* using log directory 'd:/Rcompile/CRANpkg/local/2.15/cMonkey.Rcheck'
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'cMonkey/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cMonkey' version '4.8.5'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking:
  'doMC' 'multicore'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'cMonkey' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
adjust.all.clusters: no visible binding for global variable
  'no.genome.info'
adjust.clust: no visible binding for global variable 'k.clust'
adjust.clust: no visible binding for global variable 'ratios'
adjust.clust: no visible binding for global variable
  'cluster.rows.allowed'
cluster.pclust : <anonymous>: no visible binding for global variable
  'meme.scores'
cluster.pclust: no visible binding for global variable 'mot.weights'
cluster.resid: no visible binding for global variable 'ratios'
cluster.resid: no visible binding for global variable 'row.weights'
cluster.summary: no visible binding for global variable 'mot.weights'
cluster.summary: no visible binding for global variable 'meme.scores'
cluster.summary: no visible binding for global variable 'k.clust'
cluster.summary : <anonymous>: no visible binding for global variable
  'row.scores'
cluster.summary: no visible binding for global variable 'row.scaling'
cluster.summary: no visible binding for global variable 'iter'
cluster.summary: no visible binding for global variable 'mot.scores'
cluster.summary : <anonymous>: no visible binding for global variable
  'mot.scores'
cluster.summary: no visible binding for global variable 'mot.scaling'
cluster.summary: no visible binding for global variable 'net.scores'
cluster.summary : <anonymous>: no visible binding for global variable
  'net.scores'
cluster.summary: no visible binding for global variable 'net.scaling'
cluster.summary: no visible binding for global variable
  'row.membership'
clusters.w.conds: no visible binding for global variable 'k.clust'
clusters.w.conds : <anonymous>: warning in phyper(sum(cols %in% conds),
  length(conds), attr(ratios, "ncol") - length(conds), length(cols),
  lower = F): partial argument match of 'lower' to 'lower.tail'
clusters.w.conds : <anonymous>: no visible binding for global variable
  'ratios'
clusters.w.func: no visible binding for global variable 'k.clust'
clusters.w.func: warning in get.long.names(attr(ratios, "rnames"),
  short = short): partial argument match of 'short' to 'shorter'
clusters.w.func: no visible binding for global variable 'ratios'
clusters.w.func : <anonymous>: warning in get.long.names(rows, short =
  short): partial argument match of 'short' to 'shorter'
clusters.w.func : <anonymous>: warning in phyper(length(grep(func,
  rows.l, perl = T, ignore.case = T)), n2, attr(ratios, "nrow") - n2,
  length(rows), lower = F): partial argument match of 'lower' to
  'lower.tail'
clusters.w.func : <anonymous>: no visible binding for global variable
  'ratios'
clusters.w.genes: no visible binding for global variable 'k.clust'
clusters.w.genes : <anonymous>: warning in phyper(sum(rows %in% genes),
  length(genes), attr(ratios, "nrow") - length(genes), length(rows),
  lower = F): partial argument match of 'lower' to 'lower.tail'
clusters.w.genes : <anonymous>: no visible binding for global variable
  'ratios'
cmonkey: no visible binding for global variable 'dont.init'
cmonkey.init: warning in exists(i, envir = env, inherit = F): partial
  argument match of 'inherit' to 'inherits'
cmonkey.init: warning in exists(i, envir = .GlobalEnv, inherit = F):
  partial argument match of 'inherit' to 'inherits'
cmonkey.init: warning in mget(names(formals()), env =
  as.environment(-1)): partial argument match of 'env' to 'envir'
cmonkey.init: no visible binding for global variable 'save.logfile'
cmonkey.init: no visible binding for global variable 'dont.init'
cmonkey.init: no visible binding for global variable 'n.clust.per.row'
