* using log directory 'd:/Rcompile/CRANpkg/local/2.12/cMonkey.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-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 name space information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking:
  doMC multicore
* checking if this is a source package ... OK
* checking whether package 'cMonkey' can be installed ... 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
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 '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>: no visible binding for global variable
  'ratios'
clusters.w.func: no visible binding for global variable 'k.clust'
clusters.w.func: no visible binding for global variable 'ratios'
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>: no visible binding for global variable
  'ratios'
cmonkey: no visible binding for global variable 'dont.init'
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: no visible binding for global variable 'V2'
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: 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: 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 : 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: 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.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 : 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 '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.col.scores: no visible global function definition for
  'get.row.weights'
get.col.scores: no visible binding for global variable 'cols'
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
  '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: no visible binding for global variable
  'no.genome.info'
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.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 '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>: no visible binding for global variable 'id'
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'
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 '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: no visible binding for global variable 'mast.cmd'
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.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: 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: 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: 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.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: 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: no visible binding for global variable 'row.scores'
plotStats: no visible binding for global variable 'mot.scores'
plotStats: no visible binding for global variable 'mot.scaling'
plotStats: no visible binding for global variable 'net.scores'
plotStats: no visible binding for global variable 'net.scaling'
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'
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: no visible binding for global variable
  'dust.cmd'
runMeme: no visible binding for global variable 'meme.cmd'
runMeme: no visible binding for global variable 'mot.weights'
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 'n.iter'
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 : <anonymous>: possible error in
  png(sprintf("%s/htmls/cluster%04d_profile.png", out.dir, k), width =
  128, height = 64, antialias = "subpixel"): unused argument(s)
  (antialias = "subpixel")
write.project : <anonymous>: possible error in
  png(sprintf("%s/htmls/cluster%04d_network.png", out.dir, k), width =
  64, height = 64, antialias = "subpixel"): unused argument(s)
  (antialias = "subpixel")
write.project : <anonymous>: possible error in
  png(sprintf("%s/htmls/cluster%04d_pssm%d.png", out.dir, k, pp), width
  = 128, height = 64, antialias = "subpixel"): unused argument(s)
  (antialias = "subpixel")
write.project : <anonymous>: possible error in
  png(sprintf("%s/htmls/cluster%04d_mot_posns.png", out.dir, k), width
  = 128, height = 12 + 6 * length(get.rows(k)), antialias =
  "subpixel"): unused argument(s) (antialias = "subpixel")
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: no visible binding for global variable 'cmonkey.params'
* 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 ... OK
* checking PDF version of manual ... OK