:~/RDKit/rdkit/build$ grep Boost_THREAD CMakeCache.txt >>> Boost_THREAD_LIBRARY_DEBUG:FILEPATH=/usr/lib/x86_64-linux-gn >>> u/libboost_thread.so >>> Boost_THREAD_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_64-linux- >>> gnu/libboost_thread.so >>> //ADVANCED property for variable: Boost_THREAD_LIBRARY_DEBUG >>> Boost_THREAD_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 >>> //ADVANCED property for variable: Boost_THREAD_LIBRARY_RELEASE >>> Boost_THREAD_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 >>> >>> The case-insensitive search has lines like this and many more: >>> >>> tj@vmmint:~/RDKit/rdkit/build$ grep -i boost_SERIAL CMakeCache.txt >>> rdqueries_LIB_DEPENDS:STATIC=general;GraphMol;general;RDGeom >>> etryLib;general;DataStructs;general;RDGeneral;general;RDBoos >>> t;general;/usr/lib/x86_64-linux-gnu/libpython2.7.so;gene >>> ral;/usr/lib/x86_64-linux-gnu/libboost_python.so;general;/ >>> usr/lib/x86_64-linux-gnu/libboost_thread.so;general;/ >>> usr/lib/x86_64-linux-gnu/libboost_system.so;general;/usr/ >>> lib/x86_64-linux-gnu/libpthread.so;general;/usr/lib/x86_64- >>> linux-gnu/libboost_serialization.so; >>> rdtrajectory_LIB_DEPENDS:STATIC=general;Trajectory;general;R >>> DGeometryLib;general;RDGeneral;general;GraphMol;general;/usr >>> /lib/x86_64-linux-gnu/libpython2.7.so;general;/usr/lib/x86_ >>> 64-linux-gnu/libboost_python.so;general;/usr/lib/x86_64- >>> linux-gnu/libboost_thread.so;general;/usr/lib/x86_64-linux- >>> gnu/libboost_system.so;general;/usr/lib/x86_64-linux- >>> gnu/libpthread.so;general;/usr/lib/x86_64-linux-gnu/ >>> libboost_serialization.so; >>> >>> >>> >>> >>> On Mon, Mar 19, 2018 at 3:27 AM, Greg Landrum <gre...@gm...> >>> wrote: >>> >>>> Well, I don't see anything obvious there to explain why the >>>> serialization library is being treated differently from the others. >>>> >>>> Could you please look at (and send) the output of; >>>> grep boost_THREAD CMakeCache.txt >>>> grep boost_SERIAL CMakeCache.txt >>>> >>>> Best, >>>> -greg >>>> >>>> >>>> >>>> On Sun, Mar 18, 2018 at 10:31 PM, TJ O'Donnell <tj...@ac...> wrote: >>>> >>>>> FYI I cloned https://github.com/rdkit/rdkit.git >>>>> and get the same error >>>>> >>>>> TJ >>>>> >>>>> On Sun, Mar 18, 2018 at 7:31 PM, TJ O'Donnell <tj...@ac...> wrote: >>>>> >>>>>> Thanks for the quick reply, Greg. I just did a git pull and it >>>>>> merged in lots of files. >>>>>> I may try a clone to a "fresh" folder and see how that goes. >>>>>> Anyway, here's the output from VERBOSE=1 make FilterCatalog >>>>>> >>>>>> tj@vmmint:~/RDKit/rdkit/build$ VERBOSE=1 make FilterCatalog >>>>>> /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build >>>>>> --check-build-system CMakeFiles/Makefile.cmake 0 >>>>>> make -f CMakeFiles/Makefile2 FilterCatalog >>>>>> make[1]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build >>>>>> --check-build-system CMakeFiles/Makefile.cmake 0 >>>>>> /usr/bin/cmake -E cmake_progress_start /home/tj/RDKit/rdkit/build/CMakeFiles >>>>>> 9 >>>>>> make -f CMakeFiles/Makefile2 Code/GraphMol/FilterCatalog/CM >>>>>> akeFiles/FilterCatalog.dir/all >>>>>> make[2]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make >>>>>> Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends >>>>>> "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/RDGeneral >>>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/RDGeneral >>>>>> /home/tj/RDKit/rdkit/build/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake >>>>>> --color= >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make >>>>>> Code/RDGeneral/CMakeFiles/RDGeneral.dir/build >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> make[3]: Nothing to be done for `Code/RDGeneral/CMakeFiles/RDG >>>>>> eneral.dir/build'. >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>>>> 64 >>>>>> [ 11%] Built target RDGeneral >>>>>> make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make >>>>>> Code/DataStructs/CMakeFiles/DataStructs.dir/depend >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends >>>>>> "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/DataStructs >>>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/DataStructs >>>>>> /home/tj/RDKit/rdkit/build/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake >>>>>> --color= >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make >>>>>> Code/DataStructs/CMakeFiles/DataStructs.dir/build >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> make[3]: Nothing to be done for `Code/DataStructs/CMakeFiles/D >>>>>> ataStructs.dir/build'. >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>>>> 7 >>>>>> [ 22%] Built target DataStructs >>>>>> make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make >>>>>> Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends >>>>>> "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Geometry >>>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Geometry >>>>>> /home/tj/RDKit/rdkit/build/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake >>>>>> --color= >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make >>>>>> Code/Geometry/CMakeFiles/RDGeometryLib.dir/build >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> make[3]: Nothing to be done for `Code/Geometry/CMakeFiles/RDGe >>>>>> ometryLib.dir/build'. >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>>>> 66 >>>>>> [ 33%] Built target RDGeometryLib >>>>>> make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make >>>>>> Code/GraphMol/CMakeFiles/GraphMol.dir/depend >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends >>>>>> "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol >>>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol >>>>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake >>>>>> --color= >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make >>>>>> Code/GraphMol/CMakeFiles/GraphMol.dir/build >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> make[3]: Nothing to be done for `Code/GraphMol/CMakeFiles/Grap >>>>>> hMol.dir/build'. >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>>>> 35 36 37 38 >>>>>> [ 77%] Built target GraphMol >>>>>> make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make >>>>>> Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends >>>>>> "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Subgraphs >>>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs >>>>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs/CMakeFile >>>>>> s/Subgraphs.dir/DependInfo.cmake --color= >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make >>>>>> Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> make[3]: Nothing to be done for `Code/GraphMol/Subgraphs/CMake >>>>>> Files/Subgraphs.dir/build'. >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>>>>> keFiles >>>>>> [ 77%] Built target Subgraphs >>>>>> make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make >>>>>> Code/Catalogs/CMakeFiles/Catalogs.dir/depend >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends >>>>>> "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Catalogs >>>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Catalogs >>>>>> /home/tj/RDKit/rdkit/build/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake >>>>>> --color= >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make >>>>>> Code/Catalogs/CMakeFiles/Catalogs.dir/build >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> make[3]: Nothing to be done for `Code/Catalogs/CMakeFiles/Cata >>>>>> logs.dir/build'. >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>>>>> keFiles >>>>>> [ 77%] Built target Catalogs >>>>>> make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make >>>>>> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends >>>>>> "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/SmilesParse >>>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse >>>>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse/CMakeFi >>>>>> les/SmilesParse.dir/DependInfo.cmake --color= >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make >>>>>> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> make[3]: Nothing to be done for `Code/GraphMol/SmilesParse/CMa >>>>>> keFiles/SmilesParse.dir/build'. >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>>>> 71 >>>>>> [ 88%] Built target SmilesParse >>>>>> make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make >>>>>> Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends >>>>>> "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Substruct >>>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct >>>>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct/CMakeFile >>>>>> s/SubstructMatch.dir/DependInfo.cmake --color= >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make >>>>>> Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> make[3]: Nothing to be done for `Code/GraphMol/Substruct/CMake >>>>>> Files/SubstructMatch.dir/build'. >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>>>>> keFiles >>>>>> [ 88%] Built target SubstructMatch >>>>>> make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make >>>>>> Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends >>>>>> "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/FilterCatalog >>>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog >>>>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog/CMake >>>>>> Files/FilterCatalog.dir/DependInfo.cmake --color= >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make >>>>>> Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build >>>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>>> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >>>>>> cd /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog && >>>>>> /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt >>>>>> --verbose=1 >>>>>> /usr/bin/c++ -fPIC -mpopcnt -Wno-deprecated -Wno-unused-function >>>>>> -fno-strict-aliasing -Wall -Wextra -fPIC -O3 -DNDEBUG -shared >>>>>> -Wl,-soname,libRDKitFilterCatalog.so.1 -o >>>>>> ../../../lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1 >>>>>> CMakeFiles/FilterCatalog.dir/Filters.cpp.o >>>>>> CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o >>>>>> CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o >>>>>> CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o >>>>>> CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >>>>>> ../../../lib/libRDKitSubgraphs.so.1.2018.03.1.dev1 >>>>>> ../../../lib/libRDKitSubstructMatch.so.1.2018.03.1.dev1 >>>>>> ../../../lib/libRDKitSmilesParse.so.1.2018.03.1.dev1 >>>>>> ../../../lib/libRDKitGraphMol.so.1.2018.03.1.dev1 >>>>>> ../../../lib/libRDKitRDGeometryLib.so.1.2018.03.1.dev1 >>>>>> ../../../lib/libRDKitCatalogs.so.1.2018.03.1.dev1 >>>>>> ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 >>>>>> -lBoost::serialization ../../../lib/libRDKitDataStructs.so.1.2018.03.1.dev1 >>>>>> ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 -lboost_thread >>>>>> -lboost_system -lpthread -Wl,-rpath,/home/tj/RDKit/rdkit/build/lib: >>>>>> /usr/bin/ld: cannot find -lBoost::serialization >>>>>> collect2: error: ld returned 1 exit status >>>>>> make[3]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >>>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> make[2]: *** [Code/GraphMol/FilterCatalog/C >>>>>> MakeFiles/FilterCatalog.dir/all] Error 2 >>>>>> make[2]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> make[1]: *** [Code/GraphMol/FilterCatalog/C >>>>>> MakeFiles/FilterCatalog.dir/rule] Error 2 >>>>>> make[1]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>>> make: *** [FilterCatalog] Error 2 >>>>>> >>>>>> On Sun, Mar 18, 2018 at 3:48 PM, Greg Landrum <gre...@gm... >>>>>> > wrote: >>>>>> >>>>>>> Hi TJ, >>>>>>> >>>>>>> Hrm, that's ugly. Just to confirm: Are you building the master >>>>>>> branch from github? >>>>>>> It looks like there's no fundamental problem with master; at least >>>>>>> the travis builds pass: https://travis-ci.org/rdkit/rdkit >>>>>>> >>>>>>> To help track this down, can you please send the results of doing: >>>>>>> VERBOSE=1 make FilterCatalog >>>>>>> >>>>>>> Best, >>>>>>> -greg >>>>>>> >>>>>>> >>>>>>> On Sun, Mar 18, 2018 at 11:27 PM, TJ O'Donnell <tj...@ac...> wrote: >>>>>>> >>>>>>>> I'm trying to build rdkit from the latest git source. >>>>>>>> Linux Mint 17 >>>>>>>> >>>>>>>> I get this error >>>>>>>> [ 57%] Building CXX object Code/GraphMol/FilterCatalog/CM >>>>>>>> akeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >>>>>>>> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >>>>>>>> /usr/bin/ld: cannot find -lBoost::serialization >>>>>>>> collect2: error: ld returned 1 exit status >>>>>>>> make[2]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error >>>>>>>> 1 >>>>>>>> make[1]: *** [Code/GraphMol/FilterCatalog/C >>>>>>>> MakeFiles/FilterCatalog.dir/all] Error 2 >>>>>>>> make: *** [all] Error 2 >>>>>>>> >>>>>>>> but cmake seemed to find this lib OK >>>>>>>> cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON >>>>>>>> -- The C compiler identification is GNU 4.8.4 >>>>>>>> -- The CXX compiler identification is GNU 4.8.4 >>>>>>>> .... >>>>>>>> -- Found Threads: TRUE >>>>>>>> -- Boost version: 1.54.0 >>>>>>>> -- Found the following Boost libraries: >>>>>>>> -- thread >>>>>>>> -- system >>>>>>>> -- Boost version: 1.54.0 >>>>>>>> -- Found the following Boost libraries: >>>>>>>> -- serialization >>>>>>>> == Using strict rotor definition >>>>>>>> == Updating Filters.cpp from pains file >>>>>>>> >>>>>>>> Can you help me figure out how to get past this? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> TJ >>>>>>>> >>>>>>>> ------------------------------------------------------------ >>>>>>>> ------------------ >>>>>>>> Check out the vibrant tech community on one of the world's most >>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>>>>>> _______________________________________________ >>>>>>>> Rdkit-devel mailing list >>>>>>>> Rdk...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > |
|
From: TJ O'D. <tj...@ac...> - 2018-03-19 14:22:14
|
Thanks for your attention to this. Have a good ACS meeting and enjoy New Orleans! On Mon, Mar 19, 2018 at 7:04 AM, Greg Landrum <gre...@gm...> wrote: > hmm, I'm stumped. > I'm going to have to try to reproduce the problem on a linux box. > Since I'm traveling this week (at the ACS in New Orleans), this may take a > while. > > -greg > > > On Mon, Mar 19, 2018 at 8:41 AM, TJ O'Donnell <tj...@ac...> wrote: > >> I grep'd with a slight mod to your suggestion and got these few lines. >> There are many others with all lower case boost_thread and boost_serial >> >> tj@vmmint:~/RDKit/rdkit/build$ grep Boost_SERIAL CMakeCache.txt >> Boost_SERIALIZATION_LIBRARY_DEBUG:FILEPATH=/usr/lib/x86_64- >> linux-gnu/libboost_serialization.so >> Boost_SERIALIZATION_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_64 >> -linux-gnu/libboost_serialization.so >> //ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_DEBUG >> Boost_SERIALIZATION_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 >> //ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_RELEASE >> Boost_SERIALIZATION_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 >> >> tj@vmmint:~/RDKit/rdkit/build$ grep Boost_THREAD CMakeCache.txt >> Boost_THREAD_LIBRARY_DEBUG:FILEPATH=/usr/lib/x86_64-linux- >> gnu/libboost_thread.so >> Boost_THREAD_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_64-linux- >> gnu/libboost_thread.so >> //ADVANCED property for variable: Boost_THREAD_LIBRARY_DEBUG >> Boost_THREAD_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 >> //ADVANCED property for variable: Boost_THREAD_LIBRARY_RELEASE >> Boost_THREAD_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 >> >> The case-insensitive search has lines like this and many more: >> >> tj@vmmint:~/RDKit/rdkit/build$ grep -i boost_SERIAL CMakeCache.txt >> rdqueries_LIB_DEPENDS:STATIC=general;GraphMol;general;RDGeom >> etryLib;general;DataStructs;general;RDGeneral;general; >> RDBoost;general;/usr/lib/x86_64-linux-gnu/libpython2.7.so; >> general;/usr/lib/x86_64-linux-gnu/libboost_python.so; >> general;/usr/lib/x86_64-linux-gnu/libboost_thread.so;general >> ;/usr/lib/x86_64-linux-gnu/libboost_system.so;general;/ >> usr/lib/x86_64-linux-gnu/libpthread.so;general;/usr/ >> lib/x86_64-linux-gnu/libboost_serialization.so; >> rdtrajectory_LIB_DEPENDS:STATIC=general;Trajectory;general; >> RDGeometryLib;general;RDGeneral;general;GraphMol;general;/ >> usr/lib/x86_64-linux-gnu/libpython2.7.so;general;/usr/lib/ >> x86_64-linux-gnu/libboost_python.so;general;/usr/lib/ >> x86_64-linux-gnu/libboost_thread.so;general;/usr/lib/ >> x86_64-linux-gnu/libboost_system.so;general;/usr/lib/ >> x86_64-linux-gnu/libpthread.so;general;/usr/lib/x86_64- >> linux-gnu/libboost_serialization.so; >> >> >> >> >> On Mon, Mar 19, 2018 at 3:27 AM, Greg Landrum <gre...@gm...> >> wrote: >> >>> Well, I don't see anything obvious there to explain why the >>> serialization library is being treated differently from the others. >>> >>> Could you please look at (and send) the output of; >>> grep boost_THREAD CMakeCache.txt >>> grep boost_SERIAL CMakeCache.txt >>> >>> Best, >>> -greg >>> >>> >>> >>> On Sun, Mar 18, 2018 at 10:31 PM, TJ O'Donnell <tj...@ac...> wrote: >>> >>>> FYI I cloned https://github.com/rdkit/rdkit.git >>>> and get the same error >>>> >>>> TJ >>>> >>>> On Sun, Mar 18, 2018 at 7:31 PM, TJ O'Donnell <tj...@ac...> wrote: >>>> >>>>> Thanks for the quick reply, Greg. I just did a git pull and it merged >>>>> in lots of files. >>>>> I may try a clone to a "fresh" folder and see how that goes. >>>>> Anyway, here's the output from VERBOSE=1 make FilterCatalog >>>>> >>>>> tj@vmmint:~/RDKit/rdkit/build$ VERBOSE=1 make FilterCatalog >>>>> /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build >>>>> --check-build-system CMakeFiles/Makefile.cmake 0 >>>>> make -f CMakeFiles/Makefile2 FilterCatalog >>>>> make[1]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build >>>>> --check-build-system CMakeFiles/Makefile.cmake 0 >>>>> /usr/bin/cmake -E cmake_progress_start /home/tj/RDKit/rdkit/build/CMakeFiles >>>>> 9 >>>>> make -f CMakeFiles/Makefile2 Code/GraphMol/FilterCatalog/CM >>>>> akeFiles/FilterCatalog.dir/all >>>>> make[2]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make >>>>> Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/RDGeneral >>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/RDGeneral >>>>> /home/tj/RDKit/rdkit/build/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake >>>>> --color= >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make >>>>> Code/RDGeneral/CMakeFiles/RDGeneral.dir/build >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> make[3]: Nothing to be done for `Code/RDGeneral/CMakeFiles/RDG >>>>> eneral.dir/build'. >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>>> 64 >>>>> [ 11%] Built target RDGeneral >>>>> make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make >>>>> Code/DataStructs/CMakeFiles/DataStructs.dir/depend >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/DataStructs >>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/DataStructs >>>>> /home/tj/RDKit/rdkit/build/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake >>>>> --color= >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make >>>>> Code/DataStructs/CMakeFiles/DataStructs.dir/build >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> make[3]: Nothing to be done for `Code/DataStructs/CMakeFiles/D >>>>> ataStructs.dir/build'. >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>>> 7 >>>>> [ 22%] Built target DataStructs >>>>> make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make >>>>> Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Geometry >>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Geometry >>>>> /home/tj/RDKit/rdkit/build/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake >>>>> --color= >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make >>>>> Code/Geometry/CMakeFiles/RDGeometryLib.dir/build >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> make[3]: Nothing to be done for `Code/Geometry/CMakeFiles/RDGe >>>>> ometryLib.dir/build'. >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>>> 66 >>>>> [ 33%] Built target RDGeometryLib >>>>> make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make >>>>> Code/GraphMol/CMakeFiles/GraphMol.dir/depend >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol >>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol >>>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake >>>>> --color= >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make >>>>> Code/GraphMol/CMakeFiles/GraphMol.dir/build >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> make[3]: Nothing to be done for `Code/GraphMol/CMakeFiles/Grap >>>>> hMol.dir/build'. >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>>> 35 36 37 38 >>>>> [ 77%] Built target GraphMol >>>>> make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make >>>>> Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Subgraphs >>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs >>>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs/CMakeFile >>>>> s/Subgraphs.dir/DependInfo.cmake --color= >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make >>>>> Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> make[3]: Nothing to be done for `Code/GraphMol/Subgraphs/CMake >>>>> Files/Subgraphs.dir/build'. >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>>>> keFiles >>>>> [ 77%] Built target Subgraphs >>>>> make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make >>>>> Code/Catalogs/CMakeFiles/Catalogs.dir/depend >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Catalogs >>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Catalogs >>>>> /home/tj/RDKit/rdkit/build/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake >>>>> --color= >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make >>>>> Code/Catalogs/CMakeFiles/Catalogs.dir/build >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> make[3]: Nothing to be done for `Code/Catalogs/CMakeFiles/Cata >>>>> logs.dir/build'. >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>>>> keFiles >>>>> [ 77%] Built target Catalogs >>>>> make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make >>>>> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/SmilesParse >>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse >>>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse/CMakeFi >>>>> les/SmilesParse.dir/DependInfo.cmake --color= >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make >>>>> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> make[3]: Nothing to be done for `Code/GraphMol/SmilesParse/CMa >>>>> keFiles/SmilesParse.dir/build'. >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>>> 71 >>>>> [ 88%] Built target SmilesParse >>>>> make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make >>>>> Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Substruct >>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct >>>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct/CMakeFile >>>>> s/SubstructMatch.dir/DependInfo.cmake --color= >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make >>>>> Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> make[3]: Nothing to be done for `Code/GraphMol/Substruct/CMake >>>>> Files/SubstructMatch.dir/build'. >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>>>> keFiles >>>>> [ 88%] Built target SubstructMatch >>>>> make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make >>>>> Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/FilterCatalog >>>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog >>>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog/CMake >>>>> Files/FilterCatalog.dir/DependInfo.cmake --color= >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make >>>>> Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build >>>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>>> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >>>>> cd /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog && >>>>> /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt >>>>> --verbose=1 >>>>> /usr/bin/c++ -fPIC -mpopcnt -Wno-deprecated -Wno-unused-function >>>>> -fno-strict-aliasing -Wall -Wextra -fPIC -O3 -DNDEBUG -shared >>>>> -Wl,-soname,libRDKitFilterCatalog.so.1 -o >>>>> ../../../lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1 >>>>> CMakeFiles/FilterCatalog.dir/Filters.cpp.o >>>>> CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o >>>>> CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o >>>>> CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o >>>>> CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >>>>> ../../../lib/libRDKitSubgraphs.so.1.2018.03.1.dev1 >>>>> ../../../lib/libRDKitSubstructMatch.so.1.2018.03.1.dev1 >>>>> ../../../lib/libRDKitSmilesParse.so.1.2018.03.1.dev1 >>>>> ../../../lib/libRDKitGraphMol.so.1.2018.03.1.dev1 >>>>> ../../../lib/libRDKitRDGeometryLib.so.1.2018.03.1.dev1 >>>>> ../../../lib/libRDKitCatalogs.so.1.2018.03.1.dev1 >>>>> ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 >>>>> -lBoost::serialization ../../../lib/libRDKitDataStructs.so.1.2018.03.1.dev1 >>>>> ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 -lboost_thread >>>>> -lboost_system -lpthread -Wl,-rpath,/home/tj/RDKit/rdkit/build/lib: >>>>> /usr/bin/ld: cannot find -lBoost::serialization >>>>> collect2: error: ld returned 1 exit status >>>>> make[3]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >>>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> make[2]: *** [Code/GraphMol/FilterCatalog/C >>>>> MakeFiles/FilterCatalog.dir/all] Error 2 >>>>> make[2]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> make[1]: *** [Code/GraphMol/FilterCatalog/C >>>>> MakeFiles/FilterCatalog.dir/rule] Error 2 >>>>> make[1]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>>> make: *** [FilterCatalog] Error 2 >>>>> >>>>> On Sun, Mar 18, 2018 at 3:48 PM, Greg Landrum <gre...@gm...> >>>>> wrote: >>>>> >>>>>> Hi TJ, >>>>>> >>>>>> Hrm, that's ugly. Just to confirm: Are you building the master branch >>>>>> from github? >>>>>> It looks like there's no fundamental problem with master; at least >>>>>> the travis builds pass: https://travis-ci.org/rdkit/rdkit >>>>>> >>>>>> To help track this down, can you please send the results of doing: >>>>>> VERBOSE=1 make FilterCatalog >>>>>> >>>>>> Best, >>>>>> -greg >>>>>> >>>>>> >>>>>> On Sun, Mar 18, 2018 at 11:27 PM, TJ O'Donnell <tj...@ac...> wrote: >>>>>> >>>>>>> I'm trying to build rdkit from the latest git source. >>>>>>> Linux Mint 17 >>>>>>> >>>>>>> I get this error >>>>>>> [ 57%] Building CXX object Code/GraphMol/FilterCatalog/CM >>>>>>> akeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >>>>>>> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >>>>>>> /usr/bin/ld: cannot find -lBoost::serialization >>>>>>> collect2: error: ld returned 1 exit status >>>>>>> make[2]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >>>>>>> make[1]: *** [Code/GraphMol/FilterCatalog/C >>>>>>> MakeFiles/FilterCatalog.dir/all] Error 2 >>>>>>> make: *** [all] Error 2 >>>>>>> >>>>>>> but cmake seemed to find this lib OK >>>>>>> cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON >>>>>>> -- The C compiler identification is GNU 4.8.4 >>>>>>> -- The CXX compiler identification is GNU 4.8.4 >>>>>>> .... >>>>>>> -- Found Threads: TRUE >>>>>>> -- Boost version: 1.54.0 >>>>>>> -- Found the following Boost libraries: >>>>>>> -- thread >>>>>>> -- system >>>>>>> -- Boost version: 1.54.0 >>>>>>> -- Found the following Boost libraries: >>>>>>> -- serialization >>>>>>> == Using strict rotor definition >>>>>>> == Updating Filters.cpp from pains file >>>>>>> >>>>>>> Can you help me figure out how to get past this? >>>>>>> >>>>>>> Thanks, >>>>>>> TJ >>>>>>> >>>>>>> ------------------------------------------------------------ >>>>>>> ------------------ >>>>>>> Check out the vibrant tech community on one of the world's most >>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>>>>> _______________________________________________ >>>>>>> Rdkit-devel mailing list >>>>>>> Rdk...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > |
