initial commit of version 1.2.11

9c99a93d · Claus Jonathan Fritzemeier · 59c7a4cb · 9c99a93d · 9c99a93d · 9c99a93d
Commit 9c99a93d authored Dec 17, 2014 by Claus Jonathan Fritzemeier
--- a/DESCRIPTION
+++ b/DESCRIPTION
+Package: glpkAPI
+Type: Package
+Title: R Interface to C API of GLPK
+Version: 1.2.11
+Date: 2014-11-16
+Authors@R: c(person("Gabriel", "Gelius-Dietrich", role = c("aut", "cre"), email = "geliudie@uni-duesseldorf.de"))
+Maintainer: Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
+Depends: R (>= 2.6.0)
+Imports: methods
+Description: R Interface to C API of GLPK, needs GLPK Version >= 4.42
+SystemRequirements: GLPK (>= 4.42)
+License: GPL-3
+LazyLoad: yes
+Collate: generics.R glpk_ptrClass.R glpk.R glpkAPI.R zzz.R
+Packaged: 2014-11-16 17:16:33 UTC; gabriel
+Author: Gabriel Gelius-Dietrich [aut, cre]
+NeedsCompilation: yes
+Repository: CRAN
+Date/Publication: 2014-11-16 22:12:16
--- a/NAMESPACE
+++ b/NAMESPACE
+useDynLib(glpkAPI)
+
+import(methods)
+
+exportClass("glpkPtr")
+
+export(
+# methods
+"glpkPointer",
+"glpkPtrType",
+"glpkPtrType<-",
+"isNULLpointerGLPK",
+"isGLPKpointer",
+"isTRWKSpointer",
+# function names
+addColsGLPK,
+addRowsGLPK,
+advBasisGLPK,
+bfExistsGLPK,
+bfUpdatedGLPK,
+checkDupGLPK,
+copyProbGLPK,
+cpxBasisGLPK,
+createIndexGLPK,
+delColsGLPK,
+deleteIndexGLPK,
+delProbGLPK,
+delRowsGLPK,
+eraseProbGLPK,
+factorizeGLPK,
+findColGLPK,
+findRowGLPK,
+getBfcpGLPK,
+getBheadGLPK,
+getCbindGLPK,
+getColDualGLPK,
+getColDualIptGLPK,
+getColKindGLPK,
+getColLowBndGLPK,
+getColNameGLPK,
+getColPrimGLPK,
+getColPrimIptGLPK,
+getColsDualGLPK,
+getColsDualIptGLPK,
+getColsKindGLPK,
+getColsLowBndsGLPK,
+getColsPrimGLPK,
+getColsPrimIptGLPK,
+getColsStatGLPK,
+getColStatGLPK,
+getColsUppBndsGLPK,
+getColTypeGLPK,
+getColUppBndGLPK,
+getDualStatGLPK,
+getInteriorParmGLPK,
+getMatColGLPK,
+getMatRowGLPK,
+getMIPParmGLPK,
+getNumBinGLPK,
+getNumColsGLPK,
+getNumIntGLPK,
+getNumNnzGLPK,
+getNumRowsGLPK,
+getObjCoefGLPK,
+getObjCoefsGLPK,
+getObjDirGLPK,
+getObjNameGLPK,
+getObjValGLPK,
+getObjValIptGLPK,
+getPrimStatGLPK,
+getProbNameGLPK,
+getRbindGLPK,
+getRiiGLPK,
+getRowDualGLPK,
+getRowDualIptGLPK,
+getRowLowBndGLPK,
+getRowNameGLPK,
+getRowPrimGLPK,
+getRowPrimIptGLPK,
+getRowsDualGLPK,
+getRowsDualIptGLPK,
+getRowsLowBndsGLPK,
+getRowsPrimGLPK,
+getRowsPrimIptGLPK,
+getRowsStatGLPK,
+getRowStatGLPK,
+getRowsTypesGLPK,
+getRowsUppBndsGLPK,
+getRowTypeGLPK,
+getRowUppBndGLPK,
+getSimplexParmGLPK,
+getSjjGLPK,
+getSolStatGLPK,
+getSolStatIptGLPK,
+getUnbndRayGLPK,
+initProbGLPK,
+loadMatrixGLPK,
+mipColsValGLPK,
+mipColValGLPK,
+mipObjValGLPK,
+mipRowsValGLPK,
+mipRowValGLPK,