cmonkey.init: no visible binding for global variable 'k.clust'
cmonkey.init: no visible binding for global variable 'n.iter'
cmonkey.init: no visible binding for global variable 'progs.dir'
cmonkey.init: no visible binding for global variable 'cmonkey.version'
cmonkey.init: no visible binding for global variable 'date.run'
cmonkey.init: no visible binding for global variable 'rnd.seed'
cmonkey.init: no visible binding for global variable 'rsat.species'
cmonkey.init: warning in read.delim("data/KEGG/KEGG_taxonomy.txt", sep
  = "\t", comment = "#", head = F, as.is = T): partial argument match
  of 'head' to 'header'
cmonkey.init: warning in read.delim("data/KEGG/KEGG_taxonomy.txt", sep
  = "\t", comment = "#", head = F, as.is = T): partial argument match
  of 'comment' to 'comment.char'
cmonkey.init: no visible binding for global variable 'V2'
cmonkey.init: warning in grep(rsat.spec, tmp, fixed = T, val = T):
  partial argument match of 'val' to 'value'
cmonkey.init: warning in agrep(rsat.spec, tmp, ignore = T, max.dist =
  max.dist, val = T): partial argument match of 'max.dist' to
  'max.distance'
cmonkey.init: warning in agrep(rsat.spec, tmp, ignore = T, max.dist =
  max.dist, val = T): partial argument match of 'ignore' to
  'ignore.case'
cmonkey.init: warning in agrep(rsat.spec, tmp, ignore = T, max.dist =
  max.dist, val = T): partial argument match of 'val' to 'value'
cmonkey.init: warning in read.delim(gzfile("data/GO/proteome2taxid"),
  head = F): partial argument match of 'head' to 'header'
cmonkey.init: no visible binding for global variable 'V1'
cmonkey.init: no visible binding for global variable 'cog.org'
cmonkey.init: no visible global function definition for 'kill'
cmonkey.init: no visible global function definition for 'children'
cmonkey.init: no visible binding for global variable 'SIGKILL'
cmonkey.init: no visible binding for global variable 'no.genome.info'
cmonkey.init: no visible binding for global variable 'type'
cmonkey.init: warning in grepl(paste("^", prefix, sep = ""), names,
  ignore = T, perl = T): partial argument match of 'ignore' to
  'ignore.case'
cmonkey.init: no visible binding for global variable
  'motif.upstream.scan'
cmonkey.init: no visible binding for global variable 'bg.order'
cmonkey.init: no visible binding for global variable
  'motif.upstream.search'
cmonkey.init: warning in my.tempfile("meme.tmp", suf = ".bg"): partial
  argument match of 'suf' to 'suffix'
cmonkey.init: no visible binding for global variable 'meme.cmd'
cmonkey.init: no visible binding for global variable 'net.iters'
cmonkey.init: no visible binding for global variable 'string.links'
cmonkey.init: no visible binding for global variable 'grouping.weights'
cmonkey.init: no visible binding for global variable 'protein1'
cmonkey.init: no visible binding for global variable 'protein2'
cmonkey.init: warning in which(!is.na(tmp), arr = T): partial argument
  match of 'arr' to 'arr.ind'
cmonkey.init : favorite.cluster: no visible binding for global variable
  'row.membership'
cmonkey.init : favorite.cluster: no visible binding for global variable
  'cluster.rows.allowed'
cmonkey.init: no visible binding for global variable
  'cm.func.each.iter'
cmonkey.one.iter: no visible binding for global variable
  'row.membership'
cmonkey.one.iter : <anonymous>: no visible binding for global variable
  'k.clust'
cmonkey.one.iter: no visible binding for global variable
  'col.membership'
cmonkey.one.iter: warning in get.combined.scores(quant = T): partial
  argument match of 'quant' to 'quantile.normalize'
cmonkey.one.iter: no visible binding for global variable 'iter'
cmonkey.one.iter: no visible binding for global variable 'fuzzy.index'
cmonkey.one.iter: no visible binding for global variable 'row.memb'
cmonkey.one.iter: no visible binding for global variable 'col.memb'
cmonkey.one.iter: no visible binding for global variable 'k.clust'
cmonkey.one.iter: no visible binding for global variable 'stats.iters'
