Hi Gabriele,
add -DBoost_DEBUG=ON to your cmake command to have more information
regarding the failure.
Also, does adding -DBoost_NO_BOOST_CMAKE=ON help or change things?
Cheers,
p.
On 14/05/2020 13:45, baldu...@units.it wrote:
hello
I'm clearly missing something here, but not being able to clarify
things.
After 2019_09_1b1 I'm not able to build rdkit via cmake from source
any longer
Even following the plain instructions in Install.md :
RDBASE=./rdkit
cd $RDBASE
mkdir build
cd build
cmake ..
make
doesn't work.
At cmake time I get a flood of errors related to boost like these:
----8<----
CMake Error at Code/cmake/Modules/RDKitUtils.cmake:153 (add_executable):
Target "testCoordGen" links to target "Boost::system" but the target was
not found. Perhaps a find_package() call is missing for an IMPORTED
target, or an ALIAS target is missing?
Call Stack (most recent call first):
External/CoordGen/CMakeLists.txt:108 (rdkit_test)
CMake Error at Code/cmake/Modules/RDKitUtils.cmake:153 (add_executable):
Target "testCoordGen" links to target "Boost::iostreams" but the target
was
not found. Perhaps a find_package() call is missing for an IMPORTED
target, or an ALIAS target is missing?
Call Stack (most recent call first):
External/CoordGen/CMakeLists.txt:108 (rdkit_test)
---->8----
If I ignore the above errors and continue with make, the build crashes
very soon with:
----8<----
/usr/bin/c++ -fPIC -mpopcnt -Wno-deprecated -Wno-unused-function
-fno-strict-aliasing -Wall -Wextra -fPIC -O3 -DNDEBUG -shared
-Wl,-soname,libRDKitDepictor.so.1 -o
../../../lib/libRDKitDepictor.so.1.2020.03.2
CMakeFiles/Depictor.dir/RDDepictor.cpp.o
CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o
CMakeFiles/Depictor.dir/DepictUtils.cpp.o
-Wl,-rpath,/home/balducci/tmp/install-us-d/rdkit-2020_03_2.d/rdkit/build/lib:
../../../lib/libRDKitMolAlign.so.1.2020.03.2 -lcoordgen -lmaeparser
-lBoost::system -lBoost::iostreams
../../../lib/libRDKitMolTransforms.so.1.2020.03.2
../../../lib/libRDKitEigenSolvers.so.1.2020.03.2
../../../lib/libRDKitAlignment.so.1.2020.03.2
../../../lib/libRDKitForceFieldHelpers.so.1.2020.03.2
../../../lib/libRDKitSubstructMatch.so.1.2020.03.2
../../../lib/libRDKitSmilesParse.so.1.2020.03.2
../../../lib/libRDKitForceField.so.1.2020.03.2
../../../lib/libRDKitOptimizer.so.1.2020.03.2
../../../lib/libRDKitTrajectory.so.1.2020.03.2
../../../lib/libRDKitGraphMol.so.1.2020.03.2
../../../lib/libRDKitRingDecomposerLib.so.1.2020.03.2
../../../lib/libRDKitRDGeometryLib.so.1.2020.03.2
../../../lib/libRDKitDataStructs.so.1.2020.03.2
../../../lib/libRDKitRDGeneral.so.1.2020.03.2 -lpthread
/usr/bin/ld: cannot find -lBoost::system
/usr/bin/ld: cannot find -lBoost::iostreams
collect2: error: ld returned 1 exit status
make[2]: ***
[Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make:154:
lib/libRDKitDepictor.so.1.2020.03.2] Error 1
make[2]: Leaving directory
'/home/balducci/tmp/install-us-d/rdkit-2020_03_2.d/rdkit/build'
---->8----
Apparently, the boost libs have been messed up, most probably related
with the above cmake error messages
If I try to build with ninja, the build doesn't even start:
----8<----
[...]
CMake Generate step failed. Build files cannot be regenerated correctly.
ninja: error: loading 'build.ninja': No such file or directory
---->8----
Cloning from git and using the following versions of the involved
packages:
rdkit-2020_03_2
boost-1_73_0
cmake-3.17.2
make-4.3
ninja-1.10.0
gcc-9.3.0
I can add that I obtain the same result also with boost-1_71_0
I'm enclosing a small script which allows to reproduce (or not) the
problem I'm reporting about
I suspect something wrong with my boost installation, but I'm unable
to find the culprit
I'm hoping that someone fluent in cmake can easily spot the mistake
I'm doing
Any hint will be warmly appreciated
ciao
-gabriele
----8<----
#!/bin/sh
work_dir=$(pwd)
the_tag="Release_2020_03_2"
GIT_SSL_NO_VERIFY=true \
git clone -b ${the_tag} https://github.com/rdkit/rdkit.git rdkit
RDBASE=rdkit
cd $RDBASE
mkdir build
cd build
cmake -DCMAKE_VERBOSE_MAKEFILE=ON ..
# the above command dumps a bunch of errors like:
# CMake Error at Code/cmake/Modules/RDKitUtils.cmake:153 (add_executable):
# Target "testCoordGen" links to target "Boost::iostreams" but the target
was
# not found. Perhaps a find_package() call is missing for an IMPORTED
# target, or an ALIAS target is missing?
# Call Stack (most recent call first):
# External/CoordGen/CMakeLists.txt:108 (rdkit_test)
make
#######################
# uncomment for ninja #
#######################
# cd $RDBASE
# mkdir build
# cd build
# cmake -G"Ninja" ..
# ninja -v
exit
----8<----
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