Received: by mail.netbsd.org (Postfix, from userid 605) id 22E2684F2A; Fri, 8 Jul 2022 19:48:04 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id 59DC884F1B for ; Fri, 8 Jul 2022 19:48:03 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([127.0.0.1]) by localhost (mail.netbsd.org [127.0.0.1]) (amavisd-new, port 10025) with ESMTP id J6cNb8kWJDf9 for ; Fri, 8 Jul 2022 19:47:59 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.NetBSD.org [IPv6:2001:470:a085:999:28c:faff:fe03:5984]) by mail.netbsd.org (Postfix) with ESMTP id B6A6984EA0 for ; Fri, 8 Jul 2022 19:47:59 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id AA15DFB1A; Fri, 8 Jul 2022 19:47:59 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_165730967941680" MIME-Version: 1.0 Date: Fri, 8 Jul 2022 19:47:59 +0000 From: "Dr. Thomas Orgis" Subject: CVS commit: pkgsrc/math To: pkgsrc-changes@NetBSD.org Reply-To: thor@netbsd.org X-Mailer: log_accum Message-Id: <20220708194759.AA15DFB1A@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_165730967941680 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: thor Date: Fri Jul 8 19:47:59 UTC 2022 Modified Files: pkgsrc/math: Makefile Added Files: pkgsrc/math/plumed: DESCR Makefile PLIST distinfo options.mk pkgsrc/math/plumed/patches: patch-Makefile.conf.in patch-configure patch-configure.ac Log Message: math/plumed: added package for the MD algorithm library To generate a diff of this commit: cvs rdiff -u -r1.546 -r1.547 pkgsrc/math/Makefile cvs rdiff -u -r0 -r1.1 pkgsrc/math/plumed/DESCR pkgsrc/math/plumed/Makefile \ pkgsrc/math/plumed/PLIST pkgsrc/math/plumed/distinfo \ pkgsrc/math/plumed/options.mk cvs rdiff -u -r0 -r1.1 pkgsrc/math/plumed/patches/patch-Makefile.conf.in \ pkgsrc/math/plumed/patches/patch-configure \ pkgsrc/math/plumed/patches/patch-configure.ac Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_165730967941680 Content-Disposition: inline Content-Length: 82027 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/math/Makefile diff -u pkgsrc/math/Makefile:1.546 pkgsrc/math/Makefile:1.547 --- pkgsrc/math/Makefile:1.546 Sun Jun 12 14:35:53 2022 +++ pkgsrc/math/Makefile Fri Jul 8 19:47:59 2022 @@ -1,4 +1,4 @@ -# $NetBSD: Makefile,v 1.546 2022/06/12 14:35:53 bacon Exp $ +# $NetBSD: Makefile,v 1.547 2022/07/08 19:47:59 thor Exp $ COMMENT= Mathematics @@ -362,6 +362,7 @@ SUBDIR+= pear-Numbers_Roman SUBDIR+= pear-Numbers_Words SUBDIR+= php-bcmath SUBDIR+= php-stats +SUBDIR+= plumed SUBDIR+= ppl SUBDIR+= prng SUBDIR+= pspp Added files: Index: pkgsrc/math/plumed/DESCR diff -u /dev/null pkgsrc/math/plumed/DESCR:1.1 --- /dev/null Fri Jul 8 19:47:59 2022 +++ pkgsrc/math/plumed/DESCR Fri Jul 8 19:47:59 2022 @@ -0,0 +1,9 @@ +PLUMED is an open-source, community-developed library that provides a +wide range of different methods, which include: + + enhanced-sampling algorithms free-energy methods tools to analyze the + vast amounts of data produced by molecular dynamics (MD) simulations. + +These techniques can be used in combination with a large toolbox +of collective variables that describe complex processes in physics, +chemistry, material science, and biology. Index: pkgsrc/math/plumed/Makefile diff -u /dev/null pkgsrc/math/plumed/Makefile:1.1 --- /dev/null Fri Jul 8 19:47:59 2022 +++ pkgsrc/math/plumed/Makefile Fri Jul 8 19:47:59 2022 @@ -0,0 +1,42 @@ +# $NetBSD: Makefile,v 1.1 2022/07/08 19:47:59 thor Exp $ + +DISTNAME= plumed-2.8.0 +CATEGORIES= math +MASTER_SITES= ${MASTER_SITE_GITHUB:=plumed/plumed2/releases/download/v2.8.0/} +EXTRACT_SUFX= .tgz + +MAINTAINER= thor@NetBSD.org +HOMEPAGE= https://www.plumed.org/ +COMMENT= Molecular dynamics support library +LICENSE= gnu-lgpl-v3 + +GNU_CONFIGURE= yes +USE_LANGUAGES= c c++ fortran +USE_TOOLS+= gmake bash + +TEST_TARGET= check + +CONFIGURE_ARGS+= --enable-gsl +CONFIGURE_ARGS+= --enable-external-blas --enable-external-lapack +CONFIGURE_ARGS+= LIBS='${LAPACK_LIBS}' +CONFIGURE_ARGS+= LIBRARY_PATH='${LIBRARY_PATH}:${PREFIX}/lib' +CONFIGURE_ARGS+= --enable-rpath +# Python module should be a separate package, I suppose. +# it is a versioned .so file, so differing pythons might coexist. +CONFIGURE_ARGS+= --disable-python + +SUBST_CLASSES+= envbash +SUBST_STAGE.envbash= pre-configure +SUBST_FILES.envbash= src/lib/Makefile +SUBST_SED.envbash= -e 's,/usr/bin/env bash,${BASH},' + +REPLACE_BASH+= scripts/*.sh patches/*.sh + +.include "options.mk" + +.include "../../devel/zlib/buildlink3.mk" +.include "../../mk/blas.buildlink3.mk" +.include "../../math/fftw/buildlink3.mk" +.include "../../math/gsl/buildlink3.mk" + +.include "../../mk/bsd.pkg.mk" Index: pkgsrc/math/plumed/PLIST diff -u /dev/null pkgsrc/math/plumed/PLIST:1.1 --- /dev/null Fri Jul 8 19:47:59 2022 +++ pkgsrc/math/plumed/PLIST Fri Jul 8 19:47:59 2022 @@ -0,0 +1,530 @@ +@comment $NetBSD: PLIST,v 1.1 2022/07/08 19:47:59 thor Exp $ +bin/plumed +bin/plumed-config +bin/plumed-patch +include/plumed/analysis/AnalysisBase.h +include/plumed/analysis/AverageVessel.h +include/plumed/analysis/DataCollectionObject.h +include/plumed/analysis/LandmarkSelectionBase.h +include/plumed/analysis/ReadAnalysisFrames.h +include/plumed/asmjit/arch.h +include/plumed/asmjit/arm.h +include/plumed/asmjit/asmjit.h +include/plumed/asmjit/asmjit_apibegin.h +include/plumed/asmjit/asmjit_apiend.h +include/plumed/asmjit/asmjit_build.h +include/plumed/asmjit/assembler.h +include/plumed/asmjit/base.h +include/plumed/asmjit/codebuilder.h +include/plumed/asmjit/codecompiler.h +include/plumed/asmjit/codeemitter.h +include/plumed/asmjit/codeholder.h +include/plumed/asmjit/constpool.h +include/plumed/asmjit/cpuinfo.h +include/plumed/asmjit/func.h +include/plumed/asmjit/globals.h +include/plumed/asmjit/inst.h +include/plumed/asmjit/logging.h +include/plumed/asmjit/misc_p.h +include/plumed/asmjit/moved_string.h +include/plumed/asmjit/operand.h +include/plumed/asmjit/osutils.h +include/plumed/asmjit/regalloc_p.h +include/plumed/asmjit/runtime.h +include/plumed/asmjit/simdtypes.h +include/plumed/asmjit/utils.h +include/plumed/asmjit/vmem.h +include/plumed/asmjit/x86.h +include/plumed/asmjit/x86assembler.h +include/plumed/asmjit/x86builder.h +include/plumed/asmjit/x86compiler.h +include/plumed/asmjit/x86emitter.h +include/plumed/asmjit/x86globals.h +include/plumed/asmjit/x86inst.h +include/plumed/asmjit/x86instimpl_p.h +include/plumed/asmjit/x86internal_p.h +include/plumed/asmjit/x86logging_p.h +include/plumed/asmjit/x86misc.h +include/plumed/asmjit/x86operand.h +include/plumed/asmjit/x86regalloc_p.h +include/plumed/asmjit/zone.h +include/plumed/bias/ActionRegister.h +include/plumed/bias/Bias.h +include/plumed/bias/ReweightBase.h +include/plumed/blas/blas.h +include/plumed/blas/def_external.h +include/plumed/blas/def_internal.h +include/plumed/blas/real.h +include/plumed/cltools/CLTool.h +include/plumed/cltools/CLToolRegister.h +include/plumed/colvar/ActionRegister.h +include/plumed/colvar/Colvar.h +include/plumed/colvar/CoordinationBase.h +include/plumed/colvar/PathMSDBase.h +include/plumed/config/Config.h +include/plumed/config/version.h +include/plumed/core/Action.h +include/plumed/core/ActionAnyorder.h +include/plumed/core/ActionAtomistic.h +include/plumed/core/ActionPilot.h +include/plumed/core/ActionRegister.h +include/plumed/core/ActionSet.h +include/plumed/core/ActionSetup.h +include/plumed/core/ActionShortcut.h +include/plumed/core/ActionWithArguments.h +include/plumed/core/ActionWithValue.h +include/plumed/core/ActionWithVirtualAtom.h +include/plumed/core/Atoms.h +include/plumed/core/CLTool.h +include/plumed/core/CLToolMain.h +include/plumed/core/CLToolRegister.h +include/plumed/core/Colvar.h +include/plumed/core/DataFetchingObject.h +include/plumed/core/ExchangePatterns.h +include/plumed/core/FlexibleBin.h +include/plumed/core/GREX.h +include/plumed/core/GenericMolInfo.h +include/plumed/core/MDAtoms.h +include/plumed/core/PlumedMain.h +include/plumed/core/PlumedMainInitializer.h +include/plumed/core/TargetDist.h +include/plumed/core/Value.h +include/plumed/core/WithCmd.h +include/plumed/function/ActionRegister.h +include/plumed/function/Function.h +include/plumed/gridtools/ActionWithGrid.h +include/plumed/gridtools/ActionWithInputGrid.h +include/plumed/gridtools/ActionWithIntegral.h +include/plumed/gridtools/AverageOnGrid.h +include/plumed/gridtools/ContourFindingBase.h +include/plumed/gridtools/GridPrintingBase.h +include/plumed/gridtools/GridSearch.h +include/plumed/gridtools/GridVessel.h +include/plumed/gridtools/HistogramOnGrid.h +include/plumed/isdb/MetainferenceBase.h +include/plumed/lapack/def_external.h +include/plumed/lapack/def_internal.h +include/plumed/lapack/lapack.h +include/plumed/lapack/lapack_limits.h +include/plumed/lapack/real.h +include/plumed/lepton/CompiledExpression.h +include/plumed/lepton/CustomFunction.h +include/plumed/lepton/Exception.h +include/plumed/lepton/ExpressionProgram.h +include/plumed/lepton/ExpressionTreeNode.h +include/plumed/lepton/Lepton.h +include/plumed/lepton/MSVC_erfc.h +include/plumed/lepton/Operation.h +include/plumed/lepton/ParsedExpression.h +include/plumed/lepton/Parser.h +include/plumed/lepton/windowsIncludes.h +include/plumed/mapping/Mapping.h +include/plumed/mapping/PathBase.h +include/plumed/mapping/PathReparameterization.h +include/plumed/mapping/TrigonometricPathVessel.h +include/plumed/molfile/Gromacs.h +include/plumed/molfile/endianswap.h +include/plumed/molfile/fastio.h +include/plumed/molfile/largefiles.h +include/plumed/molfile/libmolfile_plugin.h +include/plumed/molfile/molfile_plugin.h +include/plumed/molfile/periodic_table.h +include/plumed/molfile/readpdb.h +include/plumed/molfile/vmdplugin.h +include/plumed/multicolvar/ActionVolume.h +include/plumed/multicolvar/AtomValuePack.h +include/plumed/multicolvar/BridgedMultiColvarFunction.h +include/plumed/multicolvar/CatomPack.h +include/plumed/multicolvar/MultiColvarBase.h +include/plumed/multicolvar/MultiColvarFilter.h +include/plumed/multicolvar/VolumeGradientBase.h +include/plumed/reference/ArgumentOnlyDistance.h +include/plumed/reference/DRMSD.h 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+include/plumed/tools/ForwardDecl.h +include/plumed/tools/Grid.h +include/plumed/tools/HistogramBead.h +include/plumed/tools/IFile.h +include/plumed/tools/KernelFunctions.h +include/plumed/tools/Keywords.h +include/plumed/tools/LatticeReduction.h +include/plumed/tools/LinkCells.h +include/plumed/tools/Log.h +include/plumed/tools/LoopUnroller.h +include/plumed/tools/Matrix.h +include/plumed/tools/MatrixSquareBracketsAccess.h +include/plumed/tools/Minimise1DBrent.h +include/plumed/tools/MinimiseBase.h +include/plumed/tools/MolDataClass.h +include/plumed/tools/MultiValue.h +include/plumed/tools/NeighborList.h +include/plumed/tools/OFile.h +include/plumed/tools/OpenMP.h +include/plumed/tools/PDB.h +include/plumed/tools/Pbc.h +include/plumed/tools/PlumedHandle.h +include/plumed/tools/RMSD.h +include/plumed/tools/Random.h +include/plumed/tools/RootFindingBase.h +include/plumed/tools/Stopwatch.h +include/plumed/tools/Subprocess.h +include/plumed/tools/SwitchingFunction.h 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+lib/plumed/vim/help/NLINKS.txt +lib/plumed/vim/help/NOE.txt +lib/plumed/vim/help/OUTPUT_ANALYSIS_DATA_TO_COLVAR.txt +lib/plumed/vim/help/OUTPUT_ANALYSIS_DATA_TO_PDB.txt +lib/plumed/vim/help/PARABETARMSD.txt +lib/plumed/vim/help/PATH.txt +lib/plumed/vim/help/PATHMSD.txt +lib/plumed/vim/help/PBMETAD.txt +lib/plumed/vim/help/PCARMSD.txt +lib/plumed/vim/help/PCAVARS.txt +lib/plumed/vim/help/PCS.txt +lib/plumed/vim/help/PIECEWISE.txt +lib/plumed/vim/help/PLUMED.txt +lib/plumed/vim/help/POSITION.txt +lib/plumed/vim/help/PRE.txt +lib/plumed/vim/help/PRINT.txt +lib/plumed/vim/help/PRINT_DISSIMILARITY_MATRIX.txt +lib/plumed/vim/help/PROJECTION_ON_AXIS.txt +lib/plumed/vim/help/PROPERTYMAP.txt +lib/plumed/vim/help/PUCKERING.txt +lib/plumed/vim/help/RANDOM_EXCHANGES.txt +lib/plumed/vim/help/RDC.txt +lib/plumed/vim/help/READ.txt +lib/plumed/vim/help/READ_DISSIMILARITY_MATRIX.txt +lib/plumed/vim/help/RESCALE.txt +lib/plumed/vim/help/RESELECT_LANDMARKS.txt +lib/plumed/vim/help/RESET_CELL.txt +lib/plumed/vim/help/RESTART.txt +lib/plumed/vim/help/RESTRAINT.txt +lib/plumed/vim/help/REWEIGHT_BIAS.txt +lib/plumed/vim/help/REWEIGHT_METAD.txt +lib/plumed/vim/help/REWEIGHT_TEMP_PRESS.txt +lib/plumed/vim/help/REWEIGHT_WHAM.txt +lib/plumed/vim/help/RMSD.txt +lib/plumed/vim/help/SAXS.txt +lib/plumed/vim/help/SELECT.txt +lib/plumed/vim/help/SELECTOR.txt +lib/plumed/vim/help/SORT.txt +lib/plumed/vim/help/STATS.txt +lib/plumed/vim/help/TARGET.txt +lib/plumed/vim/help/TEMPLATE.txt +lib/plumed/vim/help/TETRAHEDRALPORE.txt +lib/plumed/vim/help/TIME.txt +lib/plumed/vim/help/TORSION.txt +lib/plumed/vim/help/TORSIONS.txt +lib/plumed/vim/help/UNITS.txt +lib/plumed/vim/help/UPDATE_IF.txt +lib/plumed/vim/help/UPPER_WALLS.txt +lib/plumed/vim/help/VOLUME.txt +lib/plumed/vim/help/WHAM_HISTOGRAM.txt +lib/plumed/vim/help/WHAM_WEIGHTS.txt +lib/plumed/vim/help/WHOLEMOLECULES.txt +lib/plumed/vim/help/WRAPAROUND.txt +lib/plumed/vim/help/XANGLES.txt +lib/plumed/vim/help/XDISTANCES.txt +lib/plumed/vim/help/XYDISTANCES.txt +lib/plumed/vim/help/XYTORSIONS.txt +lib/plumed/vim/help/XZDISTANCES.txt +lib/plumed/vim/help/XZTORSIONS.txt +lib/plumed/vim/help/YANGLES.txt +lib/plumed/vim/help/YDISTANCES.txt +lib/plumed/vim/help/YXTORSIONS.txt +lib/plumed/vim/help/YZDISTANCES.txt +lib/plumed/vim/help/YZTORSIONS.txt +lib/plumed/vim/help/ZANGLES.txt +lib/plumed/vim/help/ZDISTANCES.txt +lib/plumed/vim/help/ZXTORSIONS.txt +lib/plumed/vim/help/ZYTORSIONS.txt +lib/plumed/vim/scripts.vim +lib/plumed/vim/syntax/plumed.vim +lib/plumed/vim/syntax/plumedf.vim +@pkgdir lib/plumed/obj Index: pkgsrc/math/plumed/distinfo diff -u /dev/null pkgsrc/math/plumed/distinfo:1.1 --- /dev/null Fri Jul 8 19:47:59 2022 +++ pkgsrc/math/plumed/distinfo Fri Jul 8 19:47:59 2022 @@ -0,0 +1,8 @@ +$NetBSD: distinfo,v 1.1 2022/07/08 19:47:59 thor Exp $ + +BLAKE2s (plumed-2.8.0.tgz) = 77d381aab5c5e227b870cc12dfb57650c1598a044d8e0343d4341152e0826da5 +SHA512 (plumed-2.8.0.tgz) = fd426893b3b6d9ccd3103f5d799a8eff1a60c1a7756d4c1788046a9496f7aaadbfea2390c1617f5645ed63255a896d2ef78c154e3e2c5092d678ef6082be0641 +Size (plumed-2.8.0.tgz) = 107630231 bytes +SHA1 (patch-Makefile.conf.in) = db317ff45591a2aaefc95a1b93c74c8825115bef +SHA1 (patch-configure) = 34ccd63ee2151b6a7634b477ebb38a6bfcdb88f0 +SHA1 (patch-configure.ac) = 0ec5c5a7db2057c78a99ddd329a8cbc91d05e7e3 Index: pkgsrc/math/plumed/options.mk diff -u /dev/null pkgsrc/math/plumed/options.mk:1.1 --- /dev/null Fri Jul 8 19:47:59 2022 +++ pkgsrc/math/plumed/options.mk Fri Jul 8 19:47:59 2022 @@ -0,0 +1,17 @@ +# $NetBSD: options.mk,v 1.1 2022/07/08 19:47:59 thor Exp $ + +PKG_OPTIONS_VAR= PKG_OPTIONS.plumed +PKG_SUPPORTED_OPTIONS= mpi +PKG_SUGGESTED_OPTIONS= + +.include "../../mk/bsd.prefs.mk" +.include "../../mk/bsd.options.mk" + +.if !empty(PKG_OPTIONS:Mmpi) +# TODO: Have mpi.bl3 provide proper compiler names and use here. +# Needed for Intel support (mpiicpc). +CONFIGURE_ARGS+= --enable-mpi CXX=mpicxx +.include "../../mk/mpi.buildlink3.mk" +.else +CONFIGURE_ARGS+= --disable-mpi +.endif Index: pkgsrc/math/plumed/patches/patch-Makefile.conf.in diff -u /dev/null pkgsrc/math/plumed/patches/patch-Makefile.conf.in:1.1 --- /dev/null Fri Jul 8 19:47:59 2022 +++ pkgsrc/math/plumed/patches/patch-Makefile.conf.in Fri Jul 8 19:47:59 2022 @@ -0,0 +1,17 @@ +$NetBSD: patch-Makefile.conf.in,v 1.1 2022/07/08 19:47:59 thor Exp $ + +Enable rpath flags also for linking the main binary. + +--- Makefile.conf.in.orig 2022-07-08 18:34:07.530823035 +0000 ++++ Makefile.conf.in +@@ -11,8 +11,8 @@ DYNAMIC_LIBS=@LIBS@ @LDFLAGS@ @OPENMP_CX + LIBS=@STATIC_LIBS@ + SOEXT=@SOEXT@ + # LD is used only to link the plumed executable, so should be equivalent to the C++ compiler +-LD=@CXX@ @CXXFLAGS@ +-LDSHARED=@LDSHARED@ ++LD=@CXX@ @CXXFLAGS@ @RPATH@ ++LDSHARED=@LDSHARED@ @RPATH@ + GCCDEP=@CXX@ + disable_dependency_tracking=@disable_dependency_tracking@ + prefix=@prefix@ Index: pkgsrc/math/plumed/patches/patch-configure diff -u /dev/null