cmonkey.one.iter: no visible binding for global variable 'stats'
cmonkey.one.iter: no visible binding for global variable 'organism'
cmonkey.one.iter: no visible binding for global variable 'row.scores'
cmonkey.one.iter: no visible binding for global variable 'mot.scores'
cmonkey.one.iter: no visible binding for global variable 'net.scores'
cmonkey.one.iter : size.compensation.func.rows: no visible binding for
  global variable 'ratios'
cmonkey.one.iter : size.compensation.func.rows: no visible binding for
  global variable 'n.clust.per.row'
cmonkey.one.iter : size.compensation.func.rows: no visible binding for
  global variable 'k.clust'
cmonkey.one.iter : size.compensation.func.cols: no visible binding for
  global variable 'ratios'
cmonkey.one.iter : size.compensation.func.cols: no visible binding for
  global variable 'n.clust.per.col'
cmonkey.one.iter : size.compensation.func.cols: no visible binding for
  global variable 'k.clust'
cmonkey.one.iter: no visible binding for global variable
  'cluster.rows.allowed'
cmonkey.one.iter: no visible binding for global variable 'ratios'
cmonkey.one.iter: no visible binding for global variable 'plot.iters'
cmonkey.one.iter: no visible global function definition for
  'cm.func.each.iter'
cmonkey.one.iter: no visible binding for global variable
  'cm.script.each.iter'
cmonkey.one.iter: no visible global function definition for
  'stopCluster'
extend.vec: no visible binding for global variable 'n.iter'
filter.sequences: no visible binding for global variable
  'motif.upstream.search'
filter.sequences : <anonymous>: no visible binding for global variable
  'contig'
foreach.register.backend: no visible global function definition for
  'registerDoMC'
get.COG.code: no visible binding for global variable 'ratios'
get.COG.code : <anonymous>: warning in get.synonyms(gn, ignore = T):
  partial argument match of 'ignore' to 'ignore.case'
get.STRING.links: no visible binding for global variable 'genome.info'
get.STRING.links: no visible binding for global variable 'ratios'
get.STRING.links: no visible binding for global variable 'rsat.species'
get.STRING.links: warning in read.delim(paste("data/", rsat.species,
  "/string_links_FALSE_", org.id, ".tab", sep = ""), head = T, sep = "
  "): partial argument match of 'head' to 'header'
get.STRING.links : proc.string.df: warning in read.delim(file, head =
  F, sep = ""): partial argument match of 'head' to 'header'
get.STRING.links : proc.string.df: no visible binding for global
  variable 'combined_score'
get.all.scores: no visible binding for global variable 'k.clust'
get.all.scores: no visible binding for global variable 'row.scaling'
get.all.scores: no visible binding for global variable 'iter'
get.all.scores: no visible binding for global variable 'row.iters'
get.all.scores: no visible binding for global variable 'ratios'
get.all.scores: no visible binding for global variable 'row.weights'
get.all.scores: no visible binding for global variable 'row.memb'
get.all.scores: no visible binding for global variable
  'n.clust.per.col'
get.all.scores: no visible binding for global variable 'col.iters'
get.all.scores: no visible binding for global variable 'col.memb'
get.all.scores: no visible binding for global variable 'mot.weights'
get.all.scores: no visible binding for global variable 'mot.scaling'
get.all.scores: no visible binding for global variable 'meme.iters'
get.all.scores: no visible binding for global variable 'no.genome.info'
get.all.scores: no visible binding for global variable 'mot.iters'
get.all.scores: no visible binding for global variable 'net.scaling'
get.all.scores: no visible binding for global variable 'net.iters'
get.all.scores: no visible binding for global variable 'networks'
get.all.scores: no visible binding for global variable 'net.weights'
get.all.scores: no visible binding for global variable 'protein1'
get.all.scores: no visible binding for global variable 'protein2'
