Check results for 'FunNet'

using R version 2.14.1 Patched (2012-02-05 r58287)
using platform: i686-pc-linux-gnu (32-bit)
using session charset: UTF-8
checking for file ‘FunNet/DESCRIPTION’ ... OK
this is package ‘FunNet’ version ‘1.00-12’
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... NOTE
As from R 2.14.0 all packages need a namespace.
One will be generated on installation, but it is better to handcraft a
NAMESPACE file: R CMD build will produce a suitable starting point.
checking for executable files ... OK
checking whether package ‘FunNet’ can be installed ... OK
checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
R 5.1Mb
data 1.4Mb
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 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
File ‘FunNet/R/FunNet.R’:
.First.lib calls:
cat(paste("\nThis is FunNet package ", .funnet.version, " built and maintained by Corneliu Henegar.\n", "Using Gene Ontology and KEGG annotations updated on ", annot.date, ".\n\n", "FunNet(wd='', org=c('hsa','mmu','rno','sce','gga','ath','dre','cel','dme'), two.lists=TRUE, up.frame=NULL,\n", "\t genes.frame=NULL, restrict=FALSE, ref.list=NULL, logged=FALSE,\n", "\t down.frame=NULL, discriminant=FALSE, go.bp=TRUE, go.cc=TRUE, go.mf=TRUE,\n", "\t kegg=TRUE, annot.method=c('specificity','terminological','decorrelated'),\n", "\t annot.details=TRUE, direct=FALSE, enriched=TRUE, fdr=5, build.annot.net=TRUE,\n", "\t coexp.matrix=NULL, coexp.method=c('spearman','pearson','kendall','euclid'),\n", "\t estimate.th=FALSE, hard.th=NA, soft.th=NA, topological = FALSE, keep.sign=FALSE,\n", "\t level=NA, annot.clust.method=c('umilds','ucknn'), annot.prox.measure=c('dynamical',\n", "\t 'unilat.pond.norm.mean','unilat.norm.sum','norm.sum','pond.norm.mean'),\n", "\t test.recovery=FALSE, test.robust=FALSE, replace.annot=NA,random.annot=FALSE,\n", "\t build.gene.net=FALSE, gene.clust.method='hclust', gene.net.details=FALSE,\n", "\t gene.clusters=NA, alpha=0.05, RV=0.90, sigma=NA, keep.rdata=FALSE, zip=TRUE)\n\n", sep = ""))

Package startup functions should use ‘packageStartupMessage’ to
generate messages.
See section ‘Good practice’ in ?.onAttach.

.MiseEnFormeKegg: warning in gl(1, NbKmap, label = LL): partial
argument match of 'label' to 'labels'
.MiseEnFormeKeggSC: warning in gl(1, NbKmap, label = LL): partial
argument match of 'label' to 'labels'
.central.plot.one: warning in CairoPNG(file = paste(extra, taxoname, "
Centrality.png", sep = ""), height = height, width = width, res =
600): partial argument match of 'file' to 'filename'
.central.plot.two: warning in CairoPNG(file = paste(extra, taxoname, "
Centrality.png", sep = ""), height = height, width = width, res =
600): partial argument match of 'file' to 'filename'
.compute.global.distances: warning in
dudi.pca(as.matrix(marker.matrix[[i]][, match(theme.mask,
colnames(marker.matrix[[i]]))]), scale = TRUE, scan = FALSE): partial
argument match of 'scan' to 'scannf'
.compute.global.distances: warning in
dudi.pca(as.matrix(marker.matrix[[i + 1]][, match(theme.mask,
colnames(marker.matrix[[i + 1]]))]), scale = TRUE, scan = FALSE):
partial argument match of 'scan' to 'scannf'
.compute.global.distances: warning in coinertia(dudi1, dudi2, scan =
FALSE, nf = 2): partial argument match of 'scan' to 'scannf'
.dynamic.proximity: warning in coinertia(xt, xtt, scan = FALSE, nf =
ncol(marker.matrix[[steps]])): partial argument match of 'scan' to
'scannf'
.pcor.mat: warning in cov(xdata, xdata, m = method): partial argument
match of 'm' to 'method'
.pcor.mat: warning in cov(xdata, zdata, m = method): partial argument
match of 'm' to 'method'
.pcor.mat: warning in cov(zdata, zdata, m = method): partial argument
match of 'm' to 'method'
.pcor.rec: warning in cor(tdata[, 1], tdata[, 2], m = method): partial
argument match of 'm' to 'method'
.profil.plot.one: warning in CairoPNG(file = paste(extra, taxoname, "
Level ", i, ".png", sep = ""), height = 0.85 * height, width = 0.85 *
width, res = 600): partial argument match of 'file' to 'filename'
.profil.plot.one: warning in CairoPNG(file = paste(extra, taxoname,
".png", sep = ""), height = 0.85 * height, width = 0.85 * width, res
= 600): partial argument match of 'file' to 'filename'
.profil.plot.two: warning in CairoPNG(file = paste(extra, taxoname, "
Level ", i, ".png", sep = ""), height = 0.85 * height, width = 0.85 *
width, res = 600): partial argument match of 'file' to 'filename'
.profil.plot.two: warning in CairoPNG(file = paste(extra, taxoname,
".png", sep = ""), height = 0.85 * height, width = 0.85 * width, res
= 600): partial argument match of 'file' to 'filename'
.prop.alt: warning in matrix(seq(from = adjustment.args$edf.lower, by =
stepsize, len = adjustment.args$num.steps), nr =
adjustment.args$num.steps, nc = 1): partial argument match of 'nr' to
'nrow'
.prop.alt: warning in matrix(seq(from = adjustment.args$edf.lower, by =
stepsize, len = adjustment.args$num.steps), nr =
adjustment.args$num.steps, nc = 1): partial argument match of 'nc' to
'ncol'
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 contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... OK
checking data for ASCII and uncompressed saves ... OK
checking R/sysdata.rda ... OK
checking examples ... OK
checking PDF version of manual ... OK