pkgsrc/math/plumed/patches/patch-configure:1.1 --- /dev/null Fri Jul 8 19:47:59 2022 +++ pkgsrc/math/plumed/patches/patch-configure Fri Jul 8 19:47:59 2022 @@ -0,0 +1,1016 @@ +$NetBSD: patch-configure,v 1.1 2022/07/08 19:47:59 thor Exp $ + +Short out the rpath test that fails with pkgsrc wrappers. +Enable rpath flags also for linking the main binary. +Fix portability to non-bash with test = instead of test ==. + +--- configure.orig 2022-02-22 22:28:39.000000000 +0000 ++++ configure +@@ -635,6 +635,7 @@ dot + doxygen + make_doc + readelf ++RPATH + use_debug_glibcxx + OPENMP_CXXFLAGS + EGREP +@@ -754,6 +755,7 @@ target_alias + SOEXT + STATIC_LIBS + LDSHARED ++RPATH + PYTHON_BIN + BASH_COMPLETION_DIR + MPIEXEC +@@ -2433,10 +2435,10 @@ rm -f src/*.on src/*.off + if test "${enable_modules+set}" = set; then : + enableval=$enable_modules; + rm -f src/*.on src/*.off +- if test "${enableval}" == yes ; then ++ if test "${enableval}" = yes ; then + enableval=reset + fi +- if test "${enableval}" == no ; then ++ if test "${enableval}" = no ; then + enableval=none + fi + for modules_mod in `echo "${enableval}" | sed 's/:/ /g' | sed 's/+/ +/g' | sed 's/-/ -/g'` +@@ -3323,7 +3325,7 @@ case `(uname)` in + esac + + # if searching for MPI, try first mpi-like compilers +-if test $mpi == true ; then ++if test $mpi = true ; then + compilers="mpic++ mpicxx mpiicpc openmpic++ openmpicxx $compilers" + fi + +@@ -4433,7 +4435,7 @@ $as_echo "$as_me: Initial LDSHARED: $ + $as_echo "$as_me: Initial SOEXT: $SOEXT" >&6;} + + # check C++ flags +-if test $shared == true ++if test $shared = true + then + + +@@ -4543,7 +4545,7 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu + + fi + +-if test $basic_warnings == true ++if test $basic_warnings = true + then + + save_CXXFLAGS="$CXXFLAGS" +@@ -4689,7 +4691,7 @@ rm -f core conftest.err conftest.$ac_obj + + fi + +-if test $debug == true ++if test $debug = true + then + + save_CXXFLAGS="$CXXFLAGS" +@@ -4739,7 +4741,7 @@ rm -f core conftest.err conftest.$ac_obj + + fi + +-if test $gcov == true ++if test $gcov = true + then + CXX="$CXX --coverage" + LDSHARED="$LDSHARED --coverage" +@@ -4773,7 +4775,7 @@ rm -f core conftest.err conftest.$ac_obj + STATIC_LIBS="$STATIC_LIBS --coverage" + fi + +-if test $fussy == true ++if test $fussy = true + then + + save_CXXFLAGS="$CXXFLAGS" +@@ -5795,7 +5797,7 @@ lapack_found= + + # external lapack can only work with external blas + # thus, if external blas are disabled also external lapack should be disabled +-if test "$external_blas" == false && test "$external_lapack" == true ; then ++if test "$external_blas" = false && test "$external_lapack" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: Internal blas can only be used with internal lapack" >&5 + $as_echo "$as_me: Internal blas can only be used with internal lapack" >&6;} + { $as_echo "$as_me:${as_lineno-$LINENO}: Will not search for external lapack" >&5 +@@ -5804,7 +5806,7 @@ $as_echo "$as_me: Will not search for ex + fi + + # first look for blas +-if test "$external_blas" == true ; then ++if test "$external_blas" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether dgemv can be linked with no library" >&5 + $as_echo_n "checking whether dgemv can be linked with no library... " >&6; } + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +@@ -5866,7 +5868,7 @@ else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "no" >&6; } + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dgemv" >&5 + $as_echo_n "checking for library containing dgemv... " >&6; } + if ${ac_cv_search_dgemv+:} false; then : +@@ -5924,7 +5926,7 @@ if test "$ac_res" != no; then : + else + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dgemv_" >&5 + $as_echo_n "checking for library containing dgemv_... " >&6; } + if ${ac_cv_search_dgemv_+:} false; then : +@@ -6101,7 +6103,7 @@ if test "$ac_res" != no; then : + else + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dgemv_" >&5 + $as_echo_n "checking for library containing dgemv_... " >&6; } + if ${ac_cv_search_dgemv_+:} false; then : +@@ -6244,14 +6246,14 @@ if test -n "$blas_found" ; then + $as_echo "#define __PLUMED_HAS_EXTERNAL_BLAS 1" >>confdefs.h + + +-if test "$external_lapack" == true ; then ++if test "$external_lapack" = true ; then + # Then we look for lapack using same underscoring + case "$blas_found" in + (underscore) search_for=dsyevr_ ;; + (nounderscore) search_for=dsyevr ;; + esac + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + as_ac_Search=`$as_echo "ac_cv_search_$search_for" | $as_tr_sh` + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing $search_for" >&5 + $as_echo_n "checking for library containing $search_for... " >&6; } +@@ -6387,7 +6389,7 @@ fi + # in case external blas have been found, take note of their underscoring + # notice that this applies also when external blas are used with internal lapack + # in the latter case, also (internal) lapack names will be underscored consistently +-if test "$blas_found" == nounderscore ++if test "$blas_found" = nounderscore + then + $as_echo "#define F77_NO_UNDERSCORE 1" >>confdefs.h + +@@ -6443,7 +6445,7 @@ rm -f core *.core core.conftest.* gmon.o + fi + + +-if test "$sdot_returns_float" == no ; ++if test "$sdot_returns_float" = no ; + then + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether sdot returns double" >&5 +@@ -6529,7 +6531,7 @@ $as_echo "$as_me: Now we will check for + # GB + ############################################################# + +-if test $molfile_plugins == true ; then ++if test $molfile_plugins = true ; then + + # Check for molfile_plugins and use internal fallback if not found. TG + +@@ -6537,7 +6539,7 @@ if test $molfile_plugins == true ; then + $as_echo "#define __PLUMED_HAS_MOLFILE_PLUGINS 1" >>confdefs.h + + +- if test "$external_molfile_plugins" == true ; then ++ if test "$external_molfile_plugins" = true ; then + + found=ko + __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS=no +@@ -6545,7 +6547,7 @@ $as_echo "#define __PLUMED_HAS_MOLFILE_P + if test "x$ac_cv_header_libmolfile_plugin_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing molfile_dcdplugin_init" >&5 + $as_echo_n "checking for library containing molfile_dcdplugin_init... " >&6; } + if ${ac_cv_search_molfile_dcdplugin_init+:} false; then : +@@ -6665,7 +6667,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS 1" >>confdefs.h + + __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS=yes +@@ -6730,7 +6732,7 @@ fi + + mpi_found=ko + # optional libraries follow +-if test $mpi == true ; then ++if test $mpi = true ; then + + found=ko + __PLUMED_HAS_MPI=no +@@ -6738,7 +6740,7 @@ if test $mpi == true ; then + if test "x$ac_cv_header_mpi_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing MPI_Init" >&5 + $as_echo_n "checking for library containing MPI_Init... " >&6; } + if ${ac_cv_search_MPI_Init+:} false; then : +@@ -6858,7 +6860,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_MPI 1" >>confdefs.h + + __PLUMED_HAS_MPI=yes +@@ -6943,7 +6945,7 @@ $as_echo "$ac_cv_prog_cxx_openmp" >&6; } + + + +-if test $asmjit == true ; then ++if test $asmjit = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether architecture is X86/X64" >&5 + $as_echo_n "checking whether architecture is X86/X64... " >&6; } + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +@@ -6977,18 +6979,18 @@ fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + fi + +-if test $asmjit == true && test $x86_x64 == false ; then ++if test $asmjit = true && test $x86_x64 = false ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: asmjit does not support this architecture, it will be disabled" >&5 + $as_echo "$as_me: WARNING: asmjit does not support this architecture, it will be disabled" >&2;} + asmjit=false + fi + +-if test $asmjit == true ; then ++if test $asmjit = true ; then + found=ko + # asmjit calls clock_gettime and thus should be linked to rt on Linux + if test `(uname)` = Linux ; then + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing clock_gettime" >&5 + $as_echo_n "checking for library containing