+mipStatusGLPK,
+mplAllocWkspGLPK,
+mplBuildProbGLPK,
+mplFreeWkspGLPK,
+mplGenerateGLPK,
+mplPostsolveGLPK,
+mplReadDataGLPK,
+mplReadModelGLPK,
+printIptGLPK,
+printMIPGLPK,
+printRangesGLPK,
+printSolGLPK,
+readIptGLPK,
+readLPGLPK,
+readMIPGLPK,
+readMPSGLPK,
+readProbGLPK,
+readSolGLPK,
+return_codeGLPK,
+scaleProbGLPK,
+setBfcpGLPK,
+setColBndGLPK,
+setColKindGLPK,
+setColNameGLPK,
+setColsBndsGLPK,
+setColsBndsObjCoefsGLPK,
+setColsKindGLPK,
+setColsNamesGLPK,
+setColStatGLPK,
+setDefaultIptParmGLPK,
+setDefaultMIPParmGLPK,
+setDefaultSmpParmGLPK,
+setInteriorParmGLPK,
+setMatColGLPK,
+setMatRowGLPK,
+setMIPParmGLPK,
+setObjCoefGLPK,
+setObjCoefsGLPK,
+setObjDirGLPK,
+setObjNameGLPK,
+setProbNameGLPK,
+setRhsZeroGLPK,
+setRiiGLPK,
+setRowBndGLPK,
+setRowNameGLPK,
+setRowsBndsGLPK,
+setRowsNamesGLPK,
+setRowStatGLPK,
+setSimplexParmGLPK,
+setSjjGLPK,
+solveInteriorGLPK,
+solveMIPGLPK,
+solveSimplexExactGLPK,
+solveSimplexGLPK,
+sortMatrixGLPK,
+status_codeGLPK,
+stdBasisGLPK,
+termOutGLPK,
+unscaleProbGLPK,
+versionGLPK,
+warmUpGLPK,
+writeIptGLPK,
+writeLPGLPK,
+writeMIPGLPK,
+writeMPSGLPK,
+writeProbGLPK,
+writeSolGLPK,
+# parameter variable names
+BINARIZE,
+BR_TECH,
+BT_TECH,
+CB_SIZE,
+CLQ_CUTS,
+COV_CUTS,
+EPS_TOL,
+FP_HEUR,
+GLP_BF_BG,
+GLP_BF_FT,
+GLP_BF_GR,
+GLP_BR_DTH,
+GLP_BR_FFV,
+GLP_BR_LFV,
+GLP_BR_MFV,
+GLP_BR_PCH,
+GLP_BS,
+GLP_BT_BFS,
+GLP_BT_BLB,
+GLP_BT_BPH,
+GLP_BT_DFS,
+GLP_BV,
+GLP_CV,
+GLP_DB,
+GLP_DN_BRNCH,
+GLP_DUAL,
+GLP_DUALP,
+GLP_EBADB,
+GLP_EBOUND,
+GLP_ECOND,
+GLP_EDATA,
+GLP_EFAIL,
+GLP_EINSTAB,
+GLP_EITLIM,
+GLP_EMIPGAP,
+GLP_ENOCVG,
+GLP_ENODFS,
+GLP_ENOFEAS,
+GLP_ENOPFS,
+GLP_EOBJLL,
+GLP_EOBJUL,
+GLP_ERANGE,
+GLP_EROOT,
+GLP_ESING,
+GLP_ESTOP,
+GLP_ETMLIM,
+GLP_FEAS,
+GLP_FR,
+GLP_FX,
+GLP_IBINGO,
+GLP_IBRANCH,
+GLP_ICUTGEN,
+GLP_IHEUR,
+GLP_INFEAS,
+GLP_IPREPRO,
+GLP_IPT,
+GLP_IROWGEN,
+GLP_ISELECT,
+GLP_IV,
+GLP_KKT_CS,
+GLP_KKT_DB,
+GLP_KKT_DE,
+GLP_KKT_PB,
+GLP_KKT_PE,
+GLP_LO,
+GLP_MAX,
+GLP_MIN,
+GLP_MIP,
+GLP_MPS_DECK,
+GLP_MPS_FILE,
+GLP_MSG_ALL,
+GLP_MSG_DBG,
+GLP_MSG_ERR,
+GLP_MSG_OFF,
+GLP_MSG_ON,
+GLP_NF,
+GLP_NL,
+GLP_NO_BRNCH,
+GLP_NOFEAS,
+GLP_NS,
+GLP_NU,
+GLP_OFF,
+GLP_ON,
+GLP_OPT,
+GLP_ORD_AMD,
+GLP_ORD_NONE,
+GLP_ORD_QMD,
+GLP_ORD_SYMAMD,
+GLP_PP_ALL,
+GLP_PP_NONE,
+GLP_PP_ROOT,
+GLP_PRIMAL,
+GLP_PT_PSE,
+GLP_PT_STD,
+GLP_RF_CLQ,
+GLP_RF_COV,
+GLP_RF_CUT,
+GLP_RF_GMI,
+GLP_RF_LAZY,
+GLP_RF_MIR,
+GLP_RF_REG,
+GLP_RT_HAR,
+GLP_RT_STD,
+GLP_SF_2N,
+GLP_SF_AUTO,
+GLP_SF_EQ,
+GLP_SF_GM,
+GLP_SF_SKIP,
+GLP_SOL,
+GLP_UNBND,
+GLP_UNDEF,
+GLP_UP_BRNCH,
+GLP_UP,
+CB_FUNC,
+GMI_CUTS,
+IT_LIM,
+LU_SIZE,
+MAX_GRO,
+METH,
+MIP_GAP,
+MIR_CUTS,
+MSG_LEV,
+NFS_MAX,
+NRS_MAX,
