Re: [rDock-list-def] issues in installing rDock

[Sergio R. C. <sru...@gm...>]

Hi Andriy,

Please refer to https://github.com/CBDD/rDock, as the project has been
ported to GitHub and the installation steps modified.
Hope that helps.
Thanks,

Sergio

On Sat, 16 Dec 2023 at 18:06, Andriy Kovalenko <an...@ua...> wrote:

> Hello,
>
> I downloaded and started installing rDock on my Ubuntu desktop.
> Unfortunately, it interrupted with an error message - please see (1)
> below, highlighted in bold.
>
> Due to message (1), I then started installing *lpopt*.
> However, it ended up again with an error message - please see (2) below,
> highlighted in bold.
>
> Would you please help me out to resolve this issue.
>
> Sincerely,
>
>
> Dr. Andriy Kovalenko
>
> Research Assistant
> Department of Biological Sciences
> University of Alberta
> CW 405, Biological Sciences Bldg.
> Edmonton, Alberta, Canada T6G 2E9
>
> Tel:  780-940-7477 (cell)
> e-mail:  and...@ua...
>
>
> (1) andriy@andriy-Precision-Tower-5810:~/rDock-main$ *sudo make install*
> make lib
> make[1]: Entering directory '/home/andriy/rDock-main'
> g++ -Werror -pipe -std=c++14 -fPIC -O3 -ffast-math   -D_NDEBUG -shared
> -L./lib obj/RbtTriposAtomType.o obj/RbtMdlFileSink.o
> obj/RbtBaseMolecularFileSink.o obj/RbtPdbFileSource.o obj/RbtBaseIntraSF.o
> obj/RbtFilter.o obj/RbtSubject.o obj/RbtEuler.o obj/RbtPMFDirSource.o
> obj/RbtPrincipalAxes.o obj/RbtCellTokenIter.o obj/RbtDihedralTargetSF.o
> obj/RbtGATransform.o obj/RbtChromDihedralRefData.o
> obj/RbtBaseMolecularFileSource.o obj/RbtRotSF.o obj/RbtFlexAtomFactory.o
> obj/RbtNullTransform.o obj/RbtChrom.o obj/RbtSFAgg.o obj/RbtBond.o
> obj/RbtBiMolWorkSpace.o obj/RbtAtomFuncs.o obj/RbtNonBondedGrid.o
> obj/RbtChromPositionRefData.o obj/RbtAlignTransform.o
> obj/RbtSiteMapperFactory.o obj/RbtObserver.o obj/RbtModelMutator.o
> obj/RbtPsfFileSource.o obj/RbtAromIdxSF.o obj/RbtPolarSF.o
> obj/RbtBaseTransform.o obj/RbtBaseBiMolTransform.o obj/RbtSetupPolarSF.o
> obj/RbtDirectorySource.o obj/RbtPopulation.o obj/RbtCavityFillSF.o
> obj/RbtBaseUniMolTransform.o obj/RbtFilterExpressionVisitor.o
> obj/RbtCharmmTypesFileSource.o obj/RbtConstraint.o obj/RbtMOEGrid.o
> obj/RbtChromFactory.o obj/RbtMOL2FileSource.o obj/RbtNonBondedHHSGrid.o
> obj/RbtChromOccupancyElement.o obj/RbtChromElement.o
> obj/RbtChromPositionElement.o obj/RbtAtom.o obj/RbtTransformAgg.o
> obj/RbtCavityGridSF.o obj/RbtRandLigTransform.o obj/RbtModel.o
> obj/RbtCrdFileSource.o obj/RbtAnnotation.o obj/RbtDihedralSF.o
> obj/RbtSimplexTransform.o obj/RbtParser.o obj/RbtDebug.o obj/RbtPMFIdxSF.o
> obj/RbtElementFileSource.o obj/RbtLigandSiteMapper.o obj/RbtVdwIntraSF.o
