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CHECK report for AgiMicroRna on merida1

This page was generated on 2019-04-16 11:55:06 -0400 (Tue, 16 Apr 2019).

Package 36/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AgiMicroRna 2.32.0
Pedro Lopez-Romero
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/AgiMicroRna
Branch: RELEASE_3_8
Last Commit: 681ae17
Last Changed Date: 2018-10-30 11:41:45 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AgiMicroRna
Version: 2.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AgiMicroRna.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AgiMicroRna_2.32.0.tar.gz
StartedAt: 2019-04-15 22:18:56 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:25:13 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 377.0 seconds
RetCode: 0
Status:  OK 
CheckDir: AgiMicroRna.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AgiMicroRna.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AgiMicroRna_2.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/AgiMicroRna.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AgiMicroRna/DESCRIPTION’ ... OK
* this is package ‘AgiMicroRna’ version ‘2.32.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AgiMicroRna’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘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 ... NOTE
Warning: no function found corresponding to methods exports from ‘AgiMicroRna’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'affy' 'affycoretools' 'preprocessCore'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'codelink' 'gdata' 'geneplotter' 'gplots' 'gtools' 'marray'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'affy' 'affycoretools' 'limma' 'methods' 'preprocessCore'
  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 ... NOTE
Foreign function call to a different package:
  .Call("rma_c_complete_copy", ..., PACKAGE = "affy")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
DEG.print.info: no visible global function definition for 'is'
DEG.print.info: no visible global function definition for 'exprs'
HeatMapMicroRna: no visible binding for global variable 'var'
HeatMapMicroRna: no visible global function definition for 'rainbow'
HeatMapMicroRna: no visible global function definition for 'maPalette'
HeatMapMicroRna: no visible global function definition for 'heatmap.2'
HeatMapMicroRna: no visible global function definition for 'title'
MA.plot.miRNA: no visible global function definition for 'dev.new'
MA.plot.miRNA: no visible global function definition for 'plot'
MA.plot.miRNA: no visible global function definition for 'points'
MA.plot.miRNA: no visible global function definition for 'fitted'
MA.plot.miRNA: no visible global function definition for 'loess'
MA.plot.miRNA: no visible global function definition for 'legend'
MA.plot.miRNA: no visible global function definition for 'title'
PCAplotMicroRna: no visible global function definition for 'is'
PCAplotMicroRna: no visible global function definition for 'exprs'
PCAplotMicroRna: no visible global function definition for 'na.omit'
PCAplotMicroRna: no visible global function definition for 'exprs<-'
PCAplotMicroRna: no visible global function definition for 'plotPCA'
PCAplotMicroRna: no visible global function definition for 'dev.new'
RleMicroRna: no visible binding for global variable 'median'
RleMicroRna: no visible global function definition for 'par'
RleMicroRna: no visible global function definition for 'plot'
RleMicroRna: no visible global function definition for 'boxplot'
RleMicroRna: no visible global function definition for 'points'
RleMicroRna: no visible global function definition for 'lines'
RleMicroRna: no visible global function definition for 'title'
RleMicroRna: no visible global function definition for 'abline'
basicLimma: no visible global function definition for 'is'
basicLimma: no visible global function definition for 'exprs'
basicLimma: no visible global function definition for 'lmFit'
basicLimma: no visible global function definition for 'contrasts.fit'
basicLimma: no visible global function definition for 'eBayes'
boxplotMicroRna: no visible global function definition for 'par'
boxplotMicroRna: no visible global function definition for 'plot'
boxplotMicroRna: no visible global function definition for 'boxplot'
boxplotMicroRna: no visible global function definition for 'points'
boxplotMicroRna: no visible global function definition for 'lines'
boxplotMicroRna: no visible global function definition for 'title'
cv.array: no visible binding for global variable 'median'
cvArray: no visible global function definition for 'is'
esetMicroRna: no visible global function definition for 'is'
esetMicroRna: no visible global function definition for 'new'
esetMicroRna: no visible global function definition for 'dev.new'
esetMicroRna: no visible global function definition for 'exprs'
filter.IsGeneDetected: no visible global function definition for 'is'
filter.control.miRNA: no visible global function definition for 'is'
filter.wellaboveNEG.miRNA: no visible global function definition for
  'is'
filter.wellaboveNEG.miRNA: no visible binding for global variable 'sd'
filterMicroRna: no visible global function definition for 'is'
filterMicroRna: no visible global function definition for 'dev.new'
getDecideTests: no visible global function definition for 'is'
getDecideTests: no visible global function definition for 'decideTests'
hierclusMicroRna: no visible binding for global variable 'var'
hierclusMicroRna: no visible global function definition for 'dist'
hierclusMicroRna: no visible global function definition for 'as.dist'
