* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/RNAinteract.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RNAinteract/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RNAinteract' version '1.4.0'
* 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 whether package 'RNAinteract' 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
computePValues: warning in matrix(NA, nr = n, nc = sgi@C): partial
argument match of 'nr' to 'nrow'
computePValues: warning in matrix(NA, nr = n, nc = sgi@C): partial
argument match of 'nc' to 'ncol'
computePValues: warning in matrix(NA, nr = maxid, nc = maxn): partial
argument match of 'nr' to 'nrow'
computePValues: warning in matrix(NA, nr = maxid, nc = maxn): partial
argument match of 'nc' to 'ncol'
getData: warning in matrix(NA, nr = maxid, nc = maxn): partial argument
match of 'nr' to 'nrow'
getData: warning in matrix(NA, nr = maxid, nc = maxn): partial argument
match of 'nc' to 'ncol'
normalizeMainEffectTemplate: warning in matrix(NA, nr = sgi@pdim[1], nc
= sgi@pdim[2]): partial argument match of 'nr' to 'nrow'
normalizeMainEffectTemplate: warning in matrix(NA, nr = sgi@pdim[1], nc
= sgi@pdim[2]): partial argument match of 'nc' to 'ncol'
normalizePlateEffect: warning in matrix(NA, nr = pdim[1], nc =
pdim[2]): partial argument match of 'nr' to 'nrow'
normalizePlateEffect: warning in matrix(NA, nr = pdim[1], nc =
pdim[2]): partial argument match of 'nc' to 'ncol'
normalizePlateEffect: warning in matrix(M$row, nr = pdim[1], nc =
pdim[2]): partial argument match of 'nr' to 'nrow'
normalizePlateEffect: warning in matrix(M$row, nr = pdim[1], nc =
pdim[2]): partial argument match of 'nc' to 'ncol'
normalizePlateEffect: warning in matrix(M$col, nr = pdim[2], nc =
pdim[1]): partial argument match of 'nr' to 'nrow'
normalizePlateEffect: warning in matrix(M$col, nr = pdim[2], nc =
pdim[1]): partial argument match of 'nc' to 'ncol'
reportDoublePerturbation: warning in png(width = png.args$width, height
= png.args$height, file = fn.png): partial argument match of 'file'
to 'filename'
reportDoublePerturbation: warning in matrix(fn.png, nr =
length(fn.png), nc = 1): partial argument match of 'nr' to 'nrow'
reportDoublePerturbation: warning in matrix(fn.png, nr =
length(fn.png), nc = 1): partial argument match of 'nc' to 'ncol'
reportGeneLists: warning in matrix(row.names(p.value), nr =
dim(p.value)[1], nc = dim(p.value)[2]): partial argument match of
'nr' to 'nrow'
reportGeneLists: warning in matrix(row.names(p.value), nr =
dim(p.value)[1], nc = dim(p.value)[2]): partial argument match of
'nc' to 'ncol'
reportGeneLists: warning in matrix(colnames(p.value), nr =
dim(p.value)[2], nc = dim(p.value)[1]): partial argument match of
'nr' to 'nrow'
reportGeneLists: warning in matrix(colnames(p.value), nr =
dim(p.value)[2], nc = dim(p.value)[1]): partial argument match of
'nc' to 'ncol'
reportGeneLists: warning in matrix(dup, nr = nrow(p.value), nc =
ncol(p.value)): partial argument match of 'nr' to 'nrow'
reportGeneLists: warning in matrix(dup, nr = nrow(p.value), nc =
ncol(p.value)): partial argument match of 'nc' to 'ncol'
reportHeatmap: warning in png(width = png.args$width, height =
png.args$height, file = fn.png): partial argument match of 'file' to
'filename'
reportMainEffects: warning in png(width = png.args$width, height =
png.args$height, file = fn.png): partial argument match of 'file' to
'filename'
reportMainEffects: warning in matrix(fn2.png, nr = length(fn2.png), nc
= 1): partial argument match of 'nr' to 'nrow'
reportMainEffects: warning in matrix(fn2.png, nr = length(fn2.png), nc
= 1): partial argument match of 'nc' to 'ncol'
reportMainEffects: warning in matrix(fn.png, nr = 1, nc = 1): partial
argument match of 'nr' to 'nrow'
reportMainEffects: warning in matrix(fn.png, nr = 1, nc = 1): partial
argument match of 'nc' to 'ncol'
reportNetworks: warning in matrix(NA, nr = K, nc = 2): partial argument
match of 'nr' to 'nrow'
reportNetworks: warning in matrix(NA, nr = K, nc = 2): partial argument
match of 'nc' to 'ncol'
reportNetworks: warning in matrix("", nr = K, nc = 1): partial argument
match of 'nr' to 'nrow'
reportNetworks: warning in matrix("", nr = K, nc = 1): partial argument
match of 'nc' to 'ncol'
reportNetworks: warning in png(width = 150, height = 150, file =
fn.png[k, 1]): partial argument match of 'file' to 'filename'
reportScreenData: warning in png(width = png.args$width, height =
