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Bug 686860 - sci-chemistry/namd-2.10 fails to build
Summary: sci-chemistry/namd-2.10 fails to build
Status: RESOLVED PKGREMOVED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal
Assignee: Nicolas Bock
URL:
Whiteboard:
Keywords: PMASKED
Depends on: 934228
Blocks:
  Show dependency tree
 
Reported: 2019-05-27 15:23 UTC by Pacho Ramos
Modified: 2024-07-19 11:35 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
build.log (1.log,190.84 KB, text/plain)
2019-05-27 15:23 UTC, Pacho Ramos
Details

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Description Pacho Ramos gentoo-dev 2019-05-27 15:23:20 UTC
Created attachment 577882 [details]
build.log

I get:
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmoduleHybridLB.so: undefined reference to `AllocateGreedyRefineLB()'
collect2: error: ld returned 1 exit status
Fatal Error by charmc in directory /var/tmp/portage/sci-chemistry/namd-2.10/work/NAMD_2.10_Source/Linux-x86_64-g++
   Command g++ -rdynamic -D_REENTRANT -O2 -pipe -march=native -fno-stack-protector -pthread -L/usr/lib64 -fPIC -I/usr/include/charm-6.8.2 -o namd2 -L/usr/lib64 -I/usr/include/charm-6.8.2 obj/buildinfo.o obj/ComputeMoa.o obj/ComputeMsm.o obj/ComputeMsmMsa.o obj/ComputeMsmSerial.o obj/ComputeFmmSerial.o obj/msm.o obj/msm_longrng.o obj/msm_longrng_sprec.o obj/msm_setup.o obj/msm_shortrng.o obj/msm_shortrng_sprec.o obj/wkfutils.o obj/common.o obj/dcdlib.o obj/erf.o obj/fitrms.o obj/main.o obj/mainfunc.o obj/memusage.o obj/strlib.o obj/AlgSeven.o obj/AlgRecBisection.o obj/AlgNbor.o obj/AtomMap.o obj/BackEnd.o obj/BroadcastMgr.o obj/BroadcastClient.o obj/CollectionMaster.o obj/CollectionMgr.o obj/Communicate.o obj/Compute.o obj/ComputeAngles.o obj/ComputeAniso.o obj/ComputeBonds.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o obj/ComputeCrossterms.o obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.o obj/ComputeEwald.o obj/ComputeExt.o obj/ComputeGBISser.o obj/ComputeGBIS.o obj/ComputeGromacsPair.o obj/ComputeLCPO.o obj/ComputeFullDirect.o obj/ComputeHomePatch.o obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o obj/ComputeGlobalMsgs.o obj/ComputeGridForce.o obj/ComputeMap.o obj/ComputeMgr.o obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o obj/ComputeNonbondedFEP.o obj/ComputeNonbondedGo.o obj/ComputeNonbondedTI.o obj/ComputeNonbondedLES.o obj/ComputeNonbondedPProf.o obj/ComputeNonbondedTabEnergies.o obj/ComputeNonbondedCUDA.o obj/ComputeNonbondedCUDAExcl.o obj/ComputeNonbondedMIC.o obj/ComputeNonbondedMICKernel.o obj/ComputePatch.o obj/ComputePatchPair.o obj/ComputePme.o obj/OptPme.o obj/OptPmeRealSpace.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o obj/ComputeStir.o obj/ComputeTclBC.o obj/ComputeThole.o obj/ConfigList.o obj/Controller.o obj/ccsinterface.o obj/DataStream.o obj/DumpBench.o obj/FreeEnergyAssert.o obj/FreeEnergyGroup.o obj/FreeEnergyLambda.o obj/FreeEnergyLambdMgr.o obj/FreeEnergyParse.o obj/FreeEnergyRestrain.o obj/FreeEnergyRMgr.o obj/FreeEnergyVector.o obj/fstream_namd.o obj/GlobalMaster.o obj/GlobalMasterServer.o obj/GlobalMasterTest.o obj/GlobalMasterIMD.o obj/GlobalMasterTcl.o obj/GlobalMasterSMD.o obj/GlobalMasterTMD.o obj/Matrix4Symmetry.o