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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MmPalateMiRNA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MmPalateMiRNA_1.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/MmPalateMiRNA.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MmPalateMiRNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MmPalateMiRNA’ version ‘1.40.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Biobase', 'xtable', 'limma', 'statmod', 'lattice', 'vsn'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MmPalateMiRNA’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'MmPalateMiRNA' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/MmPalateMiRNA.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘limma’ ‘lattice’ ‘Biobase’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘methods’ ‘statmod’ ‘vsn’ ‘xtable’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
clustPlot: no visible global function definition for ‘par’
clustPlot: no visible global function definition for ‘axis’
clustPlot: no visible global function definition for ‘lines’
clustPlot: no visible global function definition for ‘legend’
fixOutliers : <anonymous>: no visible global function definition for
‘sd’
imputeKNN: no visible global function definition for ‘sd’
imputeKNN: no visible global function definition for ‘cor’
MADvsMedianPlot,list : <anonymous>: no visible global function
definition for ‘RG.MA’
MADvsMedianPlot,list : <anonymous>: no visible global function
definition for ‘assayData’
MADvsMedianPlot,list : <anonymous>: no visible binding for global
variable ‘mad’
MADvsMedianPlot,list : <anonymous>: no visible binding for global
variable ‘median’
MADvsMedianPlot,list: no visible global function definition for ‘stack’
MADvsMedianPlot,list : <anonymous>: no visible global function
definition for ‘pData’
MADvsMedianPlot,list : <anonymous>: no visible global function
definition for ‘featureData’
MAplot,MAList: no visible global function definition for ‘stack’
MAplot,NChannelSet: no visible global function definition for
‘assayData’
MAplot,NChannelSet: no visible global function definition for ‘stack’
checkOutliers,RGList: no visible binding for global variable ‘sd’
densityplot,RGList-missing: no visible global function definition for
‘as.formula’
densityplot,list-missing : <anonymous>: no visible global function
definition for ‘RG.MA’
densityplot,list-missing : <anonymous>: no visible global function
definition for ‘assayData’
densityplot,list-missing : <anonymous>: no visible global function
definition for ‘pData’
densityplot,list-missing : <anonymous>: no visible global function
definition for ‘featureData’
densityplot,list-missing: no visible global function definition for
‘as.formula’
levelplot,RGList-missing: no visible global function definition for
‘median’
levelplot,list-missing : <anonymous>: no visible global function
definition for ‘RG.MA’
levelplot,list-missing : <anonymous>: no visible global function
definition for ‘assayData’
levelplot,list-missing: no visible global function definition for
‘median’
Undefined global functions or variables:
RG.MA as.formula assayData axis cor featureData legend lines mad
median pData par sd stack
Consider adding
importFrom("graphics", "axis", "legend", "lines", "par")
importFrom("stats", "as.formula", "cor", "mad", "median", "sd")
importFrom("utils", "stack")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MmPalateMiRNA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fixMVs
> ### Title: 'Fix' an 'RGList' object with missing values.
> ### Aliases: fixMVs
> ### Keywords: manip
>
> ### ** Examples
>
> data(PalateData)
> mvs <- checkMVs(PalateData)
> PalateData$Rb <- fixMVs(PalateData$Rb, mvs$Rb.na, PalateData$genes$Gene)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
MmPalateMiRNA
--- call from context ---
fixMVs(PalateData$Rb, mvs$Rb.na, PalateData$genes$Gene)
--- call from argument ---
if (class(mat) != "matrix") {
stop("'mat' needs to be an 'matrix'")
}
--- R stacktrace ---
where 1: fixMVs(PalateData$Rb, mvs$Rb.na, PalateData$genes$Gene)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (mat, idx, gene.ids)
{
if (class(mat) != "matrix") {
stop("'mat' needs to be an 'matrix'")
}
gene.out <- gene.ids[idx]
col.out <- apply(mat[idx, ], 1, function(x) which(is.na(x)))
mean.vals <- vector("list", length(gene.out))
for (i in 1:length(gene.out)) {
mvals <- numeric(length(col.out[[i]]))
for (j in seq_along(col.out[[i]])) {
values <- mat[which(gene.ids == gene.out[i]), col.out[[i]][j]]
mvals[j] <- mean(values[-which(is.na(values))])
}
mean.vals[[i]] <- mvals
}
idxs <- cbind(rep(idx, sapply(col.out, length)), unlist(col.out))
mat[idxs] <- unlist(mean.vals)
return(mat)
}
<bytecode: 0x7f88219a9230>
<environment: namespace:MmPalateMiRNA>
--- function search by body ---
Function fixMVs in namespace MmPalateMiRNA has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/MmPalateMiRNA.Rcheck/00check.log’
for details.