|
From: Greg L. <gre...@gm...> - 2018-03-19 14:04:59
|
hmm, I'm stumped. I'm going to have to try to reproduce the problem on a linux box. Since I'm traveling this week (at the ACS in New Orleans), this may take a while. -greg On Mon, Mar 19, 2018 at 8:41 AM, TJ O'Donnell <tj...@ac...> wrote: > I grep'd with a slight mod to your suggestion and got these few lines. > There are many others with all lower case boost_thread and boost_serial > > tj@vmmint:~/RDKit/rdkit/build$ grep Boost_SERIAL CMakeCache.txt > Boost_SERIALIZATION_LIBRARY_DEBUG:FILEPATH=/usr/lib/x86_ > 64-linux-gnu/libboost_serialization.so > Boost_SERIALIZATION_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_ > 64-linux-gnu/libboost_serialization.so > //ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_DEBUG > Boost_SERIALIZATION_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 > //ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_RELEASE > Boost_SERIALIZATION_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 > > tj@vmmint:~/RDKit/rdkit/build$ grep Boost_THREAD CMakeCache.txt > Boost_THREAD_LIBRARY_DEBUG:FILEPATH=/usr/lib/x86_64- > linux-gnu/libboost_thread.so > Boost_THREAD_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_64- > linux-gnu/libboost_thread.so > //ADVANCED property for variable: Boost_THREAD_LIBRARY_DEBUG > Boost_THREAD_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 > //ADVANCED property for variable: Boost_THREAD_LIBRARY_RELEASE > Boost_THREAD_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 > > The case-insensitive search has lines like this and many more: > > tj@vmmint:~/RDKit/rdkit/build$ grep -i boost_SERIAL CMakeCache.txt > rdqueries_LIB_DEPENDS:STATIC=general;GraphMol;general; > RDGeometryLib;general;DataStructs;general;RDGeneral; > general;RDBoost;general;/usr/lib/x86_64-linux-gnu/libpython2.7.so > ;general;/usr/lib/x86_64-linux-gnu/libboost_python. > so;general;/usr/lib/x86_64-linux-gnu/libboost_thread.so; > general;/usr/lib/x86_64-linux-gnu/libboost_system.so; > general;/usr/lib/x86_64-linux-gnu/libpthread.so;general;/ > usr/lib/x86_64-linux-gnu/libboost_serialization.so; > rdtrajectory_LIB_DEPENDS:STATIC=general;Trajectory; > general;RDGeometryLib;general;RDGeneral;general;GraphMol; > general;/usr/lib/x86_64-linux-gnu/libpython2.7.so;general;/ > usr/lib/x86_64-linux-gnu/libboost_python.so;general;/ > usr/lib/x86_64-linux-gnu/libboost_thread.so;general;/ > usr/lib/x86_64-linux-gnu/libboost_system.so;general;/ > usr/lib/x86_64-linux-gnu/libpthread.so;general;/usr/ > lib/x86_64-linux-gnu/libboost_serialization.so; > > > > > On Mon, Mar 19, 2018 at 3:27 AM, Greg Landrum <gre...@gm...> > wrote: > >> Well, I don't see anything obvious there to explain why the serialization >> library is being treated differently from the others. >> >> Could you please look at (and send) the output of; >> grep boost_THREAD CMakeCache.txt >> grep boost_SERIAL CMakeCache.txt >> >> Best, >> -greg >> >> >> >> On Sun, Mar 18, 2018 at 10:31 PM, TJ O'Donnell <tj...@ac...> wrote: >> >>> FYI I cloned https://github.com/rdkit/rdkit.git >>> and get the same error >>> >>> TJ >>> >>> On Sun, Mar 18, 2018 at 7:31 PM, TJ O'Donnell <tj...@ac...> wrote: >>> >>>> Thanks for the quick reply, Greg. I just did a git pull and it merged >>>> in lots of files. >>>> I may try a clone to a "fresh" folder and see how that goes. >>>> Anyway, here's the output from VERBOSE=1 make FilterCatalog >>>> >>>> tj@vmmint:~/RDKit/rdkit/build$ VERBOSE=1 make FilterCatalog >>>> /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build >>>> --check-build-system CMakeFiles/Makefile.cmake 0 >>>> make -f CMakeFiles/Makefile2 FilterCatalog >>>> make[1]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build >>>> --check-build-system CMakeFiles/Makefile.cmake 0 >>>> /usr/bin/cmake -E cmake_progress_start /home/tj/RDKit/rdkit/build/CMakeFiles >>>> 9 >>>> make -f CMakeFiles/Makefile2 Code/GraphMol/FilterCatalog/CM >>>> akeFiles/FilterCatalog.dir/all >>>> make[2]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make >>>> Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/RDGeneral >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/RDGeneral >>>> /home/tj/RDKit/rdkit/build/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake >>>> --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make >>>> Code/RDGeneral/CMakeFiles/RDGeneral.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/RDGeneral/CMakeFiles/RDG >>>> eneral.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>> 64 >>>> [ 11%] Built target RDGeneral >>>> make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make >>>> Code/DataStructs/CMakeFiles/DataStructs.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/DataStructs >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/DataStructs >>>> /home/tj/RDKit/rdkit/build/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake >>>> --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make >>>> Code/DataStructs/CMakeFiles/DataStructs.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/DataStructs/CMakeFiles/D >>>> ataStructs.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>> 7 >>>> [ 22%] Built target DataStructs >>>> make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make >>>> Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Geometry >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Geometry >>>> /home/tj/RDKit/rdkit/build/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake >>>> --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make >>>> Code/Geometry/CMakeFiles/RDGeometryLib.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/Geometry/CMakeFiles/RDGe >>>> ometryLib.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>> 66 >>>> [ 33%] Built target RDGeometryLib >>>> make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make >>>> Code/GraphMol/CMakeFiles/GraphMol.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol >>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake >>>> --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make >>>> Code/GraphMol/CMakeFiles/GraphMol.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/GraphMol/CMakeFiles/Grap >>>> hMol.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>> 35 36 37 38 >>>> [ 77%] Built target GraphMol >>>> make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make >>>> Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Subgraphs >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs >>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs/CMakeFile >>>> s/Subgraphs.dir/DependInfo.cmake --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make >>>> Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/GraphMol/Subgraphs/CMake >>>> Files/Subgraphs.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>>> keFiles >>>> [ 77%] Built target Subgraphs >>>> make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make >>>> Code/Catalogs/CMakeFiles/Catalogs.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Catalogs >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Catalogs >>>> /home/tj/RDKit/rdkit/build/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake >>>> --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make >>>> Code/Catalogs/CMakeFiles/Catalogs.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/Catalogs/CMakeFiles/Cata >>>> logs.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>>> keFiles >>>> [ 77%] Built target Catalogs >>>> make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make >>>> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/SmilesParse >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse >>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse/CMakeFi >>>> les/SmilesParse.dir/DependInfo.cmake --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make >>>> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/GraphMol/SmilesParse/CMa >>>> keFiles/SmilesParse.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>> 71 >>>> [ 88%] Built target SmilesParse >>>> make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make >>>> Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Substruct >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct >>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct/CMakeFile >>>> s/SubstructMatch.dir/DependInfo.cmake --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make >>>> Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/GraphMol/Substruct/CMake >>>> Files/SubstructMatch.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>>> keFiles >>>> [ 88%] Built target SubstructMatch >>>> make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make >>>> Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/FilterCatalog >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog >>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog/CMake >>>> Files/FilterCatalog.dir/DependInfo.cmake --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make >>>> Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >>>> cd /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog && >>>> /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt >>>> --verbose=1 >>>> /usr/bin/c++ -fPIC -mpopcnt -Wno-deprecated -Wno-unused-function >>>> -fno-strict-aliasing -Wall -Wextra -fPIC -O3 -DNDEBUG -shared >>>> -Wl,-soname,libRDKitFilterCatalog.so.1 -o >>>> ../../../lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1 >>>> CMakeFiles/FilterCatalog.dir/Filters.cpp.o >>>> CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o >>>> CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o >>>> CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o >>>> CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >>>> ../../../lib/libRDKitSubgraphs.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitSubstructMatch.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitSmilesParse.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitGraphMol.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitRDGeometryLib.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitCatalogs.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 >>>> -lBoost::serialization ../../../lib/libRDKitDataStructs.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 -lboost_thread >>>> -lboost_system -lpthread -Wl,-rpath,/home/tj/RDKit/rdkit/build/lib: >>>> /usr/bin/ld: cannot find -lBoost::serialization >>>> collect2: error: ld returned 1 exit status >>>> make[3]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make[2]: *** [Code/GraphMol/FilterCatalog/C >>>> MakeFiles/FilterCatalog.dir/all] Error 2 >>>> make[2]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make[1]: *** [Code/GraphMol/FilterCatalog/C >>>> MakeFiles/FilterCatalog.dir/rule] Error 2 >>>> make[1]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make: *** [FilterCatalog] Error 2 >>>> >>>> On Sun, Mar 18, 2018 at 3:48 PM, Greg Landrum <gre...@gm...> >>>> wrote: >>>> >>>>> Hi TJ, >>>>> >>>>> Hrm, that's ugly. Just to confirm: Are you building the master branch >>>>> from github? >>>>> It looks like there's no fundamental problem with master; at least the >>>>> travis builds pass: https://travis-ci.org/rdkit/rdkit >>>>> >>>>> To help track this down, can you please send the results of doing: >>>>> VERBOSE=1 make FilterCatalog >>>>> >>>>> Best, >>>>> -greg >>>>> >>>>> >>>>> On Sun, Mar 18, 2018 at 11:27 PM, TJ O'Donnell <tj...@ac...> wrote: >>>>> >>>>>> I'm trying to build rdkit from the latest git source. >>>>>> Linux Mint 17 >>>>>> >>>>>> I get this error >>>>>> [ 57%] Building CXX object Code/GraphMol/FilterCatalog/CM >>>>>> akeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >>>>>> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >>>>>> /usr/bin/ld: cannot find -lBoost::serialization >>>>>> collect2: error: ld returned 1 exit status >>>>>> make[2]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >>>>>> make[1]: *** [Code/GraphMol/FilterCatalog/C >>>>>> MakeFiles/FilterCatalog.dir/all] Error 2 >>>>>> make: *** [all] Error 2 >>>>>> >>>>>> but cmake seemed to find this lib OK >>>>>> cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON >>>>>> -- The C compiler identification is GNU 4.8.4 >>>>>> -- The CXX compiler identification is GNU 4.8.4 >>>>>> .... >>>>>> -- Found Threads: TRUE >>>>>> -- Boost version: 1.54.0 >>>>>> -- Found the following Boost libraries: >>>>>> -- thread >>>>>> -- system >>>>>> -- Boost version: 1.54.0 >>>>>> -- Found the following Boost libraries: >>>>>> -- serialization >>>>>> == Using strict rotor definition >>>>>> == Updating Filters.cpp from pains file >>>>>> >>>>>> Can you help me figure out how to get past this? >>>>>> >>>>>> Thanks, >>>>>> TJ >>>>>> >>>>>> ------------------------------------------------------------ >>>>>> ------------------ >>>>>> Check out the vibrant tech community on one of the world's most >>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>>>> _______________________________________________ >>>>>> Rdkit-devel mailing list >>>>>> Rdk...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel >>>>>> >>>>>> >>>>> >>>> >>> >> > |
|
From: TJ O'D. <tj...@ac...> - 2018-03-19 13:41:43
|