get.clust: no visible binding for global variable 'mot.weights'
get.clust : gen.clust: no visible binding for global variable 'ratios'
get.clust : gen.clust: no visible binding for global variable
  'row.weights'
get.clust: no visible binding for global variable 'n.motifs'
get.cluster.matrix: no visible binding for global variable 'ratios'
get.clusterStack: no visible binding for global variable 'k.clust'
get.clusterStack: no visible binding for global variable 'iter'
get.col.scores: no visible global function definition for
  'get.row.weights'
get.col.scores: no visible binding for global variable 'cols'
get.cols: warning in which(cm[] == k, arr = T): partial argument match
  of 'arr' to 'arr.ind'
get.combined.scores: no visible binding for global variable
  'row.scores'
get.combined.scores: no visible binding for global variable
  'mot.scores'
get.combined.scores: no visible binding for global variable
  'net.scores'
get.combined.scores: no visible binding for global variable
  'col.scores'
get.combined.scores: no visible binding for global variable
  'row.scaling'
get.combined.scores: no visible binding for global variable 'iter'
get.combined.scores: no visible binding for global variable
  'mot.scaling'
get.combined.scores: no visible binding for global variable
  'net.scaling'
get.density.scores: no visible binding for global variable 'k.clust'
get.density.scores: no visible binding for global variable 'ratios'
get.density.scores: no visible binding for global variable 'r.scores'
get.density.scores : get.rr.scores: no visible binding for global
  variable 'ratios'
get.density.scores: no visible binding for global variable 'row.scores'
get.density.scores: no visible binding for global variable 'col.scores'
get.density.scores: no visible binding for global variable 'c.scores'
get.density.scores : get.cc.scores: no visible binding for global
  variable 'ratios'
get.gene.coords: no visible binding for global variable 'genome.info'
get.genome.info: no visible binding for global variable 'rsat.urls'
get.genome.info: no visible binding for global variable 'rsat.species'
get.genome.info: warning in read.delim(gzfile(fname), head = F, as.is =
  T, skip = nskip): partial argument match of 'head' to 'header'
get.genome.info: no visible binding for global variable
  'no.genome.info'
get.genome.info: warning in read.delim(gzfile(fname), skip = nskip,
  head = F, comment = "", as.is = F): partial argument match of 'head'
  to 'header'
get.genome.info: warning in read.delim(gzfile(fname), skip = nskip,
  head = F, comment = "", as.is = F): partial argument match of
  'comment' to 'comment.char'
get.genome.info: warning in read.delim(gzfile(fname), head = F, as.is =
  T, skip = nskip, row.names = NULL, comment = ""): partial argument
  match of 'head' to 'header'
get.genome.info: warning in read.delim(gzfile(fname), head = F, as.is =
  T, skip = nskip, row.names = NULL, comment = ""): partial argument
  match of 'comment' to 'comment.char'
get.genome.info: no visible binding for global variable 'mot.iters'
get.genome.info: no visible binding for global variable 'contig'
get.genome.info: no visible binding for global variable 'ratios'
get.long.names: no visible binding for global variable 'genome.info'
get.long.names : <anonymous>: no visible binding for global variable
  'genome.info'
get.long.names : <anonymous>: no visible binding for global variable
  'id'
get.motif.scores: no visible binding for global variable 'ratios'
get.motif.scores: no visible binding for global variable 'meme.scores'
get.network.scores: no visible binding for global variable 'networks'
get.network.scores: no visible binding for global variable 'ratios'
get.operon.predictions: no visible binding for global variable
  'genome.info'
get.operon.predictions: no visible binding for global variable
  'rsat.urls'
get.operon.predictions: no visible binding for global variable
  'rsat.species'
get.operon.predictions: no visible binding for global variable
