Check results for 'cMonkey'

using R version 2.15.1 (2012-06-22)
using platform: i386-apple-darwin9.8.0 (32-bit)
using session charset: ASCII
checking for file 'cMonkey/DESCRIPTION' ... OK
checking extension type ... Package
this is package 'cMonkey' version '4.9.2'
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... 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 for sufficient/correct file permissions ... 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 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 'k.clust'
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'
clusters.w.conds: no visible binding for global variable 'k.clust'
clusters.w.conds : <anonymous>: no visible binding for global variable
'p.val'
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 'p.val'
clusters.w.func: no visible binding for global variable 'ratios'
clusters.w.func: no visible binding for global variable 'short'
clusters.w.func : <anonymous>: no visible binding for global variable
'short'
clusters.w.func : <anonymous>: no visible binding for global variable
'p.val'
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
'p.val'
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 'no.genome.info'
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 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 global function definition for
'load.sif.interactions'
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: no visible binding for global variable 'plot.iters'
cmonkey.init : favorite.cluster: no visible binding for global variable
'k.clust'
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 'k.clust'
cmonkey.one.iter : <anonymous>: no visible binding for global variable
'ratios'
cmonkey.one.iter: no visible binding for global variable 'ratios'
cmonkey.one.iter: no visible binding for global variable 'stats.iters'
cmonkey.one.iter: no visible binding for global variable 'organism'
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'
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 'rsat.species'
get.STRING.links: no visible global function definition for
'get.string.links.NEW'
get.STRING.links.NEW: no visible binding for global variable
'genome.info'
get.STRING.links.NEW: no visible binding for global variable 'ratios'
get.STRING.links.NEW: no visible binding for global variable
'rsat.species'
get.STRING.links.NEW : 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 'ratios'
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 : <anonymous>: 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
'n.clust.per.col'
get.all.scores: no visible binding for global variable 'col.iters'
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.cols: no visible binding for global variable 'clusterStack'
get.cols: no visible binding for global variable 'ratios'
get.combined.scores: no visible binding for global variable
'row.scores'
get.combined.scores: no visible binding for global variable 'k.clust'
get.combined.scores : <anonymous>: no visible binding for global
variable 'ratios'
get.combined.scores: no visible binding for global variable 'ratios'
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 : 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 : get.cc.scores: no visible binding for global
variable 'ratios'
get.gene.coords: no visible binding for global variable 'genome.info'
get.gene.coords: no visible binding for global variable 'organism'
get.gene.regex: no visible binding for global variable 'ratios'
get.gene.regex: no visible binding for global variable 'type'
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.weights'
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
'synonym.thesaurus'
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 '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: no visible binding for global variable 'clusterStack'
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 'id'
get.sequences : <anonymous>: no visible binding for global variable
'genome.info'
get.stats: no visible binding for global variable 'k.clust'
get.stats : <anonymous>: no visible binding for global variable
'ratios'
get.stats: no visible binding for global variable 'ratios'
get.stats: no visible global function definition for
'get.old.scores.matrices'
get.stats: no visible binding for global variable 'clusterStack'
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
'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
'n.clust.per.col'
id.duplicate.clusters: no visible binding for global variable
'r.scores'
load.genome.info.MicrobesOnline: no visible binding for global variable
'taxon.id'
load.genome.info.MicrobesOnline: no visible binding for global variable
'rsat.species'
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'
motif.one.cluster: no visible binding for global variable 'meme.scores'
operon.list: no visible binding for global variable 'genome.info'
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
'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.scores'
plotScores: no visible global function definition for
'get.old.scores.matrices'
plotScores: no visible binding for global variable 'ratios'
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 'k.clust'
plotStats : <anonymous>: no visible binding for global variable
'ratios'
plotStats: no visible binding for global variable 'ratios'
plotStats: no visible global function definition for
'get.old.scores.matrices'
plotStats: no visible binding for global variable 'mot.scaling'
plotStats: no visible binding for global variable 'net.scaling'
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'
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'
row.col.membership.from.clusterStack: no visible binding for global
variable 'ratios'
row.col.membership.from.clusterStack: no visible binding for global
variable 'n.clust.per.row'
row.col.membership.from.clusterStack: no visible binding for global
variable 'n.clust.per.col'
runMeme: no visible binding for global variable 'meme.cmd'
runMeme: no visible binding for global variable 'mot.weights'
save.cmonkey.env: no visible binding for global variable 'env'
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'
set.param: no visible binding for global variable 'env'
update.all.clusters: no visible binding for global variable 'k.clust'
update.all.clusters : <anonymous>: no visible binding for global
variable 'ratios'
update.all.clusters: no visible binding for global variable 'ratios'
update.all.clusters: no visible binding for global variable
'row.scaling'
update.all.clusters: no visible binding for global variable
'fuzzy.index'
update.all.clusters: no visible binding for global variable
'col.scores'
update.all.clusters : size.compensation.func.rows: no visible binding
for global variable 'ratios'
update.all.clusters : size.compensation.func.rows: no visible binding
for global variable 'n.clust.per.row'
update.all.clusters : size.compensation.func.rows: no visible binding
for global variable 'k.clust'
update.all.clusters : size.compensation.func.cols: no visible binding
for global variable 'ratios'
update.all.clusters : size.compensation.func.cols: no visible binding
for global variable 'n.clust.per.col'
update.all.clusters : size.compensation.func.cols: no visible binding
for global variable 'k.clust'
update.all.clusters: no visible binding for global variable
'cluster.rows.allowed'
viewPssm: no visible binding for global variable 'e.val'
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: 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 ... OK
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
NOTE: There was 1 note.
See
'/Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/results/2.15/cMonkey.Rcheck/00check.log'
for details.
elapsed time (check, wall clock): 0:39