I grep'd with a slight mod to your suggestion and got these few lines. There are many others with all lower case boost_thread and boost_serial tj@vmmint:~/RDKit/rdkit/build$ grep Boost_SERIAL CMakeCache.txt Boost_SERIALIZATION_LIBRARY_DEBUG:FILEPATH=/usr/lib/x86_64-linux-gnu/libboost_serialization.so Boost_SERIALIZATION_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_64-linux-gnu/libboost_serialization.so //ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_DEBUG Boost_SERIALIZATION_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 //ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_RELEASE Boost_SERIALIZATION_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 tj@vmmint:~/RDKit/rdkit/build$ grep Boost_THREAD CMakeCache.txt Boost_THREAD_LIBRARY_DEBUG:FILEPATH=/usr/lib/x86_64-linux-gnu/libboost_thread.so Boost_THREAD_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_64-linux-gnu/libboost_thread.so //ADVANCED property for variable: Boost_THREAD_LIBRARY_DEBUG Boost_THREAD_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 //ADVANCED property for variable: Boost_THREAD_LIBRARY_RELEASE Boost_THREAD_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 The case-insensitive search has lines like this and many more: tj@vmmint:~/RDKit/rdkit/build$ grep -i boost_SERIAL CMakeCache.txt rdqueries_LIB_DEPENDS:STATIC=general;GraphMol;general;RDGeometryLib;general;DataStructs;general;RDGeneral;general;RDBoost;general;/usr/lib/x86_64-linux-gnu/ libpython2.7.so ;general;/usr/lib/x86_64-linux-gnu/libboost_python.so;general;/usr/lib/x86_64-linux-gnu/libboost_thread.so;general;/usr/lib/x86_64-linux-gnu/libboost_system.so;general;/usr/lib/x86_64-linux-gnu/libpthread.so;general;/usr/lib/x86_64-linux-gnu/libboost_serialization.so; rdtrajectory_LIB_DEPENDS:STATIC=general;Trajectory;general;RDGeometryLib;general;RDGeneral;general;GraphMol;general;/usr/lib/x86_64-linux-gnu/ libpython2.7.so ;general;/usr/lib/x86_64-linux-gnu/libboost_python.so;general;/usr/lib/x86_64-linux-gnu/libboost_thread.so;general;/usr/lib/x86_64-linux-gnu/libboost_system.so;general;/usr/lib/x86_64-linux-gnu/libpthread.so;general;/usr/lib/x86_64-linux-gnu/libboost_serialization.so; On Mon, Mar 19, 2018 at 3:27 AM, Greg Landrum <gre...@gm...> wrote: > Well, I don't see anything obvious there to explain why the serialization > library is being treated differently from the others. > > Could you please look at (and send) the output of; > grep boost_THREAD CMakeCache.txt > grep boost_SERIAL CMakeCache.txt > > Best, > -greg > > > > On Sun, Mar 18, 2018 at 10:31 PM, TJ O'Donnell <tj...@ac...> wrote: > >> FYI I cloned https://github.com/rdkit/rdkit.git >> and get the same error >> >> TJ >> >> On Sun, Mar 18, 2018 at 7:31 PM, TJ O'Donnell <tj...@ac...> wrote: >> >>> Thanks for the quick reply, Greg. I just did a git pull and it merged >>> in lots of files. >>> I may try a clone to a "fresh" folder and see how that goes. >>> Anyway, here's the output from VERBOSE=1 make FilterCatalog >>> >>> tj@vmmint:~/RDKit/rdkit/build$ VERBOSE=1 make FilterCatalog >>> /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build >>> --check-build-system CMakeFiles/Makefile.cmake 0 >>> make -f CMakeFiles/Makefile2 FilterCatalog >>> make[1]: Entering directory `/home/tj/RDKit/rdkit/build' >>> /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build >>> --check-build-system CMakeFiles/Makefile.cmake 0 >>> /usr/bin/cmake -E cmake_progress_start /home/tj/RDKit/rdkit/build/CMakeFiles >>> 9 >>> make -f CMakeFiles/Makefile2 Code/GraphMol/FilterCatalog/CM >>> akeFiles/FilterCatalog.dir/all >>> make[2]: Entering directory `/home/tj/RDKit/rdkit/build' >>> make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make >>> Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/RDGeneral >>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/RDGeneral >>> /home/tj/RDKit/rdkit/build/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake >>> --color= >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make >>> Code/RDGeneral/CMakeFiles/RDGeneral.dir/build >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> make[3]: Nothing to be done for `Code/RDGeneral/CMakeFiles/RDG >>> eneral.dir/build'. >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>> 64 >>> [ 11%] Built target RDGeneral >>> make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make >>> Code/DataStructs/CMakeFiles/DataStructs.dir/depend >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/DataStructs >>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/DataStructs >>> /home/tj/RDKit/rdkit/build/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake >>> --color= >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make >>> Code/DataStructs/CMakeFiles/DataStructs.dir/build >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> make[3]: Nothing to be done for `Code/DataStructs/CMakeFiles/D >>> ataStructs.dir/build'. >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>> 7 >>> [ 22%] Built target DataStructs >>> make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make >>> Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Geometry >>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Geometry >>> /home/tj/RDKit/rdkit/build/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake >>> --color= >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make >>> Code/Geometry/CMakeFiles/RDGeometryLib.dir/build >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> make[3]: Nothing to be done for `Code/Geometry/CMakeFiles/RDGe >>> ometryLib.dir/build'. >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>> 66 >>> [ 33%] Built target RDGeometryLib >>> make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make >>> Code/GraphMol/CMakeFiles/GraphMol.dir/depend >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol >>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol >>> /home/tj/RDKit/rdkit/build/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake >>> --color= >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make >>> Code/GraphMol/CMakeFiles/GraphMol.dir/build >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> make[3]: Nothing to be done for `Code/GraphMol/CMakeFiles/Grap >>> hMol.dir/build'. >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>> 35 36 37 38 >>> [ 77%] Built target GraphMol >>> make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make >>> Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Subgraphs >>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs >>> /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs/CMakeFile >>> s/Subgraphs.dir/DependInfo.cmake --color= >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make >>> Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> make[3]: Nothing to be done for `Code/GraphMol/Subgraphs/CMake >>> Files/Subgraphs.dir/build'. >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>> keFiles >>> [ 77%] Built target Subgraphs >>> make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make >>> Code/Catalogs/CMakeFiles/Catalogs.dir/depend >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Catalogs >>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Catalogs >>> /home/tj/RDKit/rdkit/build/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake >>> --color= >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make >>> Code/Catalogs/CMakeFiles/Catalogs.dir/build >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> make[3]: Nothing to be done for `Code/Catalogs/CMakeFiles/Cata >>> logs.dir/build'. >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>> keFiles >>> [ 77%] Built target Catalogs >>> make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make >>> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/SmilesParse >>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse >>> /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse/CMakeFi >>> les/SmilesParse.dir/DependInfo.cmake --color= >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make >>> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> make[3]: Nothing to be done for `Code/GraphMol/SmilesParse/CMa >>> keFiles/SmilesParse.dir/build'. >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>> 71 >>> [ 88%] Built target SmilesParse >>> make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make >>> Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Substruct >>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct >>> /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct/CMakeFile >>> s/SubstructMatch.dir/DependInfo.cmake --color= >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make >>> Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> make[3]: Nothing to be done for `Code/GraphMol/Substruct/CMake >>> Files/SubstructMatch.dir/build'. >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>> keFiles >>> [ 88%] Built target SubstructMatch >>> make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make >>> Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/FilterCatalog >>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog >>> /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog/CMake >>> Files/FilterCatalog.dir/DependInfo.cmake --color= >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make >>> Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build >>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >>> cd /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog && >>> /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt >>> --verbose=1 >>> /usr/bin/c++ -fPIC -mpopcnt -Wno-deprecated -Wno-unused-function >>> -fno-strict-aliasing -Wall -Wextra -fPIC -O3 -DNDEBUG -shared >>> -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1 >>> CMakeFiles/FilterCatalog.dir/Filters.cpp.o >>> CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o >>> CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o >>> CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o >>> CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >>> ../../../lib/libRDKitSubgraphs.so.1.2018.03.1.dev1 >>> ../../../lib/libRDKitSubstructMatch.so.1.2018.03.1.dev1 >>> ../../../lib/libRDKitSmilesParse.so.1.2018.03.1.dev1 >>> ../../../lib/libRDKitGraphMol.so.1.2018.03.1.dev1 >>> ../../../lib/libRDKitRDGeometryLib.so.1.2018.03.1.dev1 >>> ../../../lib/libRDKitCatalogs.so.1.2018.03.1.dev1 >>> ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 >>> -lBoost::serialization ../../../lib/libRDKitDataStructs.so.1.2018.03.1.dev1 >>> ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 -lboost_thread >>> -lboost_system -lpthread -Wl,-rpath,/home/tj/RDKit/rdkit/build/lib: >>> /usr/bin/ld: cannot find -lBoost::serialization >>> collect2: error: ld returned 1 exit status >>> make[3]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> make[2]: *** [Code/GraphMol/FilterCatalog/C >>> MakeFiles/FilterCatalog.dir/all] Error 2 >>> make[2]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> make[1]: *** [Code/GraphMol/FilterCatalog/C >>> MakeFiles/FilterCatalog.dir/rule] Error 2 >>> make[1]: Leaving directory `/home/tj/RDKit/rdkit/build' >>> make: *** [FilterCatalog] Error 2 >>> >>> On Sun, Mar 18, 2018 at 3:48 PM, Greg Landrum <gre...@gm...> >>> wrote: >>> >>>> Hi TJ, >>>> >>>> Hrm, that's ugly. Just to confirm: Are you building the master branch >>>> from github? >>>> It looks like there's no fundamental problem with master; at least the >>>> travis builds pass: https://travis-ci.org/rdkit/rdkit >>>> >>>> To help track this down, can you please send the results of doing: >>>> VERBOSE=1 make FilterCatalog >>>> >>>> Best, >>>> -greg >>>> >>>> >>>> On Sun, Mar 18, 2018 at 11:27 PM, TJ O'Donnell <tj...@ac...> wrote: >>>> >>>>> I'm trying to build rdkit from the latest git source. >>>>> Linux Mint 17 >>>>> >>>>> I get this error >>>>> [ 57%] Building CXX object Code/GraphMol/FilterCatalog/CM >>>>> akeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >>>>> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >>>>> /usr/bin/ld: cannot find -lBoost::serialization >>>>> collect2: error: ld returned 1 exit status >>>>> make[2]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >>>>> make[1]: *** [Code/GraphMol/FilterCatalog/C >>>>> MakeFiles/FilterCatalog.dir/all] Error 2 >>>>> make: *** [all] Error 2 >>>>> >>>>> but cmake seemed to find this lib OK >>>>> cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON >>>>> -- The C compiler identification is GNU 4.8.4 >>>>> -- The CXX compiler identification is GNU 4.8.4 >>>>> .... >>>>> -- Found Threads: TRUE >>>>> -- Boost version: 1.54.0 >>>>> -- Found the following Boost libraries: >>>>> -- thread >>>>> -- system >>>>> -- Boost version: 1.54.0 >>>>> -- Found the following Boost libraries: >>>>> -- serialization >>>>> == Using strict rotor definition >>>>> == Updating Filters.cpp from pains file >>>>> >>>>> Can you help me figure out how to get past this? >>>>> >>>>> Thanks, >>>>> TJ >>>>> >>>>> ------------------------------------------------------------ >>>>> ------------------ >>>>> Check out the vibrant tech community on one of the world's most >>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>>> _______________________________________________ >>>>> Rdkit-devel mailing list >>>>> Rdk...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel >>>>> >>>>> >>>> >>> >> > |
|
From: Greg L. <gre...@gm...> - 2018-03-19 10:27:53
|
