.CGstats2initpms: no visible global function definition for
  ‘rowSumsPrim’
.CI.exact : LRT : oneslice: no visible global function definition for
  ‘addmargins’
.CI.exact : LRT: no visible global function definition for ‘pchisq’
.CI.exact : wilcoxon : oneslice: no visible global function definition
  for ‘addmargins’
.CI.exact : wilcoxon: no visible global function definition for ‘pnorm’
.CI.exact : kruskal : oneslice: no visible global function definition
  for ‘addmargins’
.CI.exact : kruskal: no visible global function definition for ‘pchisq’
.CI.exact : jt : oneslice: no visible global function definition for
  ‘addmargins’
.CI.exact : jt: no visible global function definition for ‘pnorm’
.CI.exact : rcsum: no visible global function definition for
  ‘addmargins’
.CI.exact : rdev: no visible global function definition for ‘r2dtable’
.CI.exact : wdev: no visible global function definition for ‘r2dtable’
.CI.exact : kdev: no visible global function definition for ‘r2dtable’
.CI.exact : jtdev: no visible global function definition for ‘r2dtable’
.CI.exact: no visible global function definition for ‘ftable’
.CI.ordinal : LRT : oneslice: no visible global function definition for
  ‘addmargins’
.CI.ordinal : LRT: no visible global function definition for ‘pchisq’
.CI.ordinal : wilcoxon : oneslice: no visible global function
  definition for ‘addmargins’
.CI.ordinal : wilcoxon: no visible global function definition for
  ‘pnorm’
.CI.ordinal : kruskal : oneslice: no visible global function definition
  for ‘addmargins’
.CI.ordinal : kruskal: no visible global function definition for
  ‘pchisq’
.CI.ordinal : jt : oneslice: no visible global function definition for
  ‘addmargins’
.CI.ordinal : jt: no visible global function definition for ‘pnorm’
.CI.ordinal : rcsum: no visible global function definition for
  ‘addmargins’
.CI.ordinal : rdev: no visible global function definition for
  ‘r2dtable’
.CI.ordinal : wdev: no visible global function definition for
  ‘r2dtable’
.CI.ordinal : kdev: no visible global function definition for
  ‘r2dtable’
.CI.ordinal : jtdev: no visible global function definition for
  ‘r2dtable’
.CI.ordinal: no visible global function definition for ‘ftable’
.CI_MC_prim: no visible global function definition for ‘tableMargin’
.CI_MC_prim: no visible global function definition for ‘outerPrim’
.CI_MC_prim: no visible global function definition for ‘r2dtable’
.CI_MC_prim: no visible global function definition for ‘colSumsPrim’
.CI_X2_prim: no visible global function definition for ‘tableMargin’
.CI_X2_prim: no visible global function definition for ‘tablePerm’
.CI_X2_prim: no visible global function definition for ‘tableOp’
.CI_X2_prim: no visible global function definition for ‘rowSumsPrim’
.CI_X2_prim: no visible global function definition for ‘pchisq’
.add.edge_glist: no visible global function definition for ‘uniquePrim’
.add.edge_glist: no visible global function definition for
  ‘intersectPrim’
.add.edge_glist: no visible global function definition for
  ‘removeRedundant’
.add.term: no visible global function definition for ‘removeRedundant’
.add.term_glist: no visible global function definition for ‘isin’
.add.term_glist: no visible global function definition for
  ‘removeRedundant’
.aedge_glist: no visible global function definition for ‘uniquePrim’
.aedge_glist: no visible global function definition for ‘intersectPrim’
.aedge_glist: no visible global function definition for
  ‘removeRedundant’
.aterm_glist: no visible global function definition for ‘isin’
.aterm_glist: no visible global function definition for
  ‘removeRedundant’
.cModel_finalize: no visible global function definition for ‘ugList’
.cModel_finalize: no visible global function definition for
  ‘maxCliqueMAT’
.cModel_finalize: no visible global function definition for ‘mcsMAT’
.check.glist: no visible global function definition for ‘unlistPrim’
.check.glist: no visible global function definition for ‘uniquePrim’
.ciTest_mvn_internal: no visible global function definition for
  ‘pchisq’
.ciTest_mvn_internal: no visible global function definition for ‘pf’