> obj/RbtLigandFlexData.o obj/RbtAnnotationHandler.o obj/RbtPseudoAtom.o
> obj/RbtBaseObject.o obj/RbtRandPopTransform.o obj/RbtSetupPMFSF.o
> obj/RbtSolventFlexData.o obj/RbtRealGrid.o obj/RbtReceptorFlexData.o
> obj/RbtSFFactory.o obj/RbtChromDihedralElement.o obj/RbtSetupSASF.o
> obj/RbtNoeRestraint.o obj/RbtPsfFileSink.o obj/RbtSiteMapper.o
> obj/RbtPolarIntraSF.o obj/RbtSATypes.o obj/RbtBaseGrid.o obj/RbtWorkSpace.o
> obj/RbtToken.o obj/RbtSphereSiteMapper.o obj/RbtBaseIdxSF.o
> obj/RbtVdwGridSF.o obj/RbtSimAnnTransform.o obj/RbtContext.o
> obj/RbtPRMFactory.o obj/RbtChromOccupancyRefData.o obj/RbtVdwIdxSF.o
> obj/RbtBaseFileSink.o obj/RbtInteractionGrid.o obj/RbtDihedralIntraSF.o
> obj/RbtPharmaSF.o obj/RbtPMFGridSF.o obj/RbtDockingSite.o
> obj/RbtNmrRestraintFileSource.o obj/RbtRand.o obj/RbtVdwSF.o
> obj/RbtCharmmDataSource.o obj/RbtTransformFactory.o obj/RbtBaseFileSource.o
> obj/Rbt.o obj/RbtPMF.o obj/RbtMdlFileSource.o obj/RbtParamHandler.o
> obj/RbtParameterFileSource.o obj/RbtFFTGrid.o obj/RbtNmrSF.o
> obj/RbtPolarIdxSF.o obj/RbtCrdFileSink.o obj/RbtBaseSF.o
> obj/RbtBaseInterSF.o obj/RbtTetherSF.o obj/RbtStringTokenIter.o
> obj/RbtFilterExpression.o obj/RbtGenome.o obj/RbtConstSF.o obj/RbtSAIdxSF.o
> obj/simplex/NMSearch.o obj/GP/RbtGPChromosome.o obj/GP/RbtGPGenome.o
> obj/GP/RbtGPParser.o obj/GP/RbtGPFFGold.o obj/GP/RbtGPFFSpike.o
> obj/GP/RbtGPFitnessFunction.o obj/GP/RbtGPPopulation.o
> obj/GP/RbtGPFFCrossDock.o obj/GP/RbtGPFFCHK1.o obj/GP/RbtGPFFHSP90.o -o
> lib/libRbt.so -lpopt -lm -lstdc++
>
>
>
>
>
> */usr/bin/ld: cannot find -lpopt: No such file or directorycollect2:
> error: ld returned 1 exit statusmake[1]: *** [Makefile:190: lib/libRbt.so]
> Error 1make[1]: Leaving directory '/home/andriy/rDock-main'make: ***
> [Makefile:133: build_lib] Error 2*
>
> (2) andriy@andriy-Precision-Tower-5810:~/Ipopt$ ./configure
> CXX=g++-11.4.0 CC=gcc-11.4.0 F77=gfortran-11.4.0
> checking build system type... x86_64-pc-linux-gnu
> checking host system type... x86_64-pc-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a race-free mkdir -p... /usr/bin/mkdir -p
> checking for gawk... no
> checking for mawk... mawk
> checking whether make sets $(MAKE)... yes
> checking whether make supports nested variables... yes
> checking whether to enable maintainer-specific portions of Makefiles... no
> checking whether make supports the include directive... yes (GNU style)
> checking whether the C compiler works... no
>
>
> *configure: error: in `/home/andriy/Ipopt':configure: error: C compiler
> cannot create executables*See `config.log' for more details
>
>
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