Well, I don't see anything obvious there to explain why the serialization library is being treated differently from the others. Could you please look at (and send) the output of; grep boost_THREAD CMakeCache.txt grep boost_SERIAL CMakeCache.txt Best, -greg On Sun, Mar 18, 2018 at 10:31 PM, TJ O'Donnell <tj...@ac...> wrote: > FYI I cloned https://github.com/rdkit/rdkit.git > and get the same error > > TJ > > On Sun, Mar 18, 2018 at 7:31 PM, TJ O'Donnell <tj...@ac...> wrote: > >> Thanks for the quick reply, Greg. I just did a git pull and it merged in >> lots of files. >> I may try a clone to a "fresh" folder and see how that goes. >> Anyway, here's the output from VERBOSE=1 make FilterCatalog >> >> tj@vmmint:~/RDKit/rdkit/build$ VERBOSE=1 make FilterCatalog >> /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build >> --check-build-system CMakeFiles/Makefile.cmake 0 >> make -f CMakeFiles/Makefile2 FilterCatalog >> make[1]: Entering directory `/home/tj/RDKit/rdkit/build' >> /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build >> --check-build-system CMakeFiles/Makefile.cmake 0 >> /usr/bin/cmake -E cmake_progress_start /home/tj/RDKit/rdkit/build/CMakeFiles >> 9 >> make -f CMakeFiles/Makefile2 Code/GraphMol/FilterCatalog/CM >> akeFiles/FilterCatalog.dir/all >> make[2]: Entering directory `/home/tj/RDKit/rdkit/build' >> make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make >> Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/RDGeneral >> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/RDGeneral >> /home/tj/RDKit/rdkit/build/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake >> --color= >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make >> Code/RDGeneral/CMakeFiles/RDGeneral.dir/build >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> make[3]: Nothing to be done for `Code/RDGeneral/CMakeFiles/RDG >> eneral.dir/build'. >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >> 64 >> [ 11%] Built target RDGeneral >> make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make >> Code/DataStructs/CMakeFiles/DataStructs.dir/depend >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/DataStructs >> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/DataStructs >> /home/tj/RDKit/rdkit/build/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake >> --color= >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make >> Code/DataStructs/CMakeFiles/DataStructs.dir/build >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> make[3]: Nothing to be done for `Code/DataStructs/CMakeFiles/D >> ataStructs.dir/build'. >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >> 7 >> [ 22%] Built target DataStructs >> make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make >> Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Geometry >> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Geometry >> /home/tj/RDKit/rdkit/build/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake >> --color= >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make >> Code/Geometry/CMakeFiles/RDGeometryLib.dir/build >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> make[3]: Nothing to be done for `Code/Geometry/CMakeFiles/RDGe >> ometryLib.dir/build'. >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >> 66 >> [ 33%] Built target RDGeometryLib >> make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make >> Code/GraphMol/CMakeFiles/GraphMol.dir/depend >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol >> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol >> /home/tj/RDKit/rdkit/build/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake >> --color= >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make >> Code/GraphMol/CMakeFiles/GraphMol.dir/build >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> make[3]: Nothing to be done for `Code/GraphMol/CMakeFiles/Grap >> hMol.dir/build'. >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >> 35 36 37 38 >> [ 77%] Built target GraphMol >> make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make >> Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Subgraphs >> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs >> /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs/CMakeFile >> s/Subgraphs.dir/DependInfo.cmake --color= >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make >> Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> make[3]: Nothing to be done for `Code/GraphMol/Subgraphs/CMake >> Files/Subgraphs.dir/build'. >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >> keFiles >> [ 77%] Built target Subgraphs >> make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make >> Code/Catalogs/CMakeFiles/Catalogs.dir/depend >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Catalogs >> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Catalogs >> /home/tj/RDKit/rdkit/build/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake >> --color= >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make >> Code/Catalogs/CMakeFiles/Catalogs.dir/build >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> make[3]: Nothing to be done for `Code/Catalogs/CMakeFiles/Cata >> logs.dir/build'. >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >> keFiles >> [ 77%] Built target Catalogs >> make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make >> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/SmilesParse >> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse >> /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse/CMakeFi >> les/SmilesParse.dir/DependInfo.cmake --color= >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make >> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> make[3]: Nothing to be done for `Code/GraphMol/SmilesParse/CMa >> keFiles/SmilesParse.dir/build'. >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >> 71 >> [ 88%] Built target SmilesParse >> make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make >> Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Substruct >> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct >> /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct/CMakeFile >> s/SubstructMatch.dir/DependInfo.cmake --color= >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make >> Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> make[3]: Nothing to be done for `Code/GraphMol/Substruct/CMake >> Files/SubstructMatch.dir/build'. >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >> keFiles >> [ 88%] Built target SubstructMatch >> make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make >> Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/FilterCatalog >> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog >> /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog/CMake >> Files/FilterCatalog.dir/DependInfo.cmake --color= >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make >> Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build >> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >> cd /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog && >> /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt >> --verbose=1 >> /usr/bin/c++ -fPIC -mpopcnt -Wno-deprecated -Wno-unused-function >> -fno-strict-aliasing -Wall -Wextra -fPIC -O3 -DNDEBUG -shared >> -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1 >> CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o >> CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o >> CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o >> CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >> ../../../lib/libRDKitSubgraphs.so.1.2018.03.1.dev1 >> ../../../lib/libRDKitSubstructMatch.so.1.2018.03.1.dev1 >> ../../../lib/libRDKitSmilesParse.so.1.2018.03.1.dev1 >> ../../../lib/libRDKitGraphMol.so.1.2018.03.1.dev1 >> ../../../lib/libRDKitRDGeometryLib.so.1.2018.03.1.dev1 >> ../../../lib/libRDKitCatalogs.so.1.2018.03.1.dev1 >> ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 >> -lBoost::serialization ../../../lib/libRDKitDataStructs.so.1.2018.03.1.dev1 >> ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 -lboost_thread >> -lboost_system -lpthread -Wl,-rpath,/home/tj/RDKit/rdkit/build/lib: >> /usr/bin/ld: cannot find -lBoost::serialization >> collect2: error: ld returned 1 exit status >> make[3]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >> make[2]: *** [Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all] >> Error 2 >> make[2]: Leaving directory `/home/tj/RDKit/rdkit/build' >> make[1]: *** [Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/rule] >> Error 2 >> make[1]: Leaving directory `/home/tj/RDKit/rdkit/build' >> make: *** [FilterCatalog] Error 2 >> >> On Sun, Mar 18, 2018 at 3:48 PM, Greg Landrum <gre...@gm...> >> wrote: >> >>> Hi TJ, >>> >>> Hrm, that's ugly. Just to confirm: Are you building the master branch >>> from github? >>> It looks like there's no fundamental problem with master; at least the >>> travis builds pass: https://travis-ci.org/rdkit/rdkit >>> >>> To help track this down, can you please send the results of doing: >>> VERBOSE=1 make FilterCatalog >>> >>> Best, >>> -greg >>> >>> >>> On Sun, Mar 18, 2018 at 11:27 PM, TJ O'Donnell <tj...@ac...> wrote: >>> >>>> I'm trying to build rdkit from the latest git source. >>>> Linux Mint 17 >>>> >>>> I get this error >>>> [ 57%] Building CXX object Code/GraphMol/FilterCatalog/CM >>>> akeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >>>> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >>>> /usr/bin/ld: cannot find -lBoost::serialization >>>> collect2: error: ld returned 1 exit status >>>> make[2]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >>>> make[1]: *** [Code/GraphMol/FilterCatalog/C >>>> MakeFiles/FilterCatalog.dir/all] Error 2 >>>> make: *** [all] Error 2 >>>> >>>> but cmake seemed to find this lib OK >>>> cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON >>>> -- The C compiler identification is GNU 4.8.4 >>>> -- The CXX compiler identification is GNU 4.8.4 >>>> .... >>>> -- Found Threads: TRUE >>>> -- Boost version: 1.54.0 >>>> -- Found the following Boost libraries: >>>> -- thread >>>> -- system >>>> -- Boost version: 1.54.0 >>>> -- Found the following Boost libraries: >>>> -- serialization >>>> == Using strict rotor definition >>>> == Updating Filters.cpp from pains file >>>> >>>> Can you help me figure out how to get past this? >>>> >>>> Thanks, >>>> TJ >>>> >>>> ------------------------------------------------------------ >>>> ------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> _______________________________________________ >>>> Rdkit-devel mailing list >>>> Rdk...@li... >>>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel >>>> >>>> >>> >> > |
|
From: TJ O'D. <tj...@ac...> - 2018-03-19 03:32:12
|
FYI I cloned https://github.com/rdkit/rdkit.git and get the same error TJ On Sun, Mar 18, 2018 at 7:31 PM, TJ O'Donnell <tj...@ac...> wrote: > Thanks for the quick reply, Greg. I just did a git pull and it merged in > lots of files. > I may try a clone to a "fresh" folder and see how that goes. > Anyway, here's the output from VERBOSE=1 make FilterCatalog > > tj@vmmint:~/RDKit/rdkit/build$ VERBOSE=1 make FilterCatalog > /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build > --check-build-system CMakeFiles/Makefile.cmake 0 > make -f CMakeFiles/Makefile2 FilterCatalog > make[1]: Entering directory `/home/tj/RDKit/rdkit/build' > /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build > --check-build-system CMakeFiles/Makefile.cmake 0 > /usr/bin/cmake -E cmake_progress_start /home/tj/RDKit/rdkit/build/CMakeFiles > 9 > make -f CMakeFiles/Makefile2 Code/GraphMol/FilterCatalog/ > CMakeFiles/FilterCatalog.dir/all > make[2]: Entering directory `/home/tj/RDKit/rdkit/build' > make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make > Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix > Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/RDGeneral > /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/RDGeneral > /home/tj/RDKit/rdkit/build/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake > --color= > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make > Code/RDGeneral/CMakeFiles/RDGeneral.dir/build > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > make[3]: Nothing to be done for `Code/RDGeneral/CMakeFiles/ > RDGeneral.dir/build'. > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles > 64 > [ 11%] Built target RDGeneral > make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make > Code/DataStructs/CMakeFiles/DataStructs.dir/depend > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix > Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/DataStructs > /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/DataStructs > /home/tj/RDKit/rdkit/build/Code/DataStructs/CMakeFiles/ > DataStructs.dir/DependInfo.cmake --color= > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make > Code/DataStructs/CMakeFiles/DataStructs.dir/build > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > make[3]: Nothing to be done for `Code/DataStructs/CMakeFiles/ > DataStructs.dir/build'. > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles > 7 > [ 22%] Built target DataStructs > make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make > Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix > Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Geometry > /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Geometry > /home/tj/RDKit/rdkit/build/Code/Geometry/CMakeFiles/ > RDGeometryLib.dir/DependInfo.cmake --color= > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make > Code/Geometry/CMakeFiles/RDGeometryLib.dir/build > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > make[3]: Nothing to be done for `Code/Geometry/CMakeFiles/ > RDGeometryLib.dir/build'. > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles > 66 > [ 33%] Built target RDGeometryLib > make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make > Code/GraphMol/CMakeFiles/GraphMol.dir/depend > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix > Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol > /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol > /home/tj/RDKit/rdkit/build/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake > --color= > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make > Code/GraphMol/CMakeFiles/GraphMol.dir/build > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > make[3]: Nothing to be done for `Code/GraphMol/CMakeFiles/ > GraphMol.dir/build'. > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles > 35 36 37 38 > [ 77%] Built target GraphMol > make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make > Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix > Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Subgraphs > /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs > /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs/ > CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make > Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > make[3]: Nothing to be done for `Code/GraphMol/Subgraphs/ > CMakeFiles/Subgraphs.dir/build'. > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/ > CMakeFiles > [ 77%] Built target Subgraphs > make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make > Code/Catalogs/CMakeFiles/Catalogs.dir/depend > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix > Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Catalogs > /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Catalogs > /home/tj/RDKit/rdkit/build/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake > --color= > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make > Code/Catalogs/CMakeFiles/Catalogs.dir/build > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > make[3]: Nothing to be done for `Code/Catalogs/CMakeFiles/ > Catalogs.dir/build'. > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/ > CMakeFiles > [ 77%] Built target Catalogs > make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make > Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix > Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/SmilesParse > /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse > /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse/ > CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make > Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > make[3]: Nothing to be done for `Code/GraphMol/SmilesParse/ > CMakeFiles/SmilesParse.dir/build'. > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles > 71 > [ 88%] Built target SmilesParse > make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make > Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix > Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Substruct > /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct > /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct/ > CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make > Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > make[3]: Nothing to be done for `Code/GraphMol/Substruct/ > CMakeFiles/SubstructMatch.dir/build'. > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/ > CMakeFiles > [ 88%] Built target SubstructMatch > make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make > Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix > Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/FilterCatalog > /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog > /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog/ > CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make > Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build > make[3]: Entering directory `/home/tj/RDKit/rdkit/build' > Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so > cd /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog && > /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt > --verbose=1 > /usr/bin/c++ -fPIC -mpopcnt -Wno-deprecated -Wno-unused-function > -fno-strict-aliasing -Wall -Wextra -fPIC -O3 -DNDEBUG -shared -Wl,-soname,libRDKitFilterCatalog.so.1 > -o ../../../lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1 > CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o > CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o > CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o > CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/ > libRDKitSubgraphs.so.1.2018.03.1.dev1 ../../../lib/ > libRDKitSubstructMatch.so.1.2018.03.1.dev1 ../../../lib/ > libRDKitSmilesParse.so.1.2018.03.1.dev1 ../../../lib/libRDKitGraphMol.so.1.2018.03.1.dev1 > ../../../lib/libRDKitRDGeometryLib.so.1.2018.03.1.dev1 > ../../../lib/libRDKitCatalogs.so.1.2018.03.1.dev1 ../../../lib/ > libRDKitRDGeneral.so.1.2018.03.1.dev1 -lBoost::serialization ../../../lib/ > libRDKitDataStructs.so.1.2018.03.1.dev1 ../../../lib/ > libRDKitRDGeneral.so.1.2018.03.1.dev1 -lboost_thread -lboost_system > -lpthread -Wl,-rpath,/home/tj/RDKit/rdkit/build/lib: > /usr/bin/ld: cannot find -lBoost::serialization > collect2: error: ld returned 1 exit status > make[3]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 > make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' > make[2]: *** [Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all] > Error 2 > make[2]: Leaving directory `/home/tj/RDKit/rdkit/build' > make[1]: *** [Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/rule] > Error 2 > make[1]: Leaving directory `/home/tj/RDKit/rdkit/build' > make: *** [FilterCatalog] Error 2 > > On Sun, Mar 18, 2018 at 3:48 PM, Greg Landrum <gre...@gm...> > wrote: > >> Hi TJ, >> >> Hrm, that's ugly. Just to confirm: Are you building the master branch >> from github? >> It looks like there's no fundamental problem with master; at least the >> travis builds pass: https://travis-ci.org/rdkit/rdkit >> >> To help track this down, can you please send the results of doing: >> VERBOSE=1 make FilterCatalog >> >> Best, >> -greg >> >> >> On Sun, Mar 18, 2018 at 11:27 PM, TJ O'Donnell <tj...@ac...> wrote: >> >>> I'm trying to build rdkit from the latest git source. >>> Linux Mint 17 >>> >>> I get this error >>> [ 57%] Building CXX object Code/GraphMol/FilterCatalog/CM >>> akeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >>> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >>> /usr/bin/ld: cannot find -lBoost::serialization >>> collect2: error: ld returned 1 exit status >>> make[2]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >>> make[1]: *** [Code/GraphMol/FilterCatalog/C >>> MakeFiles/FilterCatalog.dir/all] Error 2 >>> make: *** [all] Error 2 >>> >>> but cmake seemed to find this lib OK >>> cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON >>> -- The C compiler identification is GNU 4.8.4 >>> -- The CXX compiler identification is GNU 4.8.4 >>> .... >>> -- Found Threads: TRUE >>> -- Boost version: 1.54.0 >>> -- Found the following Boost libraries: >>> -- thread >>> -- system >>> -- Boost version: 1.54.0 >>> -- Found the following Boost libraries: >>> -- serialization >>> == Using strict rotor definition >>> == Updating Filters.cpp from pains file >>> >>> Can you help me figure out how to get past this? >>> >>> Thanks, >>> TJ >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> Rdkit-devel mailing list >>> Rdk...@li... >>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel >>> >>> >> > |
|
From: TJ O'D. <tj...@ac...> - 2018-03-19 02:31:40
|
Thanks for the quick reply, Greg. I just did a git pull and it merged in lots of files. I may try a clone to a "fresh" folder and see how that goes. Anyway, here's the output from VERBOSE=1 make FilterCatalog tj@vmmint:~/RDKit/rdkit/build$ VERBOSE=1 make FilterCatalog /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 FilterCatalog make[1]: Entering directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /home/tj/RDKit/rdkit/build/CMakeFiles 9 make -f CMakeFiles/Makefile2 Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all make[2]: Entering directory `/home/tj/RDKit/rdkit/build' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/RDGeneral /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/RDGeneral /home/tj/RDKit/rdkit/build/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/RDGeneral/CMakeFiles/RDGeneral.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles 64 [ 11%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/DataStructs /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/DataStructs /home/tj/RDKit/rdkit/build/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/DataStructs/CMakeFiles/DataStructs.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles 7 [ 22%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Geometry /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Geometry /home/tj/RDKit/rdkit/build/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/Geometry/CMakeFiles/RDGeometryLib.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles 66 [ 33%] Built target RDGeometryLib make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol /home/tj/RDKit/rdkit/build/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/GraphMol/CMakeFiles/GraphMol.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles 35 36 37 38 [ 77%] Built target GraphMol make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Subgraphs /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles [ 77%] Built target Subgraphs make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Catalogs /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Catalogs /home/tj/RDKit/rdkit/build/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/Catalogs/CMakeFiles/Catalogs.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles [ 77%] Built target Catalogs make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/SmilesParse /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles 71 [ 88%] Built target SmilesParse make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Substruct /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' make[3]: Nothing to be done for `Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build'. make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles [ 88%] Built target SubstructMatch make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[3]: Entering directory `/home/tj/RDKit/rdkit/build' cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/FilterCatalog /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build make[3]: Entering directory `/home/tj/RDKit/rdkit/build' Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O3 -DNDEBUG -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2018.03.1.dev1 ../../../lib/libRDKitSubstructMatch.so.1.2018.03.1.dev1 ../../../lib/libRDKitSmilesParse.so.1.2018.03.1.dev1 ../../../lib/libRDKitGraphMol.so.1.2018.03.1.dev1 ../../../lib/libRDKitRDGeometryLib.so.1.2018.03.1.dev1 ../../../lib/libRDKitCatalogs.so.1.2018.03.1.dev1 ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 -lBoost::serialization ../../../lib/libRDKitDataStructs.so.1.2018.03.1.dev1 ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 -lboost_thread -lboost_system -lpthread -Wl,-rpath,/home/tj/RDKit/rdkit/build/lib: /usr/bin/ld: cannot find -lBoost::serialization collect2: error: ld returned 1 exit status make[3]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' make[2]: *** [Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all] Error 2 make[2]: Leaving directory `/home/tj/RDKit/rdkit/build' make[1]: *** [Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/rule] Error 2 make[1]: Leaving directory `/home/tj/RDKit/rdkit/build' make: *** [FilterCatalog] Error 2 On Sun, Mar 18, 2018 at 3:48 PM, Greg Landrum <gre...@gm...> wrote: > Hi TJ, > > Hrm, that's ugly. Just to confirm: Are you building the master branch from > github? > It looks like there's no fundamental problem with master; at least the > travis builds pass: https://travis-ci.org/rdkit/rdkit > > To help track this down, can you please send the results of doing: > VERBOSE=1 make FilterCatalog > > Best, > -greg > > > On Sun, Mar 18, 2018 at 11:27 PM, TJ O'Donnell <tj...@ac...> wrote: > >> I'm trying to build rdkit from the latest git source. >> Linux Mint 17 >> >> I get this error >> [ 57%] Building CXX object Code/GraphMol/FilterCatalog/CM >> akeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >> /usr/bin/ld: cannot find -lBoost::serialization >> collect2: error: ld returned 1 exit status >> make[2]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >> make[1]: *** [Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all] >> Error 2 >> make: *** [all] Error 2 >> >> but cmake seemed to find this lib OK >> cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON >> -- The C compiler identification is GNU 4.8.4 >> -- The CXX compiler identification is GNU 4.8.4 >> .... >> -- Found Threads: TRUE >> -- Boost version: 1.54.0 >> -- Found the following Boost libraries: >> -- thread >> -- system >> -- Boost version: 1.54.0 >> -- Found the following Boost libraries: >> -- serialization >> == Using strict rotor definition >> == Updating Filters.cpp from pains file >> >> Can you help me figure out how to get past this? >> >> Thanks, >> TJ >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Rdkit-devel mailing list >> Rdk...@li... >> https://lists.sourceforge.net/lists/listinfo/rdkit-devel >> >> > |
|
From: Greg L. <gre...@gm...> - 2018-03-18 22:48:38
|
Hi TJ, Hrm, that's ugly. Just to confirm: Are you building the master branch from github? It looks like there's no fundamental problem with master; at least the travis builds pass: https://travis-ci.org/rdkit/rdkit To help track this down, can you please send the results of doing: VERBOSE=1 make FilterCatalog Best, -greg On Sun, Mar 18, 2018 at 11:27 PM, TJ O'Donnell <tj...@ac...> wrote: > I'm trying to build rdkit from the latest git source. > Linux Mint 17 > > I get this error > [ 57%] Building CXX object Code/GraphMol/FilterCatalog/ > CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o > Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so > /usr/bin/ld: cannot find -lBoost::serialization > collect2: error: ld returned 1 exit status > make[2]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 > make[1]: *** [Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all] > Error 2 > make: *** [all] Error 2 > > but cmake seemed to find this lib OK > cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON > -- The C compiler identification is GNU 4.8.4 > -- The CXX compiler identification is GNU 4.8.4 > .... > -- Found Threads: TRUE > -- Boost version: 1.54.0 > -- Found the following Boost libraries: > -- thread > -- system > -- Boost version: 1.54.0 > -- Found the following Boost libraries: > -- serialization > == Using strict rotor definition > == Updating Filters.cpp from pains file > > Can you help me figure out how to get past this? > > Thanks, > TJ > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Rdkit-devel mailing list > Rdk...@li... > https://lists.sourceforge.net/lists/listinfo/rdkit-devel > > |