clock_gettime... " >&6; } + if ${ac_cv_search_clock_gettime+:} false; then : +@@ -7119,7 +7121,7 @@ $as_echo "$as_me: WARNING: cannot link c + fi + + +-if test $readdir_r == true ; then ++if test $readdir_r = true ; then + + found=ko + __PLUMED_HAS_READDIR_R=no +@@ -7127,7 +7129,7 @@ if test $readdir_r == true ; then + if test "x$ac_cv_header_dirent_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing readdir_r" >&5 + $as_echo_n "checking for library containing readdir_r... " >&6; } + if ${ac_cv_search_readdir_r+:} false; then : +@@ -7247,7 +7249,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_READDIR_R 1" >>confdefs.h + + __PLUMED_HAS_READDIR_R=yes +@@ -7257,7 +7259,7 @@ $as_echo "$as_me: WARNING: cannot enable + fi + + fi +-if test $cregex == true ; then ++if test $cregex = true ; then + + found=ko + __PLUMED_HAS_CREGEX=no +@@ -7265,7 +7267,7 @@ if test $cregex == true ; then + if test "x$ac_cv_header_regex_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing regcomp" >&5 + $as_echo_n "checking for library containing regcomp... " >&6; } + if ${ac_cv_search_regcomp+:} false; then : +@@ -7385,7 +7387,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_CREGEX 1" >>confdefs.h + + __PLUMED_HAS_CREGEX=yes +@@ -7395,7 +7397,7 @@ $as_echo "$as_me: WARNING: cannot enable + fi + + fi +-if test $dlopen == true ; then ++if test $dlopen = true ; then + + found=ko + __PLUMED_HAS_DLOPEN=no +@@ -7403,7 +7405,7 @@ if test $dlopen == true ; then + if test "x$ac_cv_header_dlfcn_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dlopen" >&5 + $as_echo_n "checking for library containing dlopen... " >&6; } + if ${ac_cv_search_dlopen+:} false; then : +@@ -7523,7 +7525,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_DLOPEN 1" >>confdefs.h + + __PLUMED_HAS_DLOPEN=yes +@@ -7534,11 +7536,11 @@ $as_echo "$as_me: WARNING: cannot enable + + fi + +-if test $rtld_default == true ; then ++if test $rtld_default = true ; then + + found=ko + __PLUMED_HAS_RTLD_DEFAULT=no +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + testlibs="" + else + testlibs="" +@@ -7577,12 +7579,12 @@ $as_echo "no" >&6; } + fi + rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +- if test $found == ok ; then ++ if test $found = ok ; then + break + fi + LIBS="$save_LIBS" + done +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_RTLD_DEFAULT 1" >>confdefs.h + + __PLUMED_HAS_RTLD_DEFAULT=yes +@@ -7594,7 +7596,7 @@ $as_echo "$as_me: WARNING: cannot enable + + fi + +-if test $chdir == true ; then ++if test $chdir = true ; then + + found=ko + __PLUMED_HAS_CHDIR=no +@@ -7602,7 +7604,7 @@ if test $chdir == true ; then + if test "x$ac_cv_header_unistd_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing chdir" >&5 + $as_echo_n "checking for library containing chdir... " >&6; } + if ${ac_cv_search_chdir+:} false; then : +@@ -7722,7 +7724,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_CHDIR 1" >>confdefs.h + + __PLUMED_HAS_CHDIR=yes +@@ -7733,11 +7735,11 @@ $as_echo "$as_me: WARNING: cannot enable + + fi + +-if test $subprocess == true ; then ++if test $subprocess = true ; then + + found=ko + __PLUMED_HAS_SUBPROCESS=no +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + testlibs="" + else + testlibs="" +@@ -7799,12 +7801,12 @@ $as_echo "no" >&6; } + fi + rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +- if test $found == ok ; then ++ if test $found = ok ; then + break + fi + LIBS="$save_LIBS" + done +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_SUBPROCESS 1" >>confdefs.h + + __PLUMED_HAS_SUBPROCESS=yes +@@ -7816,7 +7818,7 @@ $as_echo "$as_me: WARNING: cannot enable + + fi + +-if test $getcwd == true ; then ++if test $getcwd = true ; then + + found=ko + __PLUMED_HAS_GETCWD=no +@@ -7824,7 +7826,7 @@ if test $getcwd == true ; then + if test "x$ac_cv_header_unistd_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing getcwd" >&5 + $as_echo_n "checking for library containing getcwd... " >&6; } + if ${ac_cv_search_getcwd+:} false; then : +@@ -7944,7 +7946,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_GETCWD 1" >>confdefs.h + + __PLUMED_HAS_GETCWD=yes +@@ -7955,7 +7957,7 @@ $as_echo "$as_me: WARNING: cannot enable + + fi + +-if test $popen == true ; then ++if test $popen = true ; then + + found=ko + __PLUMED_HAS_POPEN=no +@@ -7963,7 +7965,7 @@ if test $popen == true ; then + if test "x$ac_cv_header_cstdio" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing popen" >&5 + $as_echo_n "checking for library containing popen... " >&6; } + if ${ac_cv_search_popen+:} false; then : +@@ -8083,7 +8085,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_POPEN 1" >>confdefs.h + + __PLUMED_HAS_POPEN=yes +@@ -8094,7 +8096,7 @@ $as_echo "$as_me: WARNING: cannot enable + + fi + +-if test $execinfo == true ; then ++if test $execinfo = true ; then + + found=ko + __PLUMED_HAS_EXECINFO=no +@@ -8102,7 +8104,7 @@ if test $execinfo == true ; then + if test "x$ac_cv_header_execinfo_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing backtrace" >&5 + $as_echo_n "checking for library containing backtrace... " >&6; } + if ${ac_cv_search_backtrace+:} false; then : +@@ -8222,7 +8224,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_EXECINFO 1" >>confdefs.h + + __PLUMED_HAS_EXECINFO=yes +@@ -8232,7 +8234,7 @@ $as_echo "$as_me: WARNING: cannot enable + fi + + fi +-if test $zlib == true ; then ++if test $zlib = true ; then + + found=ko + __PLUMED_HAS_ZLIB=no +@@ -8240,7 +8242,7 @@ if test $zlib == true ; then + if test "x$ac_cv_header_zlib_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing gzopen" >&5 + $as_echo_n "checking for library containing gzopen... " >&6; } + if ${ac_cv_search_gzopen+:} false; then : +@@ -8360,7 +8362,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_ZLIB 1" >>confdefs.h + + __PLUMED_HAS_ZLIB=yes +@@ -8371,10 +8373,10 @@ $as_echo "$as_me: WARNING: cannot enable + + fi + +-if test $gsl == true ; then ++if test $gsl = true ; then + found=ko + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing cblas_dgemv" >&5 + $as_echo_n "checking for library containing cblas_dgemv... " >&6; } + if ${ac_cv_search_cblas_dgemv+:} false; then : +@@ -8433,7 +8435,7 @@ if test "$ac_res" != no; then : + if test "x$ac_cv_header_gsl_gsl_vector_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing gsl_vector_alloc" >&5 + $as_echo_n "checking for library containing gsl_vector_alloc... " >&6; } + if ${ac_cv_search_gsl_vector_alloc+:} false; then : +@@ -8615,7 +8617,7 @@ if test "$ac_res" != no; then : + if test "x$ac_cv_header_gsl_gsl_vector_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing gsl_vector_alloc" >&5 + $as_echo_n "checking for library containing gsl_vector_alloc... " >&6; } + if ${ac_cv_search_gsl_vector_alloc+:} false; then : +@@ -8740,7 +8742,7 @@ fi + + fi + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_GSL 1" >>confdefs.h + + else +@@ -8749,11 +8751,11 @@ $as_echo "$as_me: WARNING: cannot enable + fi + fi + +-if test $boost_graph == true ; then ++if test $boost_graph = true ; then + + found=ko + __PLUMED_HAS_BOOST_GRAPH=no +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + testlibs="" + else + testlibs="" +@@ -8794,12 +8796,12 @@ $as_echo "no" >&6; } + fi + rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +- if test $found == ok ; then ++ if test $found = ok ; then + break + fi + LIBS="$save_LIBS" + done +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_BOOST_GRAPH 1" >>confdefs.h + + __PLUMED_HAS_BOOST_GRAPH=yes +@@ -8811,11 +8813,11 @@ $as_echo "$as_me: WARNING: cannot enable + + fi + +-if test $boost_serialization == true ; then ++if test $boost_serialization = true ; then + + found=ko + __PLUMED_HAS_BOOST_SERIALIZATION=no +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + testlibs="boost_serialization boost_serialization-mt" + else + testlibs="" +@@ -8854,12 +8856,12 @@ $as_echo "no" >&6; } + fi + rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +- if test $found == ok ; then ++ if test $found = ok ; then + break + fi + LIBS="$save_LIBS" + done +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_BOOST_SERIALIZATION 1" >>confdefs.h + + __PLUMED_HAS_BOOST_SERIALIZATION=yes +@@ -8872,7 +8874,7 @@ $as_echo "$as_me: WARNING: cannot enable + # notice: macports install libraries with -mt suffix + fi + +-if test $fftw == true ; then ++if test $fftw = true ; then + + found=ko + __PLUMED_HAS_FFTW=no +@@ -8880,7 +8882,7 @@ if test $fftw == true ; then + if test "x$ac_cv_header_fftw3_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing fftw_execute" >&5 + $as_echo_n "checking for library containing fftw_execute... " >&6; } + if ${ac_cv_search_fftw_execute+:} false; then : +@@ -9000,7 +9002,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_FFTW 1" >>confdefs.h + + __PLUMED_HAS_FFTW=yes +@@ -9011,7 +9013,7 @@ $as_echo "$as_me: WARNING: cannot enable + + fi + +-if test $python == true ; then ++if test $python = true ; then + # if PYTHON_BIN is defined, it is expected to be the full path to python + # Otherwise, search from a list of names: + if test -z "$PYTHON_BIN" ; then +@@ -9094,7 +9096,7 @@ $as_echo "$as_me: WARNING: cannot enable + fi + fi + +-if test "$af_ocl" == true ; then ++if test "$af_ocl" = true ; then + + found=ko + __PLUMED_HAS_ARRAYFIRE=no +@@ -9102,7 +9104,7 @@ if test "$af_ocl" == true ; then + if test "x$ac_cv_header_arrayfire_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing af_is_double" >&5 + $as_echo_n "checking for library containing af_is_double... " >&6; } + if ${ac_cv_search_af_is_double+:} false; then : +@@ -9222,7 +9224,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_ARRAYFIRE 1" >>confdefs.h + + __PLUMED_HAS_ARRAYFIRE=yes +@@ -9232,7 +9234,7 @@ $as_echo "$as_me: WARNING: cannot enable + fi + + fi +-if test "$af_cuda" == true ; then ++if test "$af_cuda" = true ; then + + found=ko + __PLUMED_HAS_ARRAYFIRE=no +@@ -9240,7 +9242,7 @@ if test "$af_cuda" == true ; then + if test "x$ac_cv_header_arrayfire_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing af_is_double" >&5 + $as_echo_n "checking for library containing af_is_double... " >&6; } + if ${ac_cv_search_af_is_double+:} false; then : +@@ -9360,7 +9362,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_ARRAYFIRE 1" >>confdefs.h + + __PLUMED_HAS_ARRAYFIRE=yes +@@ -9370,7 +9372,7 @@ $as_echo "$as_me: WARNING: cannot enable + fi + + fi +-if test "$af_cpu" == true ; then ++if test "$af_cpu" = true ; then + + found=ko + __PLUMED_HAS_ARRAYFIRE=no +@@ -9378,7 +9380,7 @@ if test "$af_cpu" == true ; then + if test "x$ac_cv_header_arrayfire_h" = xyes; then : + + +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing af_is_double" >&5 + $as_echo_n "checking for library containing af_is_double... " >&6; } + if ${ac_cv_search_af_is_double+:} false; then : +@@ -9498,7 +9500,7 @@ fi + fi + + +- if test $found == ok ; then ++ if test $found = ok ; then + $as_echo "#define __PLUMED_HAS_ARRAYFIRE 1" >>confdefs.h + + __PLUMED_HAS_ARRAYFIRE=yes +@@ -9510,7 +9512,7 @@ $as_echo "$as_me: WARNING: cannot enable + fi + + # in non-debug mode, add -DNDEBUG +-if test "$debug" == false ; then ++if test "$debug" = false ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: Release mode, adding -DNDEBUG" >&5 + $as_echo "$as_me: Release mode, adding -DNDEBUG" >&6;} + $as_echo "#define NDEBUG 1" >>confdefs.h +@@ -9521,7 +9523,7 @@ fi + # in debug-glibcxx mode, add -D_GLIBCXX_DEBUG + # also take note that we are using this to relax `make nmcheck` + use_debug_glibcxx=no +-if test "$debug_glibcxx" == true ; then ++if test "$debug_glibcxx" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: Check boundaries, adding -D_GLIBCXX_DEBUG" >&5 + $as_echo "$as_me: Check boundaries, adding -D_GLIBCXX_DEBUG" >&6;} + $as_echo "#define _GLIBCXX_DEBUG 1" >>confdefs.h +@@ -9544,7 +9546,7 @@ $as_echo "#define _REENTRANT 1" >>confde + + + +-if test "$shared" == true ; then ++if test "$shared" = true ; then + case `(uname)` in + (Darwin) + { $as_echo "$as_me:${as_lineno-$LINENO}: *** Special settings for dynamic libraries on OSX ***" >&5 +@@ -9596,7 +9598,7 @@ fi + rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext + +- if test "$bsymbolic" == true ; then ++ if test "$bsymbolic" = true ; then + + save_LDFLAGS="$LDFLAGS" + LDFLAGS="$LDFLAGS -Wl,-Bsymbolic" +@@ -9695,19 +9697,22 @@ $as_echo "no" >&6; } + fi + + +- if test "$readelf" == found ; then +- test_LDSHARED="$LDSHARED -Wl,-R -Wl,/some/random/dir/" +- $test_LDSHARED $LDFLAGS conftest.o -o conftest.$SOEXT 1>/dev/null 2>/dev/null +- if readelf -d conftest.$SOEXT | grep RPATH | grep -q /some/random/dir ; then +- LDSHARED="$LDSHARED -Wl,-R -Wl,\"$libdir:$LIBRARY_PATH\"" +- else +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: -R option seems not working, disabling rpath" >&5 +-$as_echo "$as_me: WARNING: -R option seems not working, disabling rpath" >&2;} +- fi +- else +- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: readelf not available, no way to set rpath" >&5 +-$as_echo "$as_me: WARNING: readelf not available, no way to set rpath" >&2;} +- fi ++# Believe us that we provide a toolchain that does rpath, just not accepting ++# any random directories in pkgsrc! ++# Also need rpath in LDFLAGS for plumed binary! ++# if test "$readelf" = found ; then ++# test_LDSHARED="$LDSHARED -Wl,-R -Wl,/some/random/dir/" ++# $test_LDSHARED $LDFLAGS conftest.o -o conftest.$SOEXT 1>/dev/null 2>/dev/null ++# if readelf -d conftest.$SOEXT | grep RPATH | grep -q /some/random/dir ; then ++ RPATH="-Wl,-R -Wl,\"$libdir:$LIBRARY_PATH\"" ++# else ++# { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: -R option seems not working, disabling rpath" >&5 ++#$as_echo "$as_me: WARNING: -R option seems not working, disabling rpath" >&2;} ++# fi ++# else ++# { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: readelf not available, no way to set rpath" >&5 ++#$as_echo "$as_me: WARNING: readelf not available, no way to set rpath" >&2;} ++# fi + fi + rm -f conftest.* + fi +@@ -9715,7 +9720,7 @@ fi + + + make_doc=no +-if test "$doc" == true ++if test "$doc" = true + then + + make_doc=yes +@@ -9758,10 +9763,10 @@ $as_echo "no" >&6; } + fi + + +-if test "$doxygen" == found ++if test "$doxygen" = found + then + doxygen_version=`doxygen --version | awk 'BEGIN{FS="."}{if($1>1 || ($1==1 && $2>=8)) print "ok"}'` +- if test "$doxygen_version" == ok ++ if test "$doxygen_version" = ok + then + { $as_echo "$as_me:${as_lineno-$LINENO}: Doxygen version is fine" >&5 + $as_echo "$as_me: Doxygen version is fine" >&6;} +@@ -9828,7 +9833,7 @@ fi + + + make_pdfdoc="" +-if test "$pdfdoc" == true && test "$make_doc" == yes ++if test "$pdfdoc" = true && test "$make_doc" = yes + then + { $as_echo "$as_me:${as_lineno-$LINENO}: A PDF version of the manual will be generated" >&5 + $as_echo "$as_me: A PDF version of the manual will be generated" >&6;} +@@ -9880,7 +9885,7 @@ rm -f core *.core core.conftest.