png.args$height, file = fn.png): partial argument match of 'file' to
'filename'
reportScreenData: warning in pdf(width = pdf.args$width, height =
pdf.args$height, file = fn.pdf, maxRaster = 1024): partial argument
match of 'maxRaster' to 'maxRasters'
reportScreenData: warning in png(width = png.scatter.args$width, height
= png.scatter.args$height, file = fn.scatter.rep.png): partial
argument match of 'file' to 'filename'
reportScreenData: warning in png(width = png.scatter.args$width, height
= png.scatter.args$height, file = fn.scatter.ind.png): partial
argument match of 'file' to 'filename'
reportStatistics: warning in matrix("", nr = sgi@S * sgi@C *
length(neg), nc = 3): partial argument match of 'nr' to 'nrow'
reportStatistics: warning in matrix("", nr = sgi@S * sgi@C *
length(neg), nc = 3): partial argument match of 'nc' to 'ncol'
reportStatistics: warning in matrix("", nr = sgi@S * sgi@C *
length(neg), nc = length(pos)): partial argument match of 'nr' to
'nrow'
reportStatistics: warning in matrix("", nr = sgi@S * sgi@C *
length(neg), nc = length(pos)): partial argument match of 'nc' to
'ncol'
reportStatistics: warning in matrix(NA, nr = sgi@S * sgi@C *
length(neg), nc = length(pos)): partial argument match of 'nr' to
'nrow'
reportStatistics: warning in matrix(NA, nr = sgi@S * sgi@C *
length(neg), nc = length(pos)): partial argument match of 'nc' to
'ncol'
reportStatistics: warning in png(file =
sprintf("%s/%s/%s_data_%s_%s_%s_%s.png", path, dir, prefix, n, p, s,
c)): partial argument match of 'file' to 'filename'
reportStatistics: warning in png(file =
sprintf("%s/%s/%s_density_%s_%s_%s_%s.png", path, dir, prefix, n, p,
s, c)): partial argument match of 'file' to 'filename'
reportStatistics: warning in matrix("", nr = nrow(fn.data.pdf), nc =
3): partial argument match of 'nr' to 'nrow'
reportStatistics: warning in matrix("", nr = nrow(fn.data.pdf), nc =
3): partial argument match of 'nc' to 'ncol'
reportStatistics: warning in matrix("", nr = nrow(fn.density.pdf), nc =
3): partial argument match of 'nr' to 'nrow'
reportStatistics: warning in matrix("", nr = nrow(fn.density.pdf), nc =
3): partial argument match of 'nc' to 'ncol'
reportStatistics: warning in matrix(NA, nr = sgi@C, nc = sgi@S):
partial argument match of 'nr' to 'nrow'
reportStatistics: warning in matrix(NA, nr = sgi@C, nc = sgi@S):
partial argument match of 'nc' to 'ncol'
reportStatistics: warning in png(width = 400, height = 400, file =
sprintf("%s/%s/%s-repscatter-data-%s-%s.png", path, dir, prefix, s,
c)): partial argument match of 'file' to 'filename'
reportStatistics: warning in png(width = 400, height = 400, file =
sprintf("%s/%s/%s-indscatter-data-%s-%s.png", path, dir, prefix, s,
c)): partial argument match of 'file' to 'filename'
reportStatistics: warning in matrix(NA, nr = sgi@C, nc = sgi@S * (sgi@S
- 1)/2): partial argument match of 'nr' to 'nrow'
reportStatistics: warning in matrix(NA, nr = sgi@C, nc = sgi@S * (sgi@S
- 1)/2): partial argument match of 'nc' to 'ncol'
reportStatistics: warning in png(width = 400, height = 400, file =
sprintf("%s/%s/%s-betweenscatter-data-%s-%s-%s.png", path, dir,
prefix, s1, s2, c)): partial argument match of 'file' to 'filename'
reportStatistics: warning in matrix(c(M1, M2, M3), nr = 1, nc = 3):
partial argument match of 'nr' to 'nrow'
reportStatistics: warning in matrix(c(M1, M2, M3), nr = 1, nc = 3):
partial argument match of 'nc' to 'ncol'
reportStatistics: warning in matrix(c(M1, M2, ""), nr = 1, nc = 3):
partial argument match of 'nr' to 'nrow'
reportStatistics: warning in matrix(c(M1, M2, ""), nr = 1, nc = 3):
partial argument match of 'nc' to 'ncol'
reportStatistics: warning in png(width = 400, height = 400, file =
sprintf("%s/%s/%s-repscatter-pi-%s-%s.png", path, dir, prefix, s,
c)): partial argument match of 'file' to 'filename'
reportStatistics: warning in png(width = 400, height = 400, file =
sprintf("%s/%s/%s-indscatter-pi-%s-%s.png", path, dir, prefix, s,
c)): partial argument match of 'file' to 'filename'
reportStatistics: warning in png(width = 400, height = 400, file =
sprintf("%s/%s/%s-betweenscatter-pi-%s-%s-%s.png", path, dir, prefix,
s1, s2, c)): partial argument match of 'file' to 'filename'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There was 1 note.
See
'/Users/biocbuild/bbs-2.10-bioc/meat/RNAinteract.Rcheck/00check.log'
for details.