.compareModel: no visible global function definition for ‘pchisq’
.comparemodels: no visible global function definition for ‘pchisq’
.cov.wt: no visible global function definition for ‘colSumsPrim’
.dModel_finalize: no visible global function definition for
  ‘isGSD_glist’
.dModel_sparsity: no visible global function definition for
  ‘tableMargin’
.delete.term: no visible global function definition for ‘isin’
.delete.term: no visible global function definition for
  ‘removeRedundant’
.drop.term_glist: no visible global function definition for ‘subsetof’
.drop.term_glist: no visible global function definition for ‘combnPrim’
.drop.term_glist: no visible global function definition for
  ‘unlistPrim’
.drop.term_glist : <anonymous>: no visible global function definition
  for ‘subsetof’
.drop.term_glist: no visible global function definition for
  ‘removeRedundant’
.dterm_glist: no visible global function definition for ‘subsetof’
.dterm_glist: no visible global function definition for ‘combnPrim’
.dterm_glist: no visible global function definition for ‘unlistPrim’
.dterm_glist : <anonymous>: no visible global function definition for
  ‘subsetof’
.dterm_glist: no visible global function definition for
  ‘removeRedundant’
.extendCGstats: no visible global function definition for ‘rowSumsPrim’
.ghk2pmsParms: no visible global function definition for ‘solveSPD’
.ghk2pmsParms: no visible global function definition for ‘colSumsPrim’
.glist2formula: no visible global function definition for ‘as.formula’
.list2pairs : <anonymous>: no visible global function definition for
  ‘combn’
.loglinDecDim: no visible global function definition for ‘tableMargin’
.loglinDim: no visible global function definition for ‘unlistPrim’
.loglinGenDim: no visible global function definition for ‘unlistPrim’
.mModel_finalize: no visible global function definition for
  ‘isGSD_glist’
.mModel_logLpms: no visible global function definition for ‘solveSPD’
.mModelinfoPrimitive: no visible global function definition for
  ‘removeRedundant’
.mmod_dimensionPrimitive: no visible global function definition for
  ‘glist2adjMAT’
.normalize.ghkParms: no visible global function definition for
  ‘solveSPD’
.normalize.ghkParms: no visible global function definition for
  ‘colSumsPrim’
.pFormula2: no visible global function definition for ‘combn’
.pFormula2: no visible global function definition for ‘rhsFormula2list’
.pFormula2: no visible global function definition for ‘maxCliqueMAT’
.pFormula2: no visible global function definition for ‘as.adjMAT’
.pFormula2: no visible global function definition for ‘uniquePrim’
.parse.change.list : .foo: no visible global function definition for
  ‘rhsf2list’
.parse.change.list : .foo: no visible binding for global variable
  ‘names2pairs’
.parse.change.list: no visible global function definition for
  ‘matchPrim’
.pms2ghkParms: no visible global function definition for ‘solveSPD’
.pms2ghkParms: no visible global function definition for ‘colSumsPrim’
.reduceSet : <anonymous>: no visible global function definition for
  ‘combn’
.reduceSet: no visible global function definition for ‘isin’
.rhsf2char: no visible global function definition for ‘rhsf2list’
.set.interactions : <anonymous>: no visible global function definition
  for ‘combn’
.set.interactions: no visible global function definition for
  ‘removeRedundant’
.split.by: no visible global function definition for ‘xtabs’
.subtract.fix: no visible global function definition for ‘pairs2num’
.subtract.fix: no visible global function definition for ‘na.omit’
.subtract.fix: no visible global function definition for ‘matchPrim’
.update.ghkParms: no visible global function definition for ‘tableOp2’
.weak.datamarg.cont: no visible global function definition for
  ‘rowSumsPrim’
.weak.datamarg.disc: no visible global function definition for
  ‘tableMargin’
.weak.datamarg.mix: no visible global function definition for
  ‘tableMargin’
.weak.datamarg.mix: no visible global function definition for
  ‘slice2entry’
.weak.datamarg.mix: no visible global function definition for