obj/GlobalMasterSymmetry.o obj/GlobalMasterFreeEnergy.o obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o obj/colvar.o obj/colvaratoms.o obj/colvarbias.o obj/colvarbias_abf.o obj/colvarbias_alb.o obj/colvarbias_meta.o obj/colvarbias_restraint.o obj/colvarcomp.o obj/colvarcomp_angles.o obj/colvarcomp_coordnums.o obj/colvarcomp_distances.o obj/colvarcomp_protein.o obj/colvarcomp_rotations.o obj/colvargrid.o obj/colvarmodule.o obj/colvarparse.o obj/colvarproxy_namd.o obj/colvarscript.o obj/colvartypes.o obj/colvarvalue.o obj/GridForceGrid.o obj/GromacsTopFile.o obj/heap.o obj/HomePatch.o obj/IMDOutput.o obj/InfoStream.o obj/LdbCoordinator.o obj/LJTable.o obj/Measure.o obj/MGridforceParams.o obj/MStream.o obj/MigrateAtomsMsg.o obj/Molecule.o obj/Molecule2.o obj/GoMolecule.o obj/NamdCentLB.o obj/NamdNborLB.o obj/NamdHybridLB.o obj/NamdDummyLB.o obj/NamdState.o obj/NamdOneTools.o obj/Node.o obj/Output.o obj/Parameters.o obj/ParseOptions.o obj/Patch.o obj/PatchMgr.o obj/PatchMap.o obj/PDB.o obj/PDBData.o obj/PmeKSpace.o obj/PmeRealSpace.o obj/ProcessorPrivate.o obj/ProxyMgr.o obj/ProxyPatch.o obj/Rebalancer.o obj/RecBisection.o obj/ReductionMgr.o obj/RefineOnly.o obj/RefineTorusLB.o obj/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o obj/SimParameters.o obj/SortAtoms.o obj/Sync.o obj/TclCommands.o obj/TorusLB.o obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o obj/CompressPsf.o obj/PluginIOMgr.o obj/DataExchanger.o obj/ParallelIOMgr.o obj/dcdplugin.o obj/jsplugin.o obj/namdbinplugin.o obj/pdbplugin.o obj/psfplugin.o moduleinit1819.o -lmoduleCkMulticast -lmoduleGreedyLB -lmoduleRefineLB -lmoduleHybridLB -lmoduleNeighborLB -lckmain -lck -lmemory-default -lthreads-default -lconv-cplus-y -lconv-core -ltmgr -lconv-util -lconv-partition -lmemory-default -lthreads-default -lldb-rand -lconv-ldb -lpthread -lckqt -ldl -Wl,-O1 -Wl,--as-needed -Wl,-O1 -Wl,--as-needed -ltcl8.6 -ltclstub8.6 -ldl -lfftw3f -lm -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB -lmoduleCkMulticast -lmoduleNDMeshStreamer -lmodulecompletion -lnuma -lm returned error code 1
charmc exiting...
rm -f moduleinit1819.C moduleinit1819.o
Comment 1 Larry the Git Cow gentoo-dev 2024-07-19 11:34:49 UTC
The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=140e19b020538b51f589747c5525883061c7f970

commit 140e19b020538b51f589747c5525883061c7f970
Author:     Arthur Zamarin <arthurzam@gentoo.org>
AuthorDate: 2024-07-19 11:29:05 +0000
Commit:     Arthur Zamarin <arthurzam@gentoo.org>
CommitDate: 2024-07-19 11:34:41 +0000

    sci-chemistry/namd: treeclean
    
    Bug: https://bugs.gentoo.org/686856
    Bug: https://bugs.gentoo.org/686858
    Bug: https://bugs.gentoo.org/686860
    Bug: https://bugs.gentoo.org/934228
    Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>

 profiles/package.mask                           |   6 --
 sci-chemistry/namd/Manifest                     |   1 -
 sci-chemistry/namd/files/namd-2.10-gentoo.patch | 124 ------------------------
 sci-chemistry/namd/files/namd-2.7-iml-dec.patch |  24 -----
 sci-chemistry/namd/metadata.xml                 |  12 ---
 sci-chemistry/namd/namd-2.10.ebuild             | 110 ---------------------
 6 files changed, 277 deletions(-)