  'taxon.id'
get.operon.predictions: no visible binding for global variable 'bOp'
get.operon.predictions: no visible binding for global variable
  'SysName1'
get.operon.predictions: no visible binding for global variable
  'SysName2'
get.operon.predictions: no visible binding for global variable 'ratios'
get.operon.predictions : <anonymous> : <anonymous>: no visible binding
  for global variable 'genome.info'
get.parallel: no visible binding for global variable 'k.clust'
get.parallel : out.apply: no visible binding for global variable 'l'
get.row.scores: no visible global function definition for
  'get.col.weights'
get.rows: warning in which(rm[] == k, arr = T): partial argument match
  of 'arr' to 'arr.ind'
get.sequences: no visible binding for global variable
  'motif.upstream.search'
get.sequences: no visible binding for global variable 'genome.info'
get.sequences: no visible binding for global variable 'operon.shift'
get.sequences: no visible binding for global variable 'start_pos'
get.sequences: no visible binding for global variable 'end_pos'
get.sequences: no visible binding for global variable 'name'
get.sequences : <anonymous>: no visible binding for global variable
  'genome.info'
get.stats: no visible binding for global variable 'old.row.membership'
get.stats: no visible binding for global variable 'row.memb'
get.stats : <anonymous>: no visible binding for global variable
  'k.clust'
get.stats: no visible binding for global variable 'clusterStack'
get.stats: no visible binding for global variable 'iter'
get.stats: no visible binding for global variable 'row.scores'
get.stats: no visible binding for global variable 'col.scores'
get.stats: no visible binding for global variable 'col.memb'
get.stats: no visible binding for global variable 'mot.scores'
get.stats: no visible binding for global variable 'net.scores'
get.stats: no visible binding for global variable 'row.weights'
get.stats: no visible binding for global variable 'mot.weights'
get.stats: no visible binding for global variable 'networks'
get.stats: no visible binding for global variable 'net.weights'
get.stats: no visible binding for global variable 'cluster.net.scores'
get.synonyms: no visible binding for global variable 'genome.info'
get.synonyms: no visible binding for global variable 'no.genome.info'
get.synonyms: no visible binding for global variable 'translation.tab'
get.synonyms : <anonymous>: warning in grepl(greg, id, perl = T, ignore
  = ignore.case): partial argument match of 'ignore' to 'ignore.case'
get.synonyms : <anonymous>: no visible binding for global variable 'id'
get.synonyms : <anonymous>: warning in grepl(greg, names, perl = T,
  ignore = ignore.case): partial argument match of 'ignore' to
  'ignore.case'
get.unpreprocessed.ratios: no visible binding for global variable
  'ratios.raw'
get.updated.memberships: no visible binding for global variable
  'rr.scores'
get.updated.memberships: no visible binding for global variable
  'n.clust.per.row'
get.updated.memberships: no visible binding for global variable
  'max.changes'
get.updated.memberships: no visible binding for global variable
  'maintain.seed'
get.updated.memberships: no visible binding for global variable
  'cc.scores'
get.updated.memberships: no visible binding for global variable
  'n.clust.per.col'
id.duplicate.clusters: no visible binding for global variable
  'r.scores'
id.duplicate.clusters: warning in which(cors >= cor.cutoff, arr = T):
  partial argument match of 'arr' to 'arr.ind'
load.sif.interactions: warning in read.delim(gzfile(sif.fname), sep =
  "", head = F, comment = "#"): partial argument match of 'head' to
  'header'
load.sif.interactions: warning in read.delim(gzfile(sif.fname), sep =
  "", head = F, comment = "#"): partial argument match of 'comment' to
  'comment.char'
make.pv.ev.matrix: no visible binding for global variable 'k.clust'
meme.one.cluster: no visible binding for global variable 'mot.weights'