+OBJ_LL,
+OBJ_UL,
+ORD_ALG,
+OUT_DLY,
+OUT_FRQ,
+PIV_LIM,
+PIV_TOL,
+PP_TECH,
+PRESOLVE,
+PRICING,
+R_TEST,
+RS_SIZE,
+SUHL,
+TM_LIM,
+TOL_BND,
+TOL_DJ,
+TOL_INT,
+TOL_OBJ,
+TOL_PIV,
+TYPE,
+UPD_TOL
+)
+
+
--- a/R/generics.R
+++ b/R/generics.R
+#------------------------------------------------------------------------------#
+#                             R interface to GLPK                              #
+#------------------------------------------------------------------------------#
+
+#  generics.R
+#  R interface to GLPK.
+#
+#  Copyright (C) 2011-2014 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
+#  Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+#  All right reserved.
+#  Email: geliudie@uni-duesseldorf.de
+#
+#  This file is part of glpkAPI.
+#
+#  GlpkAPI is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  GlpkAPI is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with glpkAPI  If not, see <http://www.gnu.org/licenses/>.
+
+
+#------------------------------------------------------------------------------#
+#                                   generics                                   #
+#------------------------------------------------------------------------------#
+
+setGeneric(name = "glpkPointer",
+           def  = function(object) { standardGeneric("glpkPointer") }
+)
+
+setGeneric(name = "glpkPtrType",
+           def  = function(object) { standardGeneric("glpkPtrType") }
+)
+setGeneric(name = "glpkPtrType<-",
+           def  = function(object, value) { standardGeneric("glpkPtrType<-") }
+)
+
+setGeneric(name = "isNULLpointerGLPK",
+           def  = function(object) { standardGeneric("isNULLpointerGLPK") }
+)
+
+setGeneric(name = "isGLPKpointer",
+           def  = function(object) { standardGeneric("isGLPKpointer") }
+)
+
+setGeneric(name = "isTRWKSpointer",
+           def  = function(object) { standardGeneric("isTRWKSpointer") }
+)
--- a/R/glpk.R
+++ b/R/glpk.R
+#------------------------------------------------------------------------------#
+#                             R interface to GLPK                              #
+#------------------------------------------------------------------------------#
+
+#  glpk.R
+#  R interface to GLPK.
+#
+#  Copyright (C) 2011-2014 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
+#  Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+#  All right reserved.
+#  Email: geliudie@uni-duesseldorf.de
+#
+#  This file is part of glpkAPI.
+#
+#  GlpkAPI is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  GlpkAPI is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with glpkAPI  If not, see <http://www.gnu.org/licenses/>.