|
From: TJ O'D. <tj...@ac...> - 2018-03-18 22:27:29
|
I'm trying to build rdkit from the latest git source. Linux Mint 17 I get this error [ 57%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so /usr/bin/ld: cannot find -lBoost::serialization collect2: error: ld returned 1 exit status make[2]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 make[1]: *** [Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all] Error 2 make: *** [all] Error 2 but cmake seemed to find this lib OK cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON -- The C compiler identification is GNU 4.8.4 -- The CXX compiler identification is GNU 4.8.4 .... -- Found Threads: TRUE -- Boost version: 1.54.0 -- Found the following Boost libraries: -- thread -- system -- Boost version: 1.54.0 -- Found the following Boost libraries: -- serialization == Using strict rotor definition == Updating Filters.cpp from pains file Can you help me figure out how to get past this? Thanks, TJ |
|
From: Greg L. <gre...@gm...> - 2018-03-16 05:45:23
|
Hi Jeff, On Thu, Mar 15, 2018 at 10:26 PM, jeff godden <jg...@gm...> wrote: > > > First and foremost thank you for your excellent offering of a singularly > useful set of molecular descriptors! > Thanks for the kind words. :-) > As one of the authors cited by Dr Labute (http://www.chemcomp.com/journ > al/vsadesc.htm) > , > i've appreciated RDKit's implementation of the "Labute descriptor" set. > So i've noticed that two particular descriptors in that set, specifically > SlogP_VSA9 and SMR_VSA8, appear to always return a value of 0.0 no matter > which of a > substantial > set of small molecules are tested via: > > from rdkit.Chem import Descriptors > Descriptors.SlogP_VSA9(molecule) > Descriptors.SMR_VSA8(molecule) > Let's look at the first one. SlogP_VSA9 is the sum of the VSA contributions of atoms whose contribution to SlogP falls into bin 9. In the case of the RDKit this is means an atomic SlogP contribution of between 0.3 and 0.4 (I believe that this is the same as the definition in the original paper. This RDKit bins are not always the same as the original publication, in this case they are). So we need to look for atom types that have an SlogP contribution between 0.3 and 0.4. Curiously, there don't seem to be any of these. Going back to the original Wildman and Crippen paper (the source of these values), there aren't any there either. This is "a bit" strange since the Labute article says that they picked the bins in order to have evenly distributed values. So I don't think you're doing anything wrong; there's an oddity in the definition of the bins and it looks like that descriptor is basically always going to be zero. Thanks for pointing it out. Since I have found the various "MOE like" descriptors to be quite useful in the past, it's worth considering doing another version of them where the bin definitions have been adjusted based on a larger set of molecules. Something to think about for a future version... Thanks for the great question, -greg > > All other descriptors i've tried seem to produce sensible results (with > those same molecules) > > Of course it's always possible that it's something i've mis-coded. I'm > attaching a simple python program which returns the anomalous descriptor > values for me. > > Thank you very much for all your efforts! > -- > jeff godden > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Rdkit-devel mailing list > Rdk...@li... > https://lists.sourceforge.net/lists/listinfo/rdkit-devel > > |
|
From: jeff g. <jg...@gm...> - 2018-03-15 21:26:26
|
Dear RDKit Developers , First and foremost thank you for your excellent offering of a singularly useful set of molecular descriptors! As one of the authors cited by Dr Labute ( http://www.chemcomp.com/journal/vsadesc.htm) , i've appreciated RDKit's implementation of the "Labute descriptor" set. So i've noticed that two particular descriptors in that set, specifically SlogP_VSA9 and SMR_VSA8, appear to always return a value of 0.0 no matter which of a substantial set of small molecules are tested via: from rdkit.Chem import Descriptors Descriptors.SlogP_VSA9(molecule) Descriptors.SMR_VSA8(molecule) All other descriptors i've tried seem to produce sensible results (with those same molecules) Of course it's always possible that it's something i've mis-coded. I'm attaching a simple python program which returns the anomalous descriptor values for me. Thank you very much for all your efforts! -- jeff godden |
|
From: Greg L. <gre...@gm...> - 2017-10-08 12:33:23
|
I'm pleased to announce that the next version of the RDKit -- 2017.09 -- is released. The release notes are below. The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2017_09_1 Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit). The available conda binaries for this release are: Linux 64bit: python 2.7, 3.5, 3.6 Mac OS 64bit: python 2.7, 3.5, 3.6 Windows 64bit: python 2.7, 3.5, 3.6 I left out the Win32 python2.7 build this time. If that's important to someone, let me know and I'll see if I can get it working again. Some notes on the conda builds: - These builds are tested with conda v4.3.25 and, as of the release date, are very unlikely to work with anything newer than that. This thread has more information on that: https://www.mail-archive.com/rdkit-discuss@lists. sourceforge.net/msg07315.html - The conda builds now depend on numpy 1.13 instead of 1.11. - The Mac and Linux builds now use v1.63 of boost. The rdkit conda channel has the appropriate binaries. Some things that will be finished over the next couple of days: - The conda build scripts will be updated to reflect the new version and new conda builds will be available in the RDKit channel at anaconda.org ( https://anaconda.org/rdkit). - The homebrew script - The online version of the documentation at rdkit.org Thanks to everyone who submitted bug reports and suggestions for this release! Please let me know if you find any problems with the release or have suggestions for the next one, which is scheduled for March 2018. Best Regards, -greg # Release_2017.09.1 (Changes relative to Release_2017.03.1) ## Important - The fix for bug #1567 changes the way fragment SMILES are canonicalized. MolFragmentToSmiles() and canonicalizeFragment() will now often return different results - The fix for bug #1604 changes the behavior of QueryAtom::setQuery(), which now deletes the current query before setting the new value. If you are using QueryAtom::setQuery() from C++ (or possibly Java), be sure that you are not also deleting that memory. ## Acknowledgements: Brian Cole, Peter Gedeck, Guillaume Godin, Jan Halborg Jensen, Malitha Kabir, Tuomo Kalliokoski, Brian Kelley, Noel O'Boyle, Matthew O'Meara, Pavel Polishchuk, Cameron Pye, Christian Ribeaud, Stephen Roughley, Patrick Savery, Roger Sayle, Nadine Schneider, Gregor Simm, Matt Swain, Paolo Tosco, Alain Vaucher, Sam Webb, 'phenethyl', 'xiaotaw' ## Highlights: - The new R-Group decomposition code provides a flexible and powerful tool for building R-group tables or datasets look in $RDBASE/Docs/Notebooks for example notebooks showing how to use this. - Drawing of chemical reactions has been greatly improved and is now done using the C++ rendering code. - The MaxMinPicker is dramatically faster. - New descriptors: the QED descriptor has been added as have a large collection of new 3D descriptors and implementations of the USR and USRCAT fingerprints. ## New Features and Enhancements: - Bring back USR and USRCAT descriptors (github pull #1417 from greglandrum) - Generate a warning for conflicting bond directions (github issue #1423 from greglandrum) - expose and test GetDrawCoords() (github pull #1427 from greglandrum) - Improvement suggestions for SaltRemover (github issue #1431 from ribeaud) - Remove obsolete scripts from Scripts dir (github pull #1440 from greglandrum) - Support drawing reactions from C++ (github pull #1444 from greglandrum) - QED code with unit test file (github pull #1445 from gedeck) - Add support for other datatypes to ConvertToNumpyArray (github issue #1447 from pyeguy) - - updated FindCairo.cmake (github pull #1455 from ptosco) - - fixes PgSQL CMakeLists.txt to enable conda build on Windows (github pull #1457 from ptosco) - Some cleanups to make Travis builds faster (github pull #1464 from greglandrum) - ExplainPairScore does not support includeChirality=True (github issue #1466 from xiaotaw) - Add a collection of new 3D descriptors (github pull #1467 from greglandrum) - Update cartridge documentation to use ChEMBL 23 (github issue #1491 from greglandrum) - First entry of the SubstructLibrary module (github pull #1493 from bp-kelley) - assorted fixes to get the current master branch to build on Windows (github pull #1495 from ptosco) - Support assignment of stereochemistry tags to bonds from 3D structure (github issue #1497 from gncs) - Support black and white molecule drawing (github issue #1510 from greglandrum) - Missing def_readwrite for backgroundColour in rdMolDraw2D.cpp (github issue #1519 from goraj) - Adds canonicalization of atom maps (github pull #1521 from bp-kelley) - Implement stereoisomer enumeration (github pull #1531 from greglandrum) - Add a MolBundle class (github pull #1537 from greglandrum) - Provide support for color palettes in MolDraw2D (github pull #1546 from greglandrum) - A few reaction drawing tweaks (github pull #1549 from greglandrum) - R group improvements (github pull #1552 from greglandrum) - Add a canned Atom query for heavy atom degree (github issue #1563 from greglandrum) - Adds FreeSASA adapter (github pull #1565 from bp-kelley) - Added C++ version of getBestRMS() (github pull #1568 from psavery) - SMILES lexer optimization/enhancement (github pull #1575 from greglandrum) - Update IPythonConsole and PandasTools to use new drawing code (github pull #1577 from greglandrum) - Squashes warnings on cygwin (github pull #1578 from bp-kelley) - Support continuous highlighting in drawMolecules(). (github pull #1579 from greglandrum) - Enhanced Similarity Maps depiction (github pull #1594 from gerebtzoff) ## Bug Fixes: - RDKit gets stuck on PubChem CID 102128817 (github issue #1281 from TuomoKalliokoski) - MMP code not including molecules with no cuts (github issue #1406 from greglandrum) - Fixes PandasTools to also work with pandas 0.20 (github pull #1410 from bp-kelley) - csharp input files out of date (github issue #1413 from greglandrum) - Fix cxsmiles parse on VS2008 (github pull #1415 from mcs07) - MaxMinPicker picking non-existent element (github issue #1421 from greglandrum) - _isCallable clashes with Celery (github issue #1434 from momeara) - Impossible to build the RDKit from source without Python installed (github issue #1435 from greglandrum) - RemoveHs() removes H atom attached to dummy if it came from AddHs() (github issue #1439 from DrrDom) - fix a couple failing windows tests related to temp file removal (github pull #1446 from greglandrum) - SanitizeRxn fails with a runtime exception when unused Rlabels are in product (github issue #1448 from bp-kelley) - String module conversion bug (github pull #1452 from coleb) - GetConformerRMS() documentation is misleading (github pull #1459 from greglandrum) - URANGE_CHECK not doing its job in RWMol::addBond (github issue #1461 from baoilleach) - ExplainPairScore does not support includeChirality=True (github issue #1466 from xiaotaw) - MolToSmarts does not include atom-map or isotope info for molecules built from SMILES (github issue #1472 from greglandrum) - AdjustQueryProperties() removing properties from dummy atoms (github issue #1474 from greglandrum) - Fixes lookup for HELM Monomer 'D' (github pull #1477 from bp-kelley) - Aromatic rings composed solely of dummy atoms should not be kekulized (github issue #1478 from bp-kelley) - Directly specify rotor model used in QED. (github pull #1483 from bp-kelley) - Unicode problem with pidPS tests on Mac (github issue #1490 from greglandrum) - Pattern fingerprint setting bad bits with degree zero atoms (github issue #1496 from greglandrum) - Remove xlocale header (github pull #1501 from greglandrum) - Fixes atom documentation (github pull #1505 from bp-kelley) - TypeError from PandasTools.SaveXlsxFromFrame (github issue #1507 from pyeguy) - Removes trailing spaces after \ to fix windows compilation errors (github pull #1516 from bp-kelley) - prepareMolForDrawing() not in SWIG wrappers (github issue #1522 from greglandrum) - Bond is missing IsInRing methods in Java wrapper (github issue #1535 from sroughley) - Fixes blanking of non-query atom data when QueryAtomData was being pi… (github pull #1541 from bp-kelley) - ChemicalReaction code not calling setNoImplicit() when H counts are set. (github issue #1544 from greglandrum) - Fixes failing build with MSVC (github pull #1547 from ptosco) - Kekulization error with cores from R-Group Decomposition (github issue #1550 from greglandrum) - Fixes double free for Dict::update (github pull #1571 from bp-kelley) - QueryAtom::setQuery() should delete the old query first (github pull #1604 from greglandrum) |
|
From: Greg L. <gre...@gm...> - 2017-09-29 07:31:22
