- using R Under development (unstable) (2012-08-11 r60235)
- using platform: x86_64-unknown-linux-gnu (64-bit)
- using session charset: UTF-8
- 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 ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... 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 loading without being on the library search path ... 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
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.func: warning in get.long.names(attr(ratios, "rnames"),
short = short): partial argument match of 'short' to 'shorter'
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.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'
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: 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: 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: warning in grepl(paste("^", prefix, sep = ""), names,
ignore = T, perl = T): partial argument match of 'ignore' to
'ignore.case'
cmonkey.init: warning in my.tempfile("meme.tmp", suf = ".bg"): partial
argument match of 'suf' to 'suffix'
cmonkey.init: warning in which(!is.na(tmp), arr = T): partial argument
match of 'arr' to 'arr.ind'
cmonkey.one.iter: warning in get.combined.scores(quant = T): partial
argument match of 'quant' to 'quantile.normalize'
get.COG.code : <anonymous>: warning in get.synonyms(gn, ignore = T):
partial argument match of 'ignore' to 'ignore.case'
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.cols: warning in which(cm[] == k, arr = T): partial argument match
of 'arr' to 'arr.ind'
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: 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.rows: warning in which(rm[] == k, arr = T): partial argument match
of 'arr' to 'arr.ind'
get.synonyms : <anonymous>: warning in grepl(greg, id, perl = T, ignore
= ignore.case): partial argument match of 'ignore' to 'ignore.case'
get.synonyms : <anonymous>: warning in grepl(greg, names, perl = T,
ignore = ignore.case): partial argument match of 'ignore' to
'ignore.case'
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'
meme.one.cluster: warning in my.tempfile("meme.tmp", suf = ".bg"):
partial argument match of 'suf' to 'suffix'
mkBgFile : <anonymous>: warning in grep("N", names(counts), val = T,
invert = T): partial argument match of 'val' to 'value'
plotClust: warning in get.long.names(rows, short = short.names):
partial argument match of 'short' to 'shorter'
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.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.network: warning in get.long.names(get.vertex.attribute(gr,
"name"), short = T): partial argument match of 'short' to 'shorter'
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: 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: 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: warning in grep("net.", colnames(stats), val = T): partial
argument match of 'val' to 'value'
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: warning in my.tempfile("dust", suf = ".fst"):
partial argument match of 'suf' to 'suffix'
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: 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'
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: warning in get.parallel(length(ks), para = 1): partial
argument match of 'para' to 'para.cores'
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: 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'
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 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’
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: 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 ... [1s/1s] OK
- checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/cMonkey.Rcheck/00check.log’
for details.