adjust.pheno: no visible global function definition for 'find.pheno'
approximate.UDG : pvalue: no visible global function definition for
  'pt'
approximate.UDG: no visible global function definition for 'cor'
approximate.UDG: no visible global function definition for 'combn'
bic.qtlnet: no visible global function definition for 'calc.genoprob'
cov.formula: no visible global function definition for 'as.formula'
create.cov.matrix: no visible global function definition for 'formula'
create.cov.matrix: no visible global function definition for
  'model.matrix'
dist.qtlnet: no visible global function definition for 'plot'
dist.qtlnet: no visible global function definition for 'abline'
edgematch.qtlnet: no visible global function definition for 'plot'
edgematch.qtlnet: no visible global function definition for 'abline'
edgematch.qtlnet: no visible global function definition for 'points'
est.qtlnet: no visible global function definition for 'calc.genoprob'
est.qtlnet: no visible global function definition for 'makeqtl'
est.qtlnet: no visible global function definition for 'formula'
est.qtlnet: no visible global function definition for 'fitqtl'
est.qtlnet: no visible global function definition for 'coef'
est.qtlnet: no visible global function definition for 'lm'
generate.data.graph.a : gibbs.graph.a: no visible global function
  definition for 'rnorm'
generate.data.graph.b : gibbs.graph.b: no visible global function
  definition for 'rnorm'
generate.data.graph.c : gibbs.graph.c: no visible global function
  definition for 'rnorm'
generate.qtl.markers: no visible global function definition for
  'makeqtl'
generate.qtl.markers: no visible global function definition for
  'find.marker'
geno.effect: no visible global function definition for 'rnorm'
get.graph.edges: no visible global function definition for
  'list.edge.attributes'
get.graph.edges: no visible global function definition for
  'get.edgelist'
get.graph.edges: no visible global function definition for
  'get.edge.attribute'
get.graph.vertices: no visible global function definition for
  'list.vertex.attributes'
get.graph.vertices: no visible global function definition for
  'get.vertex.attribute'
get.model.average: no visible binding for global variable
  'weighted.mean'
igraph.qdg: no visible global function definition for 'pchisq'
igraph.qtlnet: no visible global function definition for
  'igraph.options'
igraph.qtlnet: no visible global function definition for
  'graph.data.frame'
loci.qtlnet: no visible global function definition for 'calc.genoprob'
lod.score: no visible global function definition for 'compareVersion'
lod.score: no visible global function definition for 'qtlversion'
lod.score : myfitqtl: no visible global function definition for
  'fitqtl'
lod.score: no visible global function definition for 'find.pheno'
log.likelihood.s: no visible global function definition for
  'find.pheno'
log.likelihood.s: no visible global function definition for 'lm'
log.likelihood.s: no visible global function definition for 'logLik'
log.likelihood.s: no visible global function definition for 'AIC'
match.parents: no visible global function definition for 'nind'
mcmc.qtlnet: no visible global function definition for 'calc.genoprob'
mcmc.qtlnet: no visible global function definition for 'plot'
mcmc.qtlnet: no visible global function definition for 'points'
mcmc.qtlnet: no visible global function definition for 'runif'
mds.qtlnet: no visible global function definition for 'dist'
mds.qtlnet: no visible global function definition for 'cmdscale'
mds.qtlnet: no visible global function definition for 'plot'
mds.qtlnet: no visible global function definition for 'points'
newfun: no visible global function definition for 'plot'
newfun: no visible global function definition for 'points'
newfun: no visible global function definition for 'abline'
parallel.error: no visible global function definition for 'write.table'
parallel.message: no visible global function definition for
  'write.table'
parents.qtlnet: no visible global function definition for 'combn'
plot.qtlnet: no visible global function definition for 'tkplot'
plotbic.qtlnet : plotfn: no visible global function definition for
  'lines'
plotbic.qtlnet : splotfn: no visible global function definition for
  'lines'
plotbic.qtlnet : splotfn: no visible global function definition for
  'lowess'
plotbic.qtlnet: no visible global function definition for 'plot'
plotbic.qtlnet: no visible global function definition for 'title'
propose.new.node.edge: no visible global function definition for
  'runif'
pull.loci: no visible global function definition for 'create.map'
qdg: no visible global function definition for 'cor'
qdg: no visible global function definition for 'skeleton'
qdg: no visible binding for global variable 'gaussCItest'
qdg: no visible global function definition for 'argmax.geno'
qdg.sem : score.sem.models: no visible global function definition for
  'nind'
qdg.sem : score.sem.models: no visible global function definition for
  'lm'
qdg.sem : score.sem.models: no visible global function definition for
  'as.formula'
qdg.sem : score.sem.models: no visible global function definition for
  'cov'
qdg.sem : score.sem.models: no visible global function definition for
  'sem'
qtlnet.phase1: no visible global function definition for
  'calc.genoprob'
qtlnet.phase1: no visible global function definition for 'write.table'
s.formula: no visible global function definition for 'as.formula'
s.formula: no visible global function definition for 'model.matrix'
scan.genome: no visible global function definition for 'makeqtl'
scan.genome: no visible global function definition for 'lm'
scan.genome: no visible global function definition for 'AIC'
scan.genome: no visible global function definition for 'update'
scanone.summary: no visible global function definition for 'scanone'
summary.qtlnet: no visible global function definition for
  'weighted.mean'
write.qtlnet: no visible global function definition for 'write.table'
Undefined global functions or variables:
  AIC abline argmax.geno as.formula calc.genoprob cmdscale coef combn
  compareVersion cor cov create.map dist find.marker find.pheno fitqtl
  formula gaussCItest get.edge.attribute get.edgelist
  get.vertex.attribute graph.data.frame igraph.options lines
  list.edge.attributes list.vertex.attributes lm logLik lowess makeqtl
  model.matrix nind pchisq plot points pt qtlversion rnorm runif
  scanone sem skeleton title tkplot update weighted.mean write.table
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points", "title")
  importFrom("stats", "AIC", "as.formula", "cmdscale", "coef", "cor",
             "cov", "dist", "formula", "lm", "logLik", "lowess",
             "model.matrix", "pchisq", "pt", "rnorm", "runif", "update",
             "weighted.mean")
  importFrom("utils", "combn", "compareVersion", "write.table")
to your NAMESPACE file.