* gmon.o + fi + + +-if test $mpi_found == ok ; then ++if test $mpi_found = ok ; then + + program_can_run_mpi="" + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a program compiled with mpi can be run on this machine" >&5 +@@ -9919,7 +9924,7 @@ fi + + fi + +-if test $mpi_found == ok ; then ++if test $mpi_found = ok ; then + if test -n "$MPIEXEC" ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: Regtest suite will use $MPIEXEC command to run MPI tests" >&5 + $as_echo "$as_me: Regtest suite will use $MPIEXEC command to run MPI tests" >&6;} +@@ -9929,15 +9934,15 @@ $as_echo "$as_me: Regtest suite will use + fi + fi + +-if test "$SOEXT" == "dylib" ; then ++if test "$SOEXT" = "dylib" ; then + use_absolute_soname=yes + else + use_absolute_soname=no + fi + + +-if test "$absolute_soname" == true ; then +- if test "$SOEXT" == "dylib" ; then ++if test "$absolute_soname" = true ; then ++ if test "$SOEXT" = "dylib" ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: --enable-absolute-soname has no effect on OSX" >&5 + $as_echo "$as_me: WARNING: --enable-absolute-soname has no effect on OSX" >&2;} + else +@@ -9947,8 +9952,8 @@ $as_echo "$as_me: enabling absolute sona + fi + fi + +-if test "$absolute_install_name" == false ; then +- if test "$SOEXT" == "so" ; then ++if test "$absolute_install_name" = false ; then ++ if test "$SOEXT" = "so" ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: --disable-absolute-install-name has no effect on Linux" >&5 + $as_echo "$as_me: WARNING: --disable-absolute-install-name has no effect on Linux" >&2;} + else +@@ -9959,8 +9964,8 @@ $as_echo "$as_me: enabling relative inst + fi + + +-if test "$SOEXT" == "dylib" ; then +- if test "$loader_path" == true ; then ++if test "$SOEXT" = "dylib" ; then ++ if test "$loader_path" = true ; then + use_loader_path=yes + else + use_loader_path=no +@@ -9976,7 +9981,7 @@ $as_echo "$as_me: PLUMED seems to be con + $as_echo "$as_me: **************************" >&6;} + + LD_RO= +-if test "$ld_r" == true ; then ++if test "$ld_r" = true ; then + for test_LD_RO in "$($CXX --print-prog-name=ld) -r -o" "$CXX -Wl,-r -o" "ld -r -o" + do + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C++ objects can be grouped with $test_LD_RO" >&5 +@@ -10020,7 +10025,7 @@ fi + + + AR_CR= +-if test "$ar_cr" == true ; then ++if test "$ar_cr" = true ; then + for test_AR_CR in "$($CXX --print-prog-name=ar) cr" "ar cr" + do + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether static libraries can be created with $test_AR_CR" >&5 +@@ -10065,7 +10070,7 @@ fi + make_static_archive=no + + +-if test "${static_archive}" == true ; then ++if test "${static_archive}" = true ; then + if test -z "$LD_RO" || test -z "$AR_CR" ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: no way to create a static archive if ld -ro or ar cr do not work" >&5 + $as_echo "$as_me: WARNING: no way to create a static archive if ld -ro or ar cr do not work" >&2;} +@@ -10073,7 +10078,7 @@ $as_echo "$as_me: WARNING: no way to cre + fi + fi + +-if test "${static_archive}" == true ; then ++if test "${static_archive}" = true ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether static-object constructors can be linked from a static archive" >&5 + $as_echo_n "checking whether static-object constructors can be linked from a static archive... " >&6; } + +@@ -10116,7 +10121,7 @@ $as_echo "no" >&6; } + fi + fi + +-if test "${static_patch}" == true ; then ++if test "${static_patch}" = true ; then + + { $as_echo "$as_me:${as_lineno-$LINENO}: I will now check if C++ objects can be linked by C/Fortran compilers" >&5 + $as_echo "$as_me: I will now check if C++ objects can be linked by C/Fortran compilers" >&6;} +@@ -10157,7 +10162,7 @@ EOF + $CXX $CXXFLAGS -c conftest.cpp + # start search: + found= +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + testlibs="-lstdc++ -lc++ -lmpi_cxx" + else + testlibs="" +@@ -10198,7 +10203,7 @@ else + $as_echo "$as_me: Static patching is disabled, thus tests required for static patching will be skipped" >&6;} + fi + +-if test "$prefix" == NONE ++if test "$prefix" = NONE + then + prefix=/usr/local + fi +@@ -10252,7 +10257,7 @@ done + + + if test -z "$BASH_COMPLETION_DIR" && test -n "$pkgconfig_bin"; then +- if test "$prefix" == "$(pkg-config --variable=prefix bash-completion 2>/dev/null)" ++ if test "$prefix" = "$(pkg-config --variable=prefix bash-completion 2>/dev/null)" + then + { $as_echo "$as_me:${as_lineno-$LINENO}: bash-completion is installed on the same prefix where plumed will be installed" >&5 + $as_echo "$as_me: bash-completion is installed on the same prefix where plumed will be installed" >&6;} +@@ -10348,8 +10353,8 @@ $as_echo "$as_me: WARNING: **** _$progra + $as_echo "$as_me: WARNING: **** complete -F _$program_name -o default $program_name" >&2;} + fi + +-if test $mpi == true; then +- if test $mpi_found == ok; then ++if test $mpi = true; then ++ if test $mpi_found = ok; then + { $as_echo "$as_me:${as_lineno-$LINENO}: **** PLUMED will be compiled using MPI" >&5 + $as_echo "$as_me: **** PLUMED will be compiled using MPI" >&6;} + else +@@ -10361,13 +10366,13 @@ else + $as_echo "$as_me: **** PLUMED will be compiled without MPI" >&6;} + fi + +-if test $program_can_run == no ; then ++if test $program_can_run = no ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: plumed executable will not run on this machine" >&5 + $as_echo "$as_me: WARNING: plumed executable will not run on this machine" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: to patch an MD code use 'plumed-patch'" >&5 + $as_echo "$as_me: WARNING: to patch an MD code use 'plumed-patch'" >&2;} +-elif test $mpi_found == ok ; then +- if test $program_can_run_mpi == no ; then ++elif test $mpi_found = ok ; then ++ if test $program_can_run_mpi = no ; then + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: plumed executable will not run on this machine" >&5 + $as_echo "$as_me: WARNING: plumed executable will not run on this machine" >&2;} + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unless you invoke it as 'plumed --no-mpi'" >&5 Index: pkgsrc/math/plumed/patches/patch-configure.ac diff -u /dev/null pkgsrc/math/plumed/patches/patch-configure.ac:1.1 --- /dev/null Fri Jul 8 19:47:59 2022 +++ pkgsrc/math/plumed/patches/patch-configure.ac Fri Jul 8 19:47:59 2022 @@ -0,0 +1,588 @@ +$NetBSD: patch-configure.ac,v 1.1 2022/07/08 19:47:59 thor Exp $ + +Short out the rpath test that fails with pkgsrc wrappers. +Enable rpath flags also for linking the main binary. +Fix portability to non-bash with test = instead of test ==. + +Including the .ac patch here to motivate upstreaming at least +of the == stuff. + +--- configure.ac.orig 2022-02-22 22:28:39.000000000 +0000 ++++ configure.ac +@@ -89,7 +89,7 @@ AC_DEFUN([PLUMED_CHECK_LDFLAGS], [ + # same as AC_SEARCH_LIBS, but does not try any library unless $libsearch==true + # Should be used instead of AC_SEARCH_LIBS in order to make --disable-libsearch work correctly + AC_DEFUN([PLUMED_SEARCH_LIBS], [ +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + AC_SEARCH_LIBS([$1],[$2],[$3],[$4],[$5]) + else + AC_SEARCH_LIBS([$1],[],[$3],[$4],[]) +@@ -106,7 +106,7 @@ AC_DEFUN([PLUMED_CHECK_PACKAGE], [ + AC_CHECK_HEADER( [$1],[ + PLUMED_SEARCH_LIBS([$2],[$4],[found=ok]) + ]) +- if test $found == ok ; then ++ if test $found = ok ; then + AC_DEFINE([$3]) + $3=yes + else +@@ -122,7 +122,7 @@ AC_DEFUN([PLUMED_CHECK_PACKAGE], [ + AC_DEFUN([PLUMED_CHECK_CXX_PACKAGE], [ + found=ko + $3=no +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + testlibs="$4" + else + testlibs="" +@@ -141,12 +141,12 @@ AC_DEFUN([PLUMED_CHECK_CXX_PACKAGE], [ + [AC_MSG_RESULT([yes])], + [AC_MSG_RESULT([no])] + ) +- if test $found == ok ; then ++ if test $found = ok ; then + break + fi + LIBS="$save_LIBS" + done +- if test $found == ok ; then ++ if test $found = ok ; then + AC_DEFINE([$3]) + $3=yes + else +@@ -164,10 +164,10 @@ AC_ARG_ENABLE([modules], + AS_HELP_STRING([--enable-modules], [all/none/reset or : separated list such as +crystallization:-bias default: reset]), + [ + rm -f src/*.on src/*.off +- if test "${enableval}" == yes ; then ++ if test "${enableval}" = yes ; then + enableval=reset + fi +- if test "${enableval}" == no ; then ++ if test "${enableval}" = no ; then + enableval=none + fi + for modules_mod in `echo "${enableval}" | sed 's/:/ /g' | sed 's/+/ +/g' | sed 's/-/ -/g'` +@@ -313,7 +313,7 @@ case `(uname)` in + esac + + # if searching for MPI, try first mpi-like compilers +-if test $mpi == true ; then ++if test $mpi = true ; then + compilers="mpic++ mpicxx mpiicpc openmpic++ openmpicxx $compilers" + fi + +@@ -346,13 +346,13 @@ AC_MSG_NOTICE([Initial LDSHARED: $LDS + AC_MSG_NOTICE([Initial SOEXT: $SOEXT]) + + # check C++ flags +-if test $shared == true ++if test $shared = true + then + PLUMED_CHECK_CXXFLAG([-fPIC]) + PLUMED_CHECK_CFLAG([-fPIC]) + fi + +-if test $basic_warnings == true ++if test $basic_warnings = true + then + PLUMED_CHECK_CXXFLAG([-Wall]) + PLUMED_CHECK_CXXFLAG([-pedantic]) +@@ -363,12 +363,12 @@ then + PLUMED_CHECK_CXXFLAG([-std=c++$cxx_level]) + fi + +-if test $debug == true ++if test $debug = true + then + PLUMED_CHECK_CXXFLAG([-g]) + fi + +-if test $gcov == true ++if test $gcov = true + then + CXX="$CXX --coverage" + LDSHARED="$LDSHARED --coverage" +@@ -377,7 +377,7 @@ then + STATIC_LIBS="$STATIC_LIBS --coverage" + fi + +-if test $fussy == true ++if test $fussy = true + then + PLUMED_CHECK_CXXFLAG([-Wextra]) + PLUMED_CHECK_CXXFLAG([-Wfloat-equal]) +@@ -499,14 +499,14 @@ lapack_found= + + # external lapack can only work with external blas + # thus, if external blas are disabled also external lapack should be disabled +-if test "$external_blas" == false && test "$external_lapack" == true ; then ++if test "$external_blas" = false && test "$external_lapack" = true ; then + AC_MSG_NOTICE([Internal blas can only be used with internal lapack]) + AC_MSG_NOTICE([Will not search for external lapack]) + external_lapack=false + fi + + # first look for blas +-if test "$external_blas" == true ; then ++if test "$external_blas" = true ; then + AC_MSG_CHECKING([whether dgemv can be linked with no library]) + AC_LINK_IFELSE([AC_LANG_CALL([], [dgemv])],[ + AC_MSG_RESULT([yes]) +@@ -536,7 +536,7 @@ if test -n "$blas_found" ; then + + AC_DEFINE([__PLUMED_HAS_EXTERNAL_BLAS]) + +-if test "$external_lapack" == true ; then ++if test "$external_lapack" = true ; then + # Then we look for lapack using same underscoring + case "$blas_found" in + (underscore) search_for=dsyevr_ ;; +@@ -557,7 +557,7 @@ fi + # in case external blas have been found, take note of their underscoring + # notice that this applies also when external blas are used with internal lapack + # in the latter case, also (internal) lapack names will be underscored consistently +-if test "$blas_found" == nounderscore ++if test "$blas_found" = nounderscore + then + AC_DEFINE([F77_NO_UNDERSCORE]) + fi +@@ -596,7 +596,7 @@ AC_RUN_IFELSE([AC_LANG_SOURCE([PLUMED_TE + [ AC_MSG_RESULT([not checked (cross compiling)]) ] + ) + +-if test "$sdot_returns_float" == no ; ++if test "$sdot_returns_float" = no ; + then + + AC_MSG_CHECKING([whether sdot returns double]) +@@ -638,14 +638,14 @@ AC_MSG_NOTICE([Now we will check for opt + # GB + ############################################################# + +-if test $molfile_plugins == true ; then ++if test $molfile_plugins = true ; then + + # Check for molfile_plugins and use internal fallback if not found. TG + + # We always have molfile, now + AC_DEFINE([__PLUMED_HAS_MOLFILE_PLUGINS]) + +- if test "$external_molfile_plugins" == true ; then ++ if test "$external_molfile_plugins" = true ; then + PLUMED_CHECK_PACKAGE([libmolfile_plugin.h],[molfile_dcdplugin_init],[__PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS],molfile_plugin) + if test "$__PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS" != yes ; then + AC_MSG_WARN([using internal molfile_plugins, which only support dcd/xtc/trr/trj/crd files]) +@@ -662,7 +662,7 @@ AC_CHECK_LIB([dl],dlopen, [STATIC_LIBS=" + + mpi_found=ko + # optional libraries follow +-if test $mpi == true ; then ++if test $mpi = true ; then + PLUMED_CHECK_PACKAGE([mpi.h],[MPI_Init],[__PLUMED_HAS_MPI]) + if test "$__PLUMED_HAS_MPI" = yes; then + mpi_found=ok +@@ -675,7 +675,7 @@ fi + # when configuring with --disable-openmp + AC_OPENMP + +-if test $asmjit == true ; then ++if test $asmjit = true ; then + AC_MSG_CHECKING([whether architecture is X86/X64]) + AC_COMPILE_IFELSE([AC_LANG_PROGRAM([ + #if !(defined(_M_IX86 ) || defined(__X86__ ) || defined(__i386 ) || \ +@@ -692,12 +692,12 @@ this_is_not_x86_x64 + x86_x64=false]) + fi + +-if test $asmjit == true && test $x86_x64 == false ; then ++if test $asmjit = true && test $x86_x64 = false ; then + AC_MSG_WARN([asmjit does not support this architecture, it will be disabled]) + asmjit=false + fi + +-if test $asmjit == true ; then ++if test $asmjit = true ; then + found=ko + # asmjit calls clock_gettime and thus should be linked to rt on Linux + if test `(uname)` = Linux ; then +@@ -714,17 +714,17 @@ if test $asmjit == true ; then + fi + + +-if test $readdir_r == true ; then ++if test $readdir_r = true ; then + PLUMED_CHECK_PACKAGE([dirent.h],[readdir_r],[__PLUMED_HAS_READDIR_R]) + fi +-if test $cregex == true ; then ++if test $cregex = true ; then + PLUMED_CHECK_PACKAGE([regex.h],[regcomp],[__PLUMED_HAS_CREGEX]) + fi +-if test $dlopen == true ; then ++if test $dlopen = true ; then + PLUMED_CHECK_PACKAGE([dlfcn.h],[dlopen],[__PLUMED_HAS_DLOPEN]) + fi + +-if test $rtld_default == true ; then ++if test $rtld_default = true ; then + PLUMED_CHECK_CXX_PACKAGE([RTLD_DEFAULT],[ + #include + int +@@ -736,11 +736,11 @@ main () + ], [__PLUMED_HAS_RTLD_DEFAULT]) + fi + +-if test $chdir == true ; then ++if test $chdir = true ; then + PLUMED_CHECK_PACKAGE([unistd.h],[chdir],[__PLUMED_HAS_CHDIR]) + fi + +-if test $subprocess == true ; then ++if test $subprocess = true ; then + PLUMED_CHECK_CXX_PACKAGE([subprocess],[ + /* random program calling all the functions needed to manage a subprocess */ + #include +@@ -775,36 +775,36 @@ main () + ], [__PLUMED_HAS_SUBPROCESS]) + fi + +-if test $getcwd == true ; then ++if test $getcwd = true ; then + PLUMED_CHECK_PACKAGE([unistd.h],[getcwd],[__PLUMED_HAS_GETCWD]) + fi + +-if test $popen == true ; then ++if test $popen = true ; then + PLUMED_CHECK_PACKAGE([cstdio],[popen],[__PLUMED_HAS_POPEN]) + fi + +-if test $execinfo == true ; then ++if test $execinfo = true ; then + PLUMED_CHECK_PACKAGE([execinfo.h],[backtrace],[__PLUMED_HAS_EXECINFO]) + fi +-if test $zlib == true ; then ++if test $zlib = true ; then + PLUMED_CHECK_PACKAGE([zlib.h],[gzopen],[__PLUMED_HAS_ZLIB],[z]) + fi + +-if test $gsl == true ; then ++if test $gsl = true ; then + found=ko + PLUMED_SEARCH_LIBS([cblas_dgemv],[gslcblas], [ + AC_CHECK_HEADER( [gsl/gsl_vector.h], [ + PLUMED_SEARCH_LIBS([gsl_vector_alloc],[gsl],[found=ok]) + ]) + ]) +- if test $found == ok ; then ++ if test $found = ok ; then + AC_DEFINE([__PLUMED_HAS_GSL]) + else + AC_MSG_WARN([cannot enable __PLUMED_HAS_GSL]) + fi + fi + +-if test $boost_graph == true ; then ++if test $boost_graph = true ; then + PLUMED_CHECK_CXX_PACKAGE([boost graph],[ + #include + #include +@@ -818,7 +818,7 @@ main () + ], [__PLUMED_HAS_BOOST_GRAPH]) + fi + +-if test $boost_serialization == true ; then ++if test $boost_serialization = true ; then + PLUMED_CHECK_CXX_PACKAGE([boost serialization],[ + #include + #include +@@ -831,11 +831,11 @@ int main() { + # notice: macports install libraries with -mt suffix + fi + +-if test $fftw == true ; then ++if test $fftw = true ; then + PLUMED_CHECK_PACKAGE([fftw3.h],[fftw_execute],[__PLUMED_HAS_FFTW],[fftw3]) + fi + +-if test $python == true ; then ++if test $python = true ; then + # if PYTHON_BIN is defined, it is expected to be the full path to python + # Otherwise, search from a list of names: + if test -z "$PYTHON_BIN" ; then +@@ -870,18 +870,18 @@ if sys.version_info < (3,): + fi + fi + +-if test "$af_ocl" == true ; then ++if test "$af_ocl" = true ; then + PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE],[afopencl]) + fi +-if test "$af_cuda" == true ; then ++if test "$af_cuda" = true ; then + PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE],[afcuda]) + fi +-if test "$af_cpu" == true ; then ++if test "$af_cpu" = true ; then + PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE],[afcpu]) + fi + + # in non-debug mode, add -DNDEBUG +-if test "$debug" == false ; then ++if test "$debug" = false ; then + AC_MSG_NOTICE([Release mode, adding -DNDEBUG]) + AC_DEFINE([NDEBUG]) + fi +@@ -890,7 +890,7 @@ AC_SUBST(use_debug_glibcxx) + # in debug-glibcxx mode, add -D_GLIBCXX_DEBUG + # also take note that we are using this to relax `make nmcheck` + use_debug_glibcxx=no +-if test "$debug_glibcxx" == true ; then ++if test "$debug_glibcxx" = true ; then + AC_MSG_NOTICE([Check boundaries, adding -D_GLIBCXX_DEBUG]) + AC_DEFINE([_GLIBCXX_DEBUG]) + use_debug_glibcxx=yes +@@ -903,6 +903,7 @@ AC_DEFINE([_REENTRANT]) + #### Options for dynamic library to work properly #### + AC_SUBST(SOEXT) + AC_SUBST(LDSHARED) ++AC_SUBST(RPATH) + # these are libraries that should be linked also to MD engines + AC_SUBST(STATIC_LIBS) + # python executable +@@ -910,7 +911,7 @@ AC_SUBST(PYTHON_BIN) + + AC_SUBST(MPIEXEC) + +-if test "$shared" == true ; then ++if test "$shared" = true ; then + case `(uname)` in + (Darwin) + AC_MSG_NOTICE([*** Special settings for dynamic libraries on OSX ***]) +@@ -930,7 +931,7 @@ if test "$shared" == true ; then + SOEXT=so + LDSHARED="$LDSHARED -shared" + PLUMED_CHECK_LDFLAGS([-rdynamic]) +- if test "$bsymbolic" == true ; then ++ if test "$bsymbolic" = true ; then + PLUMED_CHECK_LDFLAGS([-Wl,-Bsymbolic]) + fi + ;; +@@ -961,17 +962,20 @@ then + rm -f conftest.