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BioC 3.3: CHECK report for AgiMicroRna on moscato2

This page was generated on 2016-10-13 12:49:08 -0700 (Thu, 13 Oct 2016).

Package 33/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AgiMicroRna 2.22.0
Pedro Lopez-Romero
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/AgiMicroRna
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AgiMicroRna
Version: 2.22.0
Command: rm -rf AgiMicroRna.buildbin-libdir AgiMicroRna.Rcheck && mkdir AgiMicroRna.buildbin-libdir AgiMicroRna.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AgiMicroRna.buildbin-libdir AgiMicroRna_2.22.0.tar.gz >AgiMicroRna.Rcheck\00install.out 2>&1 && cp AgiMicroRna.Rcheck\00install.out AgiMicroRna-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=AgiMicroRna.buildbin-libdir --install="check:AgiMicroRna-install.out" --force-multiarch --no-vignettes --timings AgiMicroRna_2.22.0.tar.gz
StartedAt: 2016-10-13 00:50:39 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:01:04 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 624.6 seconds
RetCode: 0
Status:  OK  
CheckDir: AgiMicroRna.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf AgiMicroRna.buildbin-libdir AgiMicroRna.Rcheck && mkdir AgiMicroRna.buildbin-libdir AgiMicroRna.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AgiMicroRna.buildbin-libdir AgiMicroRna_2.22.0.tar.gz >AgiMicroRna.Rcheck\00install.out 2>&1 && cp AgiMicroRna.Rcheck\00install.out AgiMicroRna-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=AgiMicroRna.buildbin-libdir --install="check:AgiMicroRna-install.out" --force-multiarch