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CHECK report for MmPalateMiRNA on tokay2

This page was generated on 2020-10-17 11:57:10 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE MmPalateMiRNA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1111/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MmPalateMiRNA 1.38.0
Guy Brock
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/MmPalateMiRNA
Branch: RELEASE_3_11
Last Commit: 9b18d94
Last Changed Date: 2020-04-27 14:27:32 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR  OK 

Summary

Package: MmPalateMiRNA
Version: 1.38.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MmPalateMiRNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MmPalateMiRNA_1.38.0.tar.gz
StartedAt: 2020-10-17 06:10:22 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:11:45 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 83.7 seconds
RetCode: 1
Status:  ERROR  
CheckDir: MmPalateMiRNA.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MmPalateMiRNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MmPalateMiRNA_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MmPalateMiRNA.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MmPalateMiRNA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MmPalateMiRNA' version '1.38.0'
* 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 whether package 'MmPalateMiRNA' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MADvsMedianPlot.Rd:29: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MADvsMedianPlot.Rd:30: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MADvsMedianPlot.Rd:36: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MADvsMedianPlot.Rd:40: file link 'densityplot' in package 'lattice' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MADvsMedianPlot.Rd:49: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MADvsMedianPlot.Rd:50: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MAplot.Rd:29: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MAplot.Rd:30: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:29: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:33: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:34: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:35: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:36: file link 'lattice-package' in package 'lattice' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/checkMVs.Rd:9: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/checkMVs.Rd:13: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/checkMVs.Rd:22: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/checkOutliers.Rd:8: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/checkOutliers.Rd:13: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/checkOutliers.Rd:23: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/densityplot.Rd:32: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/densityplot.Rd:33: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/densityplot.Rd:34: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/densityplot.Rd:40: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/densityplot.Rd:44: file link 'densityplot' in package 'lattice' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/densityplot.Rd:51: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/densityplot.Rd:60: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/densityplot.Rd:61: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/filterArray.Rd:8: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/filterArray.Rd:12: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/filterArray.Rd:26: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/filterArray.Rd:57: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/levelplot.Rd:37: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/levelplot.Rd:38: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/levelplot.Rd:39: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/levelplot.Rd:45: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/levelplot.Rd:59: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/levelplot.Rd:68: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/levelplot.Rd:69: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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: 0x091ab338>
<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

** running examples for arch 'x64' ... 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: 0x0000000010d7c4c8>
<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: 2 ERRORs, 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/MmPalateMiRNA.Rcheck/00check.log'
for details.


Installation output

MmPalateMiRNA.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/MmPalateMiRNA_1.38.0.tar.gz && rm -rf MmPalateMiRNA.buildbin-libdir && mkdir MmPalateMiRNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MmPalateMiRNA.buildbin-libdir MmPalateMiRNA_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MmPalateMiRNA_1.38.0.zip && rm MmPalateMiRNA_1.38.0.tar.gz MmPalateMiRNA_1.38.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  506k  100  506k    0     0  7502k      0 --:--:-- --:--:-- --:--:-- 8310k

install for i386

* installing *source* package 'MmPalateMiRNA' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MmPalateMiRNA'
    finding HTML links ... done
    MADvsMedianPlot                         html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MADvsMedianPlot.Rd:29: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MADvsMedianPlot.Rd:30: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/MADvsMedianPlot.Rd:36: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
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    MAplot                                  html  
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    MmPalateMiRNA-package                   html  
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    PalateData                              html  
    finding level-2 HTML links ... done

    checkMVs                                html  
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    checkOutliers                           html  
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    clustPlot                               html  
    densityplot                             html  
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    filterArray                             html  
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    fixMVs                                  html  
    fixOutliers                             html  
    imputeKNN                               html  
    levelplot                               html  
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Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp4c3Gah/R.INSTALL1530e34c70/MmPalateMiRNA/man/levelplot.Rd:45: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
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** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MmPalateMiRNA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MmPalateMiRNA' as MmPalateMiRNA_1.38.0.zip
* DONE (MmPalateMiRNA)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MmPalateMiRNA' successfully unpacked and MD5 sums checked

Tests output


Example timings

MmPalateMiRNA.Rcheck/examples_i386/MmPalateMiRNA-Ex.timings

nameusersystemelapsed
MADvsMedianPlot1.070.061.13
MAplot0.670.050.72
PalateData0.080.000.08
checkMVs0.160.010.17
checkOutliers0.730.000.74
clustPlot0.280.020.29
densityplot0.710.050.75
filterArray0.090.000.10

MmPalateMiRNA.Rcheck/examples_x64/MmPalateMiRNA-Ex.timings

nameusersystemelapsed
MADvsMedianPlot1.000.031.06
MAplot0.470.020.49
PalateData0.060.000.06
checkMVs0.150.000.16
checkOutliers0.690.000.69
clustPlot0.270.010.28
densityplot0.620.060.69
filterArray0.080.000.08