$SOEXT + readelf="" + AC_CHECK_PROG([readelf],[readelf],[found]) +- if test "$readelf" == found ; then +- test_LDSHARED="$LDSHARED -Wl,-R -Wl,/some/random/dir/" +- $test_LDSHARED $LDFLAGS conftest.o -o conftest.$SOEXT 1>/dev/null 2>/dev/null +- if readelf -d conftest.$SOEXT | grep RPATH | grep -q /some/random/dir ; then +- LDSHARED="$LDSHARED -Wl,-R -Wl,\"$libdir:$LIBRARY_PATH\"" +- else +- AC_MSG_WARN([-R option seems not working, disabling rpath]) +- fi +- else +- AC_MSG_WARN([readelf not available, no way to set rpath]) +- fi ++# Believe us that we provide a toolchain that does rpath, just not accepting ++# any random directories in pkgsrc! ++# Also need rpath in LDFLAGS for plumed binary! ++# if test "$readelf" = found ; then ++# test_LDSHARED="$LDSHARED -Wl,-R -Wl,/some/random/dir/" ++# $test_LDSHARED $LDFLAGS conftest.o -o conftest.$SOEXT 1>/dev/null 2>/dev/null ++# if readelf -d conftest.$SOEXT | grep RPATH | grep -q /some/random/dir ; then ++ RPATH="-Wl,-R -Wl,\"$libdir:$LIBRARY_PATH\"" ++# else ++# AC_MSG_WARN([-R option seems not working, disabling rpath]) ++# fi ++# else ++# AC_MSG_WARN([readelf not available, no way to set rpath]) ++# fi + fi + rm -f conftest.* + fi +@@ -979,17 +983,17 @@ fi + + AC_SUBST(make_doc) + make_doc=no +-if test "$doc" == true ++if test "$doc" = true + then + + make_doc=yes + + ### Look for doxygen + AC_CHECK_PROG([doxygen],[doxygen],[found]) +-if test "$doxygen" == found ++if test "$doxygen" = found + then + doxygen_version=`doxygen --version | awk 'BEGIN{FS="."}{if($1>1 || ($1==1 && $2>=8)) print "ok"}'` +- if test "$doxygen_version" == ok ++ if test "$doxygen_version" = ok + then + AC_MSG_NOTICE([Doxygen version is fine]) + else +@@ -1015,7 +1019,7 @@ fi + + AC_SUBST(make_pdfdoc) + make_pdfdoc="" +-if test "$pdfdoc" == true && test "$make_doc" == yes ++if test "$pdfdoc" = true && test "$make_doc" = yes + then + AC_MSG_NOTICE([A PDF version of the manual will be generated]) + make_pdfdoc=yes +@@ -1049,7 +1053,7 @@ int main(int argc,char*argv[[]]){ + [ program_can_run=no ; AC_MSG_RESULT([no (cross compiling)]) ] + ) + +-if test $mpi_found == ok ; then ++if test $mpi_found = ok ; then + AC_SUBST(program_can_run_mpi) + program_can_run_mpi="" + AC_MSG_CHECKING([whether a program compiled with mpi can be run on this machine]) +@@ -1072,7 +1076,7 @@ int main(int argc,char*argv[[]]){ + ) + fi + +-if test $mpi_found == ok ; then ++if test $mpi_found = ok ; then + if test -n "$MPIEXEC" ; then + AC_MSG_NOTICE([Regtest suite will use $MPIEXEC command to run MPI tests]) + else +@@ -1080,15 +1084,15 @@ if test $mpi_found == ok ; then + fi + fi + +-if test "$SOEXT" == "dylib" ; then ++if test "$SOEXT" = "dylib" ; then + use_absolute_soname=yes + else + use_absolute_soname=no + fi + + AC_SUBST(use_absolute_soname) +-if test "$absolute_soname" == true ; then +- if test "$SOEXT" == "dylib" ; then ++if test "$absolute_soname" = true ; then ++ if test "$SOEXT" = "dylib" ; then + AC_MSG_WARN([--enable-absolute-soname has no effect on OSX]) + else + AC_MSG_NOTICE([enabling absolute soname. Full path will be hardcoded in plumed library soname]) +@@ -1096,8 +1100,8 @@ if test "$absolute_soname" == true ; the + fi + fi + +-if test "$absolute_install_name" == false ; then +- if test "$SOEXT" == "so" ; then ++if test "$absolute_install_name" = false ; then ++ if test "$SOEXT" = "so" ; then + AC_MSG_WARN([--disable-absolute-install-name has no effect on Linux]) + else + AC_MSG_NOTICE([enabling relative install_name. You will have to set DYLD_LIBRARY_PATH yor plumed libraries to be found at runtime]) +@@ -1106,8 +1110,8 @@ if test "$absolute_install_name" == fals + fi + + AC_SUBST(use_loader_path) +-if test "$SOEXT" == "dylib" ; then +- if test "$loader_path" == true ; then ++if test "$SOEXT" = "dylib" ; then ++ if test "$loader_path" = true ; then + use_loader_path=yes + else + use_loader_path=no +@@ -1121,7 +1125,7 @@ AC_MSG_NOTICE([PLUMED seems to be config + AC_MSG_NOTICE([**************************]) + AC_SUBST(LD_RO) + LD_RO= +-if test "$ld_r" == true ; then ++if test "$ld_r" = true ; then + for test_LD_RO in "$($CXX --print-prog-name=ld) -r -o" "$CXX -Wl,-r -o" "ld -r -o" + do + AC_MSG_CHECKING([whether C++ objects can be grouped with $test_LD_RO]) +@@ -1162,7 +1166,7 @@ fi + + AC_SUBST(AR_CR) + AR_CR= +-if test "$ar_cr" == true ; then ++if test "$ar_cr" = true ; then + for test_AR_CR in "$($CXX --print-prog-name=ar) cr" "ar cr" + do + AC_MSG_CHECKING([whether static libraries can be created with $test_AR_CR]) +@@ -1204,14 +1208,14 @@ fi + make_static_archive=no + AC_SUBST(make_static_archive) + +-if test "${static_archive}" == true ; then ++if test "${static_archive}" = true ; then + if test -z "$LD_RO" || test -z "$AR_CR" ; then + AC_MSG_WARN([no way to create a static archive if ld -ro or ar cr do not work]) + static_archive=false + fi + fi + +-if test "${static_archive}" == true ; then ++if test "${static_archive}" = true ; then + AC_MSG_CHECKING([whether static-object constructors can be linked from a static archive]) + + magic_token=c1bc476d093a3a5c67b4530e6c54c633593fe9aa +@@ -1251,7 +1255,7 @@ EOF + fi + fi + +-if test "${static_patch}" == true ; then ++if test "${static_patch}" = true ; then + + AC_MSG_NOTICE([I will now check if C++ objects can be linked by C/Fortran compilers]) + AC_MSG_NOTICE([This is relevant if you want to use plumed patch --static on a non-C++ code]) +@@ -1290,7 +1294,7 @@ EOF + $CXX $CXXFLAGS -c conftest.cpp + # start search: + found= +- if test "${libsearch}" == true ; then ++ if test "${libsearch}" = true ; then + testlibs="-lstdc++ -lc++ -lmpi_cxx" + else + testlibs="" +@@ -1324,7 +1328,7 @@ else + AC_MSG_NOTICE([Static patching is disabled, thus tests required for static patching will be skipped]) + fi + +-if test "$prefix" == NONE ++if test "$prefix" = NONE + then + prefix=/usr/local + fi +@@ -1334,7 +1338,7 @@ pkgconfig_bin="" + AC_PATH_PROGS(pkgconfig_bin,pkg-config) + + if test -z "$BASH_COMPLETION_DIR" && test -n "$pkgconfig_bin"; then +- if test "$prefix" == "$(pkg-config --variable=prefix bash-completion 2>/dev/null)" ++ if test "$prefix" = "$(pkg-config --variable=prefix bash-completion 2>/dev/null)" + then + AC_MSG_NOTICE([bash-completion is installed on the same prefix where plumed will be installed]) + if pkg-config --variable=completionsdir bash-completion 2>/dev/null >/dev/null ; then +@@ -1401,8 +1405,8 @@ if test -z "$BASH_COMPLETION_DIR" ; then + AC_MSG_WARN([**** complete -F _$program_name -o default $program_name]) + fi + +-if test $mpi == true; then +- if test $mpi_found == ok; then ++if test $mpi = true; then ++ if test $mpi_found = ok; then + AC_MSG_NOTICE([**** PLUMED will be compiled using MPI]) + else + AC_MSG_WARN([**** PLUMED will NOT be compiled using MPI because MPI have not been found!]) +@@ -1411,11 +1415,11 @@ else + AC_MSG_NOTICE([**** PLUMED will be compiled without MPI]) + fi + +-if test $program_can_run == no ; then ++if test $program_can_run = no ; then + AC_MSG_WARN([plumed executable will not run on this machine]) + AC_MSG_WARN([to patch an MD code use 'plumed-patch']) +-elif test $mpi_found == ok ; then +- if test $program_can_run_mpi == no ; then ++elif test $mpi_found = ok ; then ++ if test $program_can_run_mpi = no ; then + AC_MSG_WARN([plumed executable will not run on this machine]) + AC_MSG_WARN([unless you invoke it as 'plumed --no-mpi']) + AC_MSG_WARN([all command line tools are thus available as 'plumed --no-mpi name-of-the-tool']) --_----------=_165730967941680--