hierclusMicroRna: no visible global function definition for 'cor'
hierclusMicroRna: no visible global function definition for 'hclust'
hierclusMicroRna: no visible global function definition for 'plot'
hierclusMicroRna: no visible global function definition for 'title'
mvaBASIC: no visible binding for global variable 'median'
mvaBASIC: no visible global function definition for 'plot'
mvaBASIC: no visible global function definition for 'title'
mvaBASIC: no visible global function definition for 'abline'
mvaMicroRna: no visible binding for global variable 'median'
mvaMicroRna: no visible global function definition for 'plot'
mvaMicroRna: no visible global function definition for 'points'
mvaMicroRna: no visible global function definition for 'fitted'
mvaMicroRna: no visible global function definition for 'loess'
mvaMicroRna: no visible global function definition for 'title'
mvaMicroRna: no visible global function definition for 'abline'
mvaMicroRna: no visible global function definition for 'legend'
plotDensityMicroRna: no visible global function definition for
  'rainbow'
plotDensityMicroRna: no visible global function definition for
  'density'
plotDensityMicroRna: no visible global function definition for 'plot'
plotDensityMicroRna: no visible global function definition for 'lines'
plotDensityMicroRna: no visible global function definition for 'title'
plotDensityMicroRna: no visible global function definition for 'legend'
pvalHistogram: no visible global function definition for 'p.adjust'
pvalHistogram: no visible global function definition for 'hist'
pvalHistogram: no visible global function definition for 'dev.new'
qcPlots: no visible global function definition for 'is'
qcPlots: no visible global function definition for 'dev.new'
read.agiMicroRna: no visible global function definition for
  'read.columns'
read.agiMicroRna: no visible global function definition for 'new'
readMicroRnaAFE: no visible global function definition for 'is'
readTargets: no visible global function definition for 'read.table'
rmaMicroRna: no visible global function definition for 'is'
rmaMicroRna: no visible global function definition for
  'rma.background.correct'
rmaMicroRna: no visible global function definition for
  'normalizeBetweenArrays'
rmaMicroRna: no visible binding for global variable 'median'
significantMicroRna: no visible global function definition for 'is'
significantMicroRna: no visible global function definition for 'exprs'
significantMicroRna: no visible global function definition for
  'p.adjust'
tgsMicroRna: no visible global function definition for 'is'
tgsMicroRna: no visible global function definition for 'dev.new'
tgsNormalization: no visible global function definition for 'is'
tgsNormalization: no visible global function definition for 'dev.new'
tgsNormalization: no visible global function definition for
  'normalizeBetweenArrays'
write.LIST.miRNA: no visible global function definition for 'is'
write.LIST.miRNA: no visible global function definition for
  'write.table'
write.control.out.miRNA: no visible global function definition for 'is'
write.control.out.miRNA: no visible global function definition for
  'write.table'
write.filt.out.miRNA: no visible global function definition for 'is'
write.filt.out.miRNA: no visible global function definition for
  'write.table'
writeEset: no visible global function definition for 'is'
writeEset: no visible global function definition for 'exprs'
writeEset: no visible global function definition for 'featureNames'
writeEset: no visible global function definition for 'write.table'
show,uRNAList: no visible global function definition for 'slotNames'
show,uRNAList: no visible global function definition for 'slot'
Undefined global functions or variables:
  abline as.dist boxplot contrasts.fit cor decideTests density dev.new
  dist eBayes exprs exprs<- featureNames fitted hclust heatmap.2 hist
  is legend lines lmFit loess maPalette median na.omit new
  normalizeBetweenArrays p.adjust par plot plotPCA points rainbow
  read.columns read.table rma.background.correct sd slot slotNames
  title var write.table
Consider adding
  importFrom("grDevices", "dev.new", "rainbow")
  importFrom("graphics", "abline", "boxplot", "hist", "legend", "lines",
             "par", "plot", "points", "title")
  importFrom("methods", "is", "new", "slot", "slotNames")
  importFrom("stats", "as.dist", "cor", "density", "dist", "fitted",
             "hclust", "loess", "median", "na.omit", "p.adjust", "sd",
             "var")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
mvaMicroRna 13.351  0.243  13.704
rmaMicroRna  5.681  0.489   6.220
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/AgiMicroRna.Rcheck/00check.log’
for details.



Installation output

AgiMicroRna.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AgiMicroRna
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘AgiMicroRna’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AgiMicroRna)

Tests output


Example timings

AgiMicroRna.Rcheck/AgiMicroRna-Ex.timings

nameusersystemelapsed
HeatMapMicroRna0.7050.1330.860
PCAplotMicroRna0.1240.0090.133
RleMicroRna1.2740.0971.376
basicLimma000
boxplotMicroRna0.2990.0240.326
cvArray0.0000.0000.001
filterMicroRna0.4590.0540.517
getDecideTests0.0000.0010.001
hierclusMicroRna0.0130.0040.018
mvaBASIC1.5430.0541.607
mvaMicroRna13.351 0.24313.704
plotDensityMicroRna0.2140.0130.228
pvalHistogram000
qcPlots000
readMicroRnaAFE000
rmaMicroRna5.6810.4896.220
significantMicroRna0.5730.0340.612
tgsMicroRna0.1720.0110.186
tgsNormalization0.0010.0000.001
uRNAList0.0000.0010.000
writeEset000