meme.one.cluster: no visible binding for global variable 'meme.cmd'
meme.one.cluster: no visible binding for global variable 'n.motifs'
meme.one.cluster: no visible binding for global variable 'iter'
meme.one.cluster : get.meme.consensus: no visible binding for global
  variable 'iter'
meme.one.cluster: no visible binding for global variable 'meme.scores'
meme.one.cluster: no visible binding for global variable 'bg.order'
meme.one.cluster: no visible binding for global variable
  'motif.upstream.scan'
meme.one.cluster: no visible binding for global variable
  'cluster.rows.allowed'
meme.one.cluster: no visible binding for global variable 'recalc.bg'
meme.one.cluster: warning in my.tempfile("meme.tmp", suf = ".bg"):
  partial argument match of 'suf' to 'suffix'
meme.one.cluster: no visible binding for global variable 'mast.cmd'
mkBgFile : <anonymous>: warning in grep("N", names(counts), val = T,
  invert = T): partial argument match of 'val' to 'value'
mkTempMemeFiles: no visible binding for global variable 'mot.weights'
mkTempMemeFiles: no visible binding for global variable 'meme.cmd'
motif.all.clusters: no visible binding for global variable 'k.clust'
motif.all.clusters: no visible binding for global variable
  'mot.weights'
motif.all.clusters: no visible binding for global variable
  'meme.scores'
motif.all.clusters : <anonymous>: no visible binding for global
  variable 'l'
motif.all.clusters: no visible binding for global variable 'iter'
motif.one.cluster: no visible binding for global variable 'mot.weights'
plotClust: no visible binding for global variable 'organism'
plotClust: no visible binding for global variable 'mot.weights'
plotClust: no visible binding for global variable 'meme.scores'
plotClust: no visible binding for global variable 'mot.iters'
plotClust: no visible binding for global variable 'no.genome.info'
plotClust: no visible binding for global variable 'motif.upstream.scan'
plotClust: no visible binding for global variable 'net.iters'
plotClust: no visible binding for global variable 'networks'
plotClust: warning in get.long.names(rows, short = short.names):
  partial argument match of 'short' to 'shorter'
plotClust: no visible binding for global variable 'genome.info'
plotCluster: no visible binding for global variable 'ratios'
plotCluster: no visible binding for global variable 'organism'
plotCluster: warning in rect(ind, range.r[1] + 0.05, ind +
  sum(colnames(rats) %in% colnames(ratios[[rats.names[i]]])),
  range.r[2] - 0.05, col = col, dens = NA): partial argument match of
  'dens' to 'density'
plotCluster: no visible binding for global variable 'col.rug'
plotCluster.all.conds: no visible binding for global variable 'ratios'
plotCluster.all.conds: no visible binding for global variable
  'organism'
plotCluster.all.conds: no visible global function definition for
  'grey.image'
plotCluster.all.conds: warning in rect(ind, range.r[1] + 0.01, ind +
  sum(cols %in% colnames(ratios[[i]])), range.r[2] - 0.01, col = col,
  dens = NA): partial argument match of 'dens' to 'density'
plotCluster.all.conds: no visible binding for global variable 'col.rug'
plotCluster.motif: no visible binding for global variable 'ratios'
plotCluster.motif: no visible binding for global variable 'organism'
plotCluster.motif: no visible binding for global variable
  'cmonkey.version'
plotCluster.motif: no visible binding for global variable 'date.run'
plotCluster.motif: no visible binding for global variable 'iter'
plotCluster.network: no visible binding for global variable 'networks'
plotCluster.network: no visible binding for global variable
  'genome.info'
plotCluster.network: no visible binding for global variable 'protein1'
plotCluster.network: no visible binding for global variable 'protein2'
plotCluster.network: warning in get.long.names(get.vertex.attribute(gr,
  "name"), short = T): partial argument match of 'short' to 'shorter'