  ‘rowSumsPrim’
.weak.datamarg.mix: no visible global function definition for
  ‘nextCell’
.weak.modelmarg.cont: no visible global function definition for
  ‘rowSumsPrim’
.weak.modelmarg.disc: no visible global function definition for
  ‘tableMargin’
.weak.modelmarg.mix: no visible global function definition for
  ‘tableMargin’
.weak.modelmarg.mix: no visible global function definition for
  ‘slice2entry’
.weak.modelmarg.mix: no visible global function definition for
  ‘rowSumsPrim’
.weak.modelmarg.mix: no visible global function definition for
  ‘nextCell’
CGstats_internal: no visible global function definition for ‘xtabs’
CGstats_internal: no visible global function definition for ‘cov.wt’
backward: no visible global function definition for ‘isGSD_glist’
backward: no visible global function definition for ‘glist2adjMAT’
backward: no visible global function definition for ‘pairs2num’
backward: no visible global function definition for ‘update’
ciTest_df: no visible global function definition for ‘rhsFormula2list’
ciTest_df: no visible global function definition for ‘uniquePrim’
ciTest_df: no visible global function definition for ‘xtabs’
ciTest_df: no visible global function definition for ‘cov.wt’
ciTest_mvn: no visible global function definition for ‘rhsFormula2list’
ciTest_ordinal: no visible global function definition for
  ‘rhsFormula2list’
ciTest_table: no visible global function definition for ‘tableMargin’
ciTest_table: no visible global function definition for
  ‘rhsFormula2list’
cmod: no visible global function definition for ‘cov.wt’
compareGC: no visible global function definition for ‘unlistPrim’
compareGC : <anonymous>: no visible global function definition for
  ‘isin’
compareGCpairs: no visible binding for global variable ‘combnPrim’
compareModels.iModel: no visible global function definition for
  ‘logLik’
compareModels.iModel: no visible global function definition for
  ‘pchisq’
dmod: no visible global function definition for ‘xtabs’
dmod: no visible global function definition for ‘tableMargin’
effloglin: no visible global function definition for ‘ugList’
effloglin: no visible global function definition for ‘triangulateMAT’
effloglin: no visible global function definition for ‘ripMAT’
effloglin : <anonymous>: no visible global function definition for
  ‘tableMargin’
effloglin: no visible global function definition for ‘uniquePrim’
effloglin : <anonymous>: no visible global function definition for
  ‘parray’
effloglin: no visible global function definition for ‘propagateLS’
effloglin: no visible global function definition for ‘tableMargin’
effloglin: no visible global function definition for ‘tableOp2’
effloglin: no visible global function definition for ‘unlistPrim’
effloglin: no visible global function definition for ‘tableOp’
effloglin: no visible global function definition for ‘tablePerm’
fit.dModel: no visible global function definition for ‘loglin’
fit.dModel: no visible global function definition for ‘ripMAT’
fit.dModel: no visible global function definition for ‘glist2adjMAT’
fit.mModel: no visible global function definition for ‘loglin’
fit.mModel: no visible global function definition for ‘rowSumsPrim’
fit.mModel: no visible global function definition for ‘colwiseProd’
forward: no visible global function definition for ‘isGSD_glist’
forward: no visible global function definition for ‘glist2adjMAT’
forward: no visible global function definition for ‘pairs2num’
forward: no visible global function definition for ‘update’
getEdges.graphNEL: no visible global function definition for
  ‘as.adjMAT’
getEdges.list: no visible global function definition for ‘glist2adjMAT’
getInEdgesMAT: no visible global function definition for ‘edgeListMAT’
getInEdgesMAT: no visible global function definition for ‘mcsmarkedMAT’
getOutEdgesMAT: no visible global function definition for
  ‘nonEdgeListMAT’
getOutEdgesMAT: no visible global function definition for
  ‘mcsmarkedMAT’
ggmfit: no visible global function definition for ‘uniquePrim’
ggmfitr: no visible global function definition for ‘ellK’
