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BioC 3.5: CHECK report for AgiMicroRna on malbec2

This page was generated on 2017-08-16 13:13:25 -0400 (Wed, 16 Aug 2017).

Package 32/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AgiMicroRna 2.26.0
Pedro Lopez-Romero
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/AgiMicroRna
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AgiMicroRna
Version: 2.26.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings AgiMicroRna_2.26.0.tar.gz
StartedAt: 2017-08-15 21:04:16 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:09:48 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 331.7 seconds
RetCode: 0
Status:  OK 
CheckDir: AgiMicroRna.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings AgiMicroRna_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/AgiMicroRna.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AgiMicroRna/DESCRIPTION’ ... OK
* this is package ‘AgiMicroRna’ version ‘2.26.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
mvaMicroRna 13.068  0.084  13.158
rmaMicroRna  6.740  0.012   6.777
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/AgiMicroRna.Rcheck/00check.log’
for details.


AgiMicroRna.Rcheck/00install.out:

* installing *source* package ‘AgiMicroRna’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (AgiMicroRna)

AgiMicroRna.Rcheck/AgiMicroRna-Ex.timings:

nameusersystemelapsed
HeatMapMicroRna0.9800.1881.819
PCAplotMicroRna0.1400.0040.146
RleMicroRna0.8440.0080.852
basicLimma0.0000.0000.001
boxplotMicroRna0.1920.0040.199
cvArray000
filterMicroRna0.3960.0080.403
getDecideTests000
hierclusMicroRna0.0280.0000.026
mvaBASIC1.0080.0121.020
mvaMicroRna13.068 0.08413.158
plotDensityMicroRna0.2040.0040.206
pvalHistogram000
qcPlots000
readMicroRnaAFE0.0000.0000.001
rmaMicroRna6.7400.0126.777
significantMicroRna1.0680.0401.296
tgsMicroRna0.1920.0080.200
tgsNormalization0.0000.0000.001
uRNAList0.0040.0000.001
writeEset000