plotCluster.network: no visible binding for global variable 'organism'
plotClusterMotifPositions: no visible binding for global variable
  'organism'
plotClusterMotifPositions: no visible binding for global variable
  'gene'
plotClusterMotifPositions: no visible binding for global variable
  'genome.info'
plotClusterMotifPositions: no visible binding for global variable
  'motif.upstream.search'
plotClusterMotifPositions: no visible binding for global variable
  'row.scores'
plotClusterMotifPositions: no visible binding for global variable
  'rr.scores'
plotClusterMotifPositions: no visible binding for global variable
  'motif.upstream.scan'
plotClusterMotifPositions: no visible binding for global variable
  'posns'
plotClusterMotifPositions: no visible binding for global variable
  'all.tfs'
plotScores: no visible binding for global variable 'row.membership'
plotScores: no visible binding for global variable 'ratios'
plotScores: no visible binding for global variable 'row.scores'
plotScores: no visible binding for global variable 'mot.scores'
plotScores: no visible binding for global variable 'no.genome.info'
plotScores: no visible binding for global variable 'net.scores'
plotStats: no visible binding for global variable 'row.membership'
plotStats : <anonymous>: no visible binding for global variable
  'k.clust'
plotStats: warning in matplot(stats[, "iter"], stats[, grep("resid",
  colnames(stats), val = T)], typ = "l", xlab = "iter", ylab = "Mean
  resid", main = sprintf("Iter: %d", iter), lty = 1): partial argument
  match of 'typ' to 'type'
plotStats: warning in grep("resid", colnames(stats), val = T): partial
  argument match of 'val' to 'value'
plotStats : <anonymous>: warning in grep("resid", colnames(stats), val
  = T): partial argument match of 'val' to 'value'
plotStats: no visible binding for global variable 'row.scores'
plotStats: no visible binding for global variable 'mot.scores'
plotStats: warning in grep("p.clust", colnames(stats), val = T):
  partial argument match of 'val' to 'value'
plotStats: warning in matplot(stats[, "iter"], tmp, typ = "l", xlab =
  "iter", ylab = "Mean motif p-value", main = sprintf("Motif scaling:
  %.3f", mot.scaling[max(1, iter - 1)]), lty = 1): partial argument
  match of 'typ' to 'type'
plotStats: no visible binding for global variable 'mot.scaling'
plotStats: no visible binding for global variable 'net.scores'
plotStats: warning in grep("net.", colnames(stats), val = T, fixed =
  T): partial argument match of 'val' to 'value'
plotStats: warning in matplot(stats[, "iter"], tmp, typ = "l", xlab =
  "iter", ylab = "Mean net-score", main = sprintf("Net scaling: %.3f",
  net.scaling[max(1, iter - 1)]), lty = 1): partial argument match of
  'typ' to 'type'
plotStats: no visible binding for global variable 'net.scaling'
plotStats: warning in grep("net.", colnames(stats), val = T): partial
  argument match of 'val' to 'value'
plotStats: no visible binding for global variable 'k.clust'
plotStats : plot.all.clusterMotifPositions: no visible binding for
  global variable 'k.clust'
plotStats : plot.all.clusterMotifPositions: no visible binding for
  global variable 'mot.weights'
plotStats : plot.all.clusterMotifPositions: no visible binding for
  global variable 'meme.scores'
plotStats : plot.all.clusterMotifPositions: no visible binding for
  global variable 'genome.info'
plotStats : plot.all.clusterMotifPositions: no visible binding for
  global variable 'motif.upstream.scan'
plotStats: no visible binding for global variable 'meme.scores'
plotStats: no visible binding for global variable 'col.membership'
plotStats: no visible binding for global variable 'ratios'
quantile.normalize.scores: warning in rank(scores[[n]][, ], ties =
  "min", na = "keep"): partial argument match of 'na' to 'na.last'
quantile.normalize.scores: warning in rank(scores[[n]][, ], ties =
  "min", na = "keep"): partial argument match of 'ties' to
  'ties.method'
remove.low.complexity: no visible binding for global variable