|
Dear all, This morning I tagged the beta of the 2017.09 RDKit release in github: https://github.com/rdkit/rdkit/releases/tag/Release_2017_09_1b1 I will try to get some conda builds up over the next day or so. These will use the beta label so that they do not install by default; you'll need to run "conda install" as follows: conda install -c rdkit/label/beta rdkit python=3.6 Be sure to confirm that it's installing the right version when you are prompted (if there's no build available, it will pick the current production release instead). You can check to see if a build is available for your platform/python version here: https://anaconda.org/rdkit/rdkit/files?version=2017.09.1.b1 Note that I've done the conda linux builds using a Centos7 system - in the past I've used Centos6 - if this causes compatibility problems or if you think that this is a bad idea please let me know and I will switch back to Centos6 for the builds. The relevant section of the release notes is below. As usual, if you have time to try out the new release I would love feedback. If nothing major comes up, I plan to do the actual release a week from today. Best, -greg # Release_2017.09.1 (Changes relative to Release_2017.03.1) ## Important - The fix for bug #1567 changes the way fragment SMILES are canonicalized. MolFragmentToSmiles() and canonicalizeFragment() will now often return different results ## Acknowledgements: Brian Cole, Peter Gedeck, Guillaume Godin, Malitha Kabir, Tuomo Kalliokoski, Brian Kelley, Noel O'Boyle, Matthew O'Meara, Pavel Polishchuk, Cameron Pye, Christian Ribeaud, Stephen Roughley, Patrick Savery, Roger Sayle, Nadine Schneider, Matt Swain, Paolo Tosco, Alain Vaucher, Sam Webb, 'phenethyl', 'xiaotaw' ## Highlights: - The new R-Group decomposition code provides a flexible and powerful tool for building R-group tables or datasets look in $RDBASE/Docs/Notebooks for example notebooks showing how to use this. - Drawing of chemical reactions has been greatly improved and is now done using the C++ rendering code. - The MaxMinPicker is dramatically faster. - New descriptors: the QED descriptor has been added as have a large collection of new 3D descriptors and implementations of the USR and USRCAT fingerprints. ## New Features and Enhancements: - Bring back USR and USRCAT descriptors (github pull #1417 from greglandrum) - Generate a warning for conflicting bond directions (github issue #1423 from greglandrum) - expose and test GetDrawCoords() (github pull #1427 from greglandrum) - Improvement suggestions for SaltRemover (github issue #1431 from ribeaud) - Remove obsolete scripts from Scripts dir (github pull #1440 from greglandrum) - Support drawing reactions from C++ (github pull #1444 from greglandrum) - QED code with unit test file (github pull #1445 from gedeck) - Add support for other datatypes to ConvertToNumpyArray (github issue #1447 from pyeguy) - - updated FindCairo.cmake (github pull #1455 from ptosco) - - fixes PgSQL CMakeLists.txt to enable conda build on Windows (github pull #1457 from ptosco) - Some cleanups to make Travis builds faster (github pull #1464 from greglandrum) - ExplainPairScore does not support includeChirality=True (github issue #1466 from xiaotaw) - Add a collection of new 3D descriptors (github pull #1467 from greglandrum) - Update cartridge documentation to use ChEMBL 23 (github issue #1491 from greglandrum) - First entry of the SubstructLibrary module (github pull #1493 from bp-kelley) - assorted fixes to get the current master branch to build on Windows (github pull #1495 from ptosco) - Support black and white molecule drawing (github issue #1510 from greglandrum) - Missing def_readwrite for backgroundColour in rdMolDraw2D.cpp (github issue #1519 from goraj) - Adds canonicalization of atom maps (github pull #1521 from bp-kelley) - Implement stereoisomer enumeration (github pull #1531 from greglandrum) - Add a MolBundle class (github pull #1537 from greglandrum) - Provide support for color palettes in MolDraw2D (github pull #1546 from greglandrum) - A few reaction drawing tweaks (github pull #1549 from greglandrum) - R group improvements (github pull #1552 from greglandrum) - Add a canned Atom query for heavy atom degree (github issue #1563 from greglandrum) - Adds FreeSASA adapter (github pull #1565 from bp-kelley) - Added C++ version of getBestRMS() (github pull #1568 from psavery) - SMILES lexer optimization/enhancement (github pull #1575 from greglandrum) - Update IPythonConsole and PandasTools to use new drawing code (github pull #1577 from greglandrum) - Squashes warnings on cygwin (github pull #1578 from bp-kelley) - Support continuous highlighting in drawMolecules(). (github pull #1579 from greglandrum) - Enhanced Similarity Maps depiction (github pull #1594 from gerebtzoff) ## Bug Fixes: - RDKit gets stuck on PubChem CID 102128817 (github issue #1281 from TuomoKalliokoski) - MMP code not including molecules with no cuts (github issue #1406 from greglandrum) - Fixes PandasTools to also work with pandas 0.20 (github pull #1410 from bp-kelley) - csharp input files out of date (github issue #1413 from greglandrum) - Fix cxsmiles parse on VS2008 (github pull #1415 from mcs07) - MaxMinPicker picking non-existent element (github issue #1421 from greglandrum) - _isCallable clashes with Celery (github issue #1434 from momeara) - Impossible to build the RDKit from source without Python installed (github issue #1435 from greglandrum) - RemoveHs() removes H atom attached to dummy if it came from AddHs() (github issue #1439 from DrrDom) - fix a couple failing windows tests related to temp file removal (github pull #1446 from greglandrum) - SanitizeRxn fails with a runtime exception when unused Rlabels are in product (github issue #1448 from bp-kelley) - String module conversion bug (github pull #1452 from coleb) - GetConformerRMS() documentation is misleading (github pull #1459 from greglandrum) - URANGE_CHECK not doing its job in RWMol::addBond (github issue #1461 from baoilleach) - ExplainPairScore does not support includeChirality=True (github issue #1466 from xiaotaw) - MolToSmarts does not include atom-map or isotope info for molecules built from SMILES (github issue #1472 from greglandrum) - AdjustQueryProperties() removing properties from dummy atoms (github issue #1474 from greglandrum) - Fixes lookup for HELM Monomer 'D' (github pull #1477 from bp-kelley) - Aromatic rings composed solely of dummy atoms should not be kekulized (github issue #1478 from bp-kelley) - Directly specify rotor model used in QED. (github pull #1483 from bp-kelley) - Unicode problem with pidPS tests on Mac (github issue #1490 from greglandrum) - Pattern fingerprint setting bad bits with degree zero atoms (github issue #1496 from greglandrum) - Remove xlocale header (github pull #1501 from greglandrum) - Fixes atom documentation (github pull #1505 from bp-kelley) - TypeError from PandasTools.SaveXlsxFromFrame (github issue #1507 from pyeguy) - Removes trailing spaces after \ to fix windows compilation errors (github pull #1516 from bp-kelley) - prepareMolForDrawing() not in SWIG wrappers (github issue #1522 from greglandrum) - Bond is missing IsInRing methods in Java wrapper (github issue #1535 from sroughley) - Fixes blanking of non-query atom data when QueryAtomData was being pi… (github pull #1541 from bp-kelley) - - Fixes failing build with MSVC (github pull #1547 from ptosco) - Kekulization error with cores from R-Group Decomposition (github issue #1550 from greglandrum) - Fixes double free for Dict::update (github pull #1571 from bp-kelley) |
|
From: Igor F. <igo...@gm...> - 2017-09-09 14:12:11
|
Greg,
I figured out what the problem is:
getStringSize() calculates the pixel height/width of a given atom label.
For labels such as NH3+ the argument this function is getting is
NH<sub>3</sub><sup>+</sup>
which makes for a very long sting, which throws off the scale calculation.
I am not sure why it works correctly with the drawers other than SVG but
for wxWidgets I need to clean from the label <sub>, <sup>, </sub>, and
</sup>
before computing the string width.
Hope this helps to someone who might have the same problem.
Best regards,
Igor
On Fri, Sep 8, 2017 at 8:29 AM, Igor Filippov <igo...@gm...>
wrote:
> Great - thanks, I'll try it!
>
> Igor
>
> On Fri, Sep 8, 2017 at 8:27 AM, Greg Landrum <gre...@gm...>
> wrote:
>
>>
>> On Fri, Sep 8, 2017 at 2:10 PM, Igor Filippov <igo...@gm...>
>> wrote:
>>
>>>
>>>>
>>>> Could it be that you didn't generate coordinates for the molecule?
>>>>
>>>> The result is the same for me whether I load the molecule from an SD
>>> file with coordinates, or generate 2D or 3D coordinates on the fly.
>>> Does it display correctly for you?
>>>
>>
>> Yeah, This snippet:
>>
>> In [21]: m = Chem.MolFromSmiles('NC(=O)C(N)CCCC[NH3+]')
>>
>> In [22]: nm = Draw.PrepareMolForDrawing(m)
>>
>> In [23]: d = Draw.MolDraw2DCairo(200,200)
>>
>> In [24]: d.DrawMolecule(nm)
>>
>> In [25]: d.FinishDrawing()
>>
>> In [26]: open('blah.png','wb+').write(d.GetDrawingText())
>> Out[26]: 2730
>>
>>
>> Produces the png file that's attached.
>>
>>
>>> BTW: rdMolDraw2D.PrepareMolForDrawing() is a useful function to know
>>>> about.
>>>>
>>> I am doing it from c++, is there an equivalent there?
>>>
>>
>> Sure, here's some testing code that uses it:
>> https://github.com/rdkit/rdkit/blob/9af90524a41825b67ffb19cd
>> bff9b363d5a7ca7e/Code/GraphMol/MolDraw2D/test1.cpp#L987
>>
>> There are a bunch of other examples in that file too.
>>
>> -greg
>>
>>
>
|
|
From: Igor F. <igo...@gm...> - 2017-09-08 12:29:38
|
Great - thanks, I'll try it!
Igor
On Fri, Sep 8, 2017 at 8:27 AM, Greg Landrum <gre...@gm...> wrote:
>
> On Fri, Sep 8, 2017 at 2:10 PM, Igor Filippov <igo...@gm...>
> wrote:
>
>>
>>>
>>> Could it be that you didn't generate coordinates for the molecule?
>>>
>>> The result is the same for me whether I load the molecule from an SD
>> file with coordinates, or generate 2D or 3D coordinates on the fly.
>> Does it display correctly for you?
>>
>
> Yeah, This snippet:
>
> In [21]: m = Chem.MolFromSmiles('NC(=O)C(N)CCCC[NH3+]')
>
> In [22]: nm = Draw.PrepareMolForDrawing(m)
>
> In [23]: d = Draw.MolDraw2DCairo(200,200)
>
> In [24]: d.DrawMolecule(nm)
>
> In [25]: d.FinishDrawing()
>
> In [26]: open('blah.png','wb+').write(d.GetDrawingText())
> Out[26]: 2730
>
>
> Produces the png file that's attached.
>
>
>> BTW: rdMolDraw2D.PrepareMolForDrawing() is a useful function to know
>>> about.
>>>
>> I am doing it from c++, is there an equivalent there?
>>
>
> Sure, here's some testing code that uses it:
> https://github.com/rdkit/rdkit/blob/9af90524a41825b67ffb19cdbff9b3
> 63d5a7ca7e/Code/GraphMol/MolDraw2D/test1.cpp#L987
>
> There are a bunch of other examples in that file too.
>
> -greg
>
>
|
|
From: Greg L. <gre...@gm...> - 2017-09-08 12:27:41
|
On Fri, Sep 8, 2017 at 2:10 PM, Igor Filippov <igo...@gm...>
wrote:
>
>>
>> Could it be that you didn't generate coordinates for the molecule?
>>
>> The result is the same for me whether I load the molecule from an SD file
> with coordinates, or generate 2D or 3D coordinates on the fly.
> Does it display correctly for you?
>
Yeah, This snippet:
In [21]: m = Chem.MolFromSmiles('NC(=O)C(N)CCCC[NH3+]')
In [22]: nm = Draw.PrepareMolForDrawing(m)
In [23]: d = Draw.MolDraw2DCairo(200,200)
In [24]: d.DrawMolecule(nm)
In [25]: d.FinishDrawing()
In [26]: open('blah.png','wb+').write(d.GetDrawingText())
Out[26]: 2730
Produces the png file that's attached.
> BTW: rdMolDraw2D.PrepareMolForDrawing() is a useful function to know
>> about.
>>
> I am doing it from c++, is there an equivalent there?
>
Sure, here's some testing code that uses it:
https://github.com/rdkit/rdkit/blob/9af90524a41825b67ffb19cdbff9b363d5a7ca7e/Code/GraphMol/MolDraw2D/test1.cpp#L987
There are a bunch of other examples in that file too.
-greg
|
|
From: Igor F. <igo...@gm...> - 2017-09-08 12:10:54
|
Greg, Thank you for the quick reply. > Could it be that you didn't generate coordinates for the molecule? > > The result is the same for me whether I load the molecule from an SD file with coordinates, or generate 2D or 3D coordinates on the fly. Does it display correctly for you? > BTW: rdMolDraw2D.PrepareMolForDrawing() is a useful function to know > about. > I am doing it from c++, is there an equivalent there? Best regards, Igor > > -greg > > > On Thu, Sep 7, 2017 at 2:16 PM, Igor Filippov <igo...@gm...> > wrote: > >> Dear Colleagues, >> >> I seem to remember there already was a discussion about this, >> but I cannot find the relevant email thread, nor recall what was the >> conclusion. >> >> When I try to draw the following molecule I am getting an image of a few >> pixels in size, quite >> unusable. >> >> NC(=O)C(N)CCCC[NH3+] >> >> Has anyone else seen this problem? >> >> Best regards, >> Igor >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Rdkit-devel mailing list >> Rdk...@li... >> https://lists.sourceforge.net/lists/listinfo/rdkit-devel >> >> > |
|
From: Greg L. <gre...@gm...> - 2017-09-08 08:55:00
|
Hi Igor, Could it be that you didn't generate coordinates for the molecule? BTW: rdMolDraw2D.PrepareMolForDrawing() is a useful function to know about. -greg On Thu, Sep 7, 2017 at 2:16 PM, Igor Filippov <igo...@gm...> wrote: > Dear Colleagues, > > I seem to remember there already was a discussion about this, > but I cannot find the relevant email thread, nor recall what was the > conclusion. > > When I try to draw the following molecule I am getting an image of a few > pixels in size, quite > unusable. > > NC(=O)C(N)CCCC[NH3+] > > Has anyone else seen this problem? > > Best regards, > Igor > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Rdkit-devel mailing list > Rdk...@li... > https://lists.sourceforge.net/lists/listinfo/rdkit-devel > > |
4 messages has been excluded from this view by a project administrator.