ghk2phkParms: no visible global function definition for ‘solveSPD’
ghk2phkParms: no visible global function definition for ‘colSumsPrim’
iplot.iModel: no visible global function definition for ‘ugList’
iplot.iModel: no visible global function definition for ‘plot’
loglinDecDim: no visible global function definition for ‘ripMAT’
loglinDecDim: no visible global function definition for ‘glist2adjMAT’
mmod: no visible global function definition for ‘intersectPrim’
phk2ghkParms: no visible global function definition for ‘solveSPD’
phk2ghkParms: no visible global function definition for ‘colSumsPrim’
phk2pmsParms: no visible global function definition for ‘solveSPD’
plot.iModel: no visible global function definition for ‘ugList’
plot.iModel: no visible global function definition for ‘plot’
pms2phkParms: no visible global function definition for ‘solveSPD’
print.compareiModels: no visible global function definition for ‘str’
print.iModelsummary: no visible global function definition for ‘str’
stepwise.iModel: no visible global function definition for
  ‘isGSD_glist’
summary.citest: no visible global function definition for ‘str’
summary.iModel: no visible global function definition for ‘getCliques’
summary.iModel: no visible global function definition for ‘ugList’
testInEdges: no visible global function definition for ‘glist2adjMAT’
testOutEdges: no visible global function definition for ‘glist2adjMAT’
testadd.iModel: no visible global function definition for
  ‘rhsFormula2list’
testadd.iModel: no visible global function definition for
  ‘glist2adjMAT’
testadd.iModel: no visible global function definition for ‘subsetof’
testadd.iModel: no visible global function definition for
  ‘maxCliqueMAT’
testadd.iModel: no visible global function definition for ‘mcsMAT’
testadd.iModel: no visible global function definition for ‘isin’
testadd.iModel: no visible global function definition for ‘setdiffPrim’
testadd.iModel: no visible global function definition for ‘update’
testdelete.iModel: no visible global function definition for
  ‘rhsFormula2list’
testdelete.iModel: no visible global function definition for
  ‘glist2adjMAT’
testdelete.iModel: no visible global function definition for ‘subsetof’
testdelete.iModel: no visible global function definition for
  ‘maxCliqueMAT’
testdelete.iModel: no visible global function definition for ‘mcsMAT’
testdelete.iModel: no visible global function definition for ‘isin’
testdelete.iModel: no visible global function definition for
  ‘setdiffPrim’
testdelete.iModel: no visible global function definition for ‘update’
coerce,cModel-graphNEL: no visible global function definition for
  ‘ugList’
coerce,cModel-igraph: no visible global function definition for
  ‘ugList’
coerce,cModel-matrix: no visible global function definition for
  ‘ugList’
coerce,dModel-graphNEL: no visible global function definition for
  ‘ugList’
coerce,dModel-igraph: no visible global function definition for
  ‘ugList’
coerce,dModel-matrix: no visible global function definition for
  ‘ugList’
coerce,mModel-graphNEL: no visible global function definition for
  ‘ugList’
coerce,mModel-igraph: no visible global function definition for
  ‘ugList’
coerce,mModel-matrix: no visible global function definition for
  ‘ugList’
Undefined global functions or variables:
  addmargins as.adjMAT as.formula colSumsPrim colwiseProd combn
  combnPrim cov.wt edgeListMAT ellK ftable getCliques glist2adjMAT
  intersectPrim isGSD_glist isin logLik loglin matchPrim maxCliqueMAT
  mcsMAT mcsmarkedMAT na.omit names2pairs nextCell nonEdgeListMAT
  outerPrim pairs2num parray pchisq pf plot pnorm propagateLS r2dtable
  removeRedundant rhsFormula2list rhsf2list ripMAT rowSumsPrim
  setdiffPrim slice2entry solveSPD str subsetof tableMargin tableOp
  tableOp2 tablePerm triangulateMAT ugList uniquePrim unlistPrim update
  xtabs
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "addmargins", "as.formula", "cov.wt", "ftable",
             "logLik", "loglin", "na.omit", "pchisq", "pf", "pnorm",
             "r2dtable", "update", "xtabs")
  importFrom("utils", "combn", "str")
to your NAMESPACE file.