  'mot.weights'
remove.low.complexity: no visible binding for global variable
  'meme.cmd'
remove.low.complexity: warning in my.tempfile("dust", suf = ".fst"):
  partial argument match of 'suf' to 'suffix'
remove.low.complexity: no visible binding for global variable
  'dust.cmd'
runMast: warning in my.tempfile("mast.tmp", suf = ".fst"): partial
  argument match of 'suf' to 'suffix'
runMast: warning in my.tempfile("mast.tmp", suf = ".bg"): partial
  argument match of 'suf' to 'suffix'
runMast: warning in my.tempfile("meme.tmp", suf = ".out"): partial
  argument match of 'suf' to 'suffix'
runMeme: no visible binding for global variable 'meme.cmd'
runMeme: no visible binding for global variable 'mot.weights'
runMeme: warning in my.tempfile("meme.tmp", suf = ".fst"): partial
  argument match of 'suf' to 'suffix'
runMeme: warning in my.tempfile("meme.tmp", suf = ".bg"): partial
  argument match of 'suf' to 'suffix'
save.cmonkey.env: warning in ls(env = globalenv()): partial argument
  match of 'env' to 'envir'
seed.clusters: no visible global function definition for
  'seed.clusters.custom'
seed.clusters: no visible binding for global variable 'networks'
seed.clusters: no visible binding for global variable 'ratios'
seed.clusters : <anonymous>: no visible binding for global variable
  'n.clust.per.row'
seed.clusters : <anonymous>: no visible binding for global variable
  'ratios'
seed.clusters: no visible binding for global variable 'n.clust.per.row'
seed.clusters : <anonymous>: no visible binding for global variable
  'n.clust.per.col'
set.param: no visible binding for global variable 'cmonkey.params'
viewPssm: no visible binding for global variable 'colMap'
viewPssm: no visible binding for global variable 'colLet'
write.project: no visible binding for global variable 'mot.weights'
write.project: no visible binding for global variable
  'cmonkey.filename'
write.project: no visible binding for global variable 'iter'
write.project: no visible binding for global variable 'n.iter'
write.project : <anonymous>: warning in get.long.names(rows, short =
  T): partial argument match of 'short' to 'shorter'
write.project : <anonymous>: warning in get.long.names(rows, short =
  F): partial argument match of 'short' to 'shorter'
write.project : <anonymous>: warning in grep("^NP_", refseq.names, val
  = T): partial argument match of 'val' to 'value'
write.project : <anonymous>: no visible binding for global variable
  'meme.scores'
write.project : <anonymous>: no visible binding for global variable
  'cmonkey.filename'
write.project : <anonymous>: no visible binding for global variable
  'rsat.species'
write.project: warning in get.parallel(length(ks), para = 1): partial
  argument match of 'para' to 'para.cores'
write.project: no visible binding for global variable 'meme.scores'
write.project: no visible binding for global variable 'k.clust'
write.project: no visible binding for global variable 'no.genome.info'
write.project : <anonymous>: warning in get.long.names(rows[[k]], short
  = T): partial argument match of 'short' to 'shorter'
write.project : <anonymous>: warning in get.long.names(rows[[k]], short
  = F): partial argument match of 'short' to 'shorter'
write.project: no visible binding for global variable 'cmonkey.params'
write.project: warning in list.files(paste(out.dir, "/svgs", sep = ""),
  full = T): partial argument match of 'full' to 'full.names'
write.project: warning in list.files(sprintf("%s/htmls", out.dir),
  pattern = glob2rx("*.html"), full = T): partial argument match of
  'full' to 'full.names'
write.project: warning in list.files(out.dir, pattern =
  glob2rx("*.html"), full = T): partial argument match of 'full' to
  'full.names'
* checking Rd files ... NOTE
prepare_Rd: cMonkey-package.Rd:37-39: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
NOTE: There were 3 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/cMonkey.Rcheck/00check.log'
for details.