+
+
+#------------------------------------------------------------------------------#
+#                       global variables (from glpk.h [4.42])                  #
+#------------------------------------------------------------------------------#
+
+
+# simplex integer parameters (not from glpk.h, self defined)
+MSG_LEV  <- 101
+METH     <- 102
+PRICING  <- 103
+R_TEST   <- 104
+IT_LIM   <- 105
+TM_LIM   <- 106
+OUT_FRQ  <- 107
+OUT_DLY  <- 108
+PRESOLVE <- 109
+
+# simplex double parameters (not from glpk.h, self defined)
+TOL_BND  <- 201
+TOL_DJ   <- 202
+TOL_PIV  <- 203
+OBJ_LL   <- 204
+OBJ_UL   <- 205
+
+# additional interior integer parameters (not from glpk.h, self defined)
+ORD_ALG  <- 301
+
+# basis factorization integer control parameters (not from glpk.h, self defined)
+TYPE     <- 401
+LU_SIZE  <- 402
+PIV_LIM  <- 403
+SUHL     <- 404
+NFS_MAX  <- 405
+NRS_MAX  <- 406
+RS_SIZE  <- 407
+
+# basis factorization double control parameters (not from glpk.h, self defined)
+PIV_TOL  <- 501
+EPS_TOL  <- 502
+MAX_GRO  <- 503
+UPD_TOL  <- 504
+
+# MIP integer parameters (not from glpk.h, self defined)
+BR_TECH  <- 601
+BT_TECH  <- 602
+PP_TECH  <- 603
+FP_HEUR  <- 604
+GMI_CUTS <- 605
+MIR_CUTS <- 606
+COV_CUTS <- 607
+CLQ_CUTS <- 608
+CB_SIZE  <- 609
+BINARIZE <- 610
+
+# MIP double parameters (not from glpk.h, self defined)
+TOL_INT  <- 701
+TOL_OBJ  <- 702
+MIP_GAP  <- 703
+
+# use callback routine glpkCallback in MIP
+CB_FUNC  <- 651
+
+
+#------------------------------------------------------------------------------#
+
+# LP/MIP problem object
+# optimization direction flag:
+GLP_MIN <- 1  # minimization
+GLP_MAX <- 2  # maximization
+
+# kind of structural variable:
+GLP_CV <- 1  # continuous variable
+GLP_IV <- 2  # integer variable
+GLP_BV <- 3  # binary variable
+
+# type of auxiliary/structural variable:
+GLP_FR <- 1  # free variable
+GLP_LO <- 2  # variable with lower bound
+GLP_UP <- 3  # variable with upper bound
+GLP_DB <- 4  # double-bounded variable
+GLP_FX <- 5  # fixed variable
+
+# status of auxiliary/structural variable:
+GLP_BS <- 1  # basic variable
+GLP_NL <- 2  # non-basic variable on lower bound
+GLP_NU <- 3  # non-basic variable on upper bound
+GLP_NF <- 4  # non-basic free variable
+GLP_NS <- 5  # non-basic fixed variable
+
+# scaling options:
+GLP_SF_GM   <- 0x01  # perform geometric mean scaling
+GLP_SF_EQ   <- 0x10  # perform equilibration scaling
+GLP_SF_2N   <- 0x20  # round scale factors to power of two
+GLP_SF_SKIP <- 0x40  # skip if problem is well scaled
+GLP_SF_AUTO <- 0x80  # choose scaling options automatically
+
+# solution indicator:
+GLP_SOL <- 1  # basic solution
+GLP_IPT <- 2  # interior-point solution
+GLP_MIP <- 3  # mixed integer solution
+
+# solution status:
+GLP_UNDEF  <- 1  # solution is undefined
+GLP_FEAS   <- 2  # solution is feasible
+GLP_INFEAS <- 3  # solution is infeasible
+GLP_NOFEAS <- 4  # no feasible solution exists
+GLP_OPT    <- 5  # solution is optimal
+GLP_UNBND  <- 6  # solution is unbounded
+
+
+#------------------------------------------------------------------------------#
+# basis factorization control parameters
+# type
+GLP_BF_FT  <- 0x01  # LUF + Forrest-Tomlin
+GLP_BF_BG  <- 0x02  # LUF + Schur compl. + Bartels-Golub
+GLP_BF_GR  <- 0x03  # LUF + Schur compl. + Givens rotation
+GLP_BF_LUF <- 0x00  # plain LU-factorization
+GLP_BF_BTF <- 0x10  # block triangular LU-factorization
+
+#------------------------------------------------------------------------------#
+# simplex method control parameters
+# msg_lev           # message level:
+GLP_MSG_OFF <- 0    # no output
+GLP_MSG_ERR <- 1    # warning and error messages only
+GLP_MSG_ON  <- 2    # normal output
+GLP_MSG_ALL <- 3    # full output
+GLP_MSG_DBG <- 4    # debug output
+
+# meth              # simplex method option:
+GLP_PRIMAL <- 1     # use primal simplex
+GLP_DUALP  <- 2     # use dual; if it fails, use primal
+GLP_DUAL   <- 3     # use dual simplex
+
+# pricing           # pricing technique:
+GLP_PT_STD <- 0x11  # standard (Dantzig rule)
+GLP_PT_PSE <- 0x22  # projected steepest edge
+
+# r_test            # ratio test technique:
+GLP_RT_STD <- 0x11  # standard (textbook)
+GLP_RT_HAR <- 0x22  # two-pass Harris' ratio test
+
+
+#------------------------------------------------------------------------------#
+# interior-point solver control parameters
+# ord_alg            # ordering algorithm:
+GLP_ORD_NONE   <- 0  # natural (original) ordering
+GLP_ORD_QMD    <- 1  # quotient minimum degree (QMD)
+GLP_ORD_AMD    <- 2  # approx. minimum degree (AMD)
+GLP_ORD_SYMAMD <- 3  # approx. minimum degree (SYMAMD)
+
+
+#------------------------------------------------------------------------------#
+# integer optimizer control parameters
+# br_tech        # branching technique:
+GLP_BR_FFV <- 1  # first fractional variable
+GLP_BR_LFV <- 2  # last fractional variable
+GLP_BR_MFV <- 3  # most fractional variable
+GLP_BR_DTH <- 4  # heuristic by Driebeck and Tomlin
+GLP_BR_PCH <- 5  # hybrid pseudocost heuristic
+
+# bt_tech        # backtracking technique:
+GLP_BT_DFS <- 1  # depth first search
+GLP_BT_BFS <- 2  # breadth first search
+GLP_BT_BLB <- 3  # best local bound
+GLP_BT_BPH <- 4  # best projection heuristic
+
+# pp_tech         # preprocessing technique:
+GLP_PP_NONE <- 0  # disable preprocessing
+GLP_PP_ROOT <- 1  # preprocessing only on root level
+GLP_PP_ALL  <- 2  # preprocessing on all levels
+
+
+#------------------------------------------------------------------------------#
+# additional row attributes
+# the row origin flag:
+GLP_RF_REG  <- 0  # regular constraint
+GLP_RF_LAZY <- 1  # "lazy" constraint
+GLP_RF_CUT  <- 2  # cutting plane constraint
+
+# the row class descriptor:
+# klass
+GLP_RF_GMI <- 1  # Gomory's mixed integer cut
+GLP_RF_MIR <- 2  # mixed integer rounding cut
+GLP_RF_COV <- 3  # mixed cover cut
+GLP_RF_CLQ <- 4  # clique cut
+
+
+#------------------------------------------------------------------------------#
+# enable/disable flag:
+GLP_ON  <- 1  # enable something
+GLP_OFF <- 0  # disable something
+
+
+#------------------------------------------------------------------------------#
+# reason codes:
+GLP_IROWGEN <- 0x01  # request for row generation
+GLP_IBINGO  <- 0x02  # better integer solution found
+GLP_IHEUR   <- 0x03  # request for heuristic solution
+GLP_ICUTGEN <- 0x04  # request for cut generation
+GLP_IBRANCH <- 0x05  # request for branching
+GLP_ISELECT <- 0x06  # request for subproblem selection
+GLP_IPREPRO <- 0x07  # request for preprocessing
+
+
+#------------------------------------------------------------------------------#
+# branch selection indicator:
+GLP_NO_BRNCH <- 0  # select no branch
+GLP_DN_BRNCH <- 1  # select down-branch
+GLP_UP_BRNCH <- 2  # select up-branch
+
+
+#------------------------------------------------------------------------------#
+# return codes:
+GLP_EBADB   <- 0x01  # invalid basis
+GLP_ESING   <- 0x02  # singular matrix
+GLP_ECOND   <- 0x03  # ill-conditioned matrix
+GLP_EBOUND  <- 0x04  # invalid bounds
+GLP_EFAIL   <- 0x05  # solver failed
+GLP_EOBJLL  <- 0x06  # objective lower limit reached
+GLP_EOBJUL  <- 0x07  # objective upper limit reached
+GLP_EITLIM  <- 0x08  # iteration limit exceeded
+GLP_ETMLIM  <- 0x09  # time limit exceeded
+GLP_ENOPFS  <- 0x0A  # no primal feasible solution
+GLP_ENODFS  <- 0x0B  # no dual feasible solution
+GLP_EROOT   <- 0x0C  # root LP optimum not provided
+GLP_ESTOP   <- 0x0D  # search terminated by application
+GLP_EMIPGAP <- 0x0E  # relative mip gap tolerance reached
+GLP_ENOFEAS <- 0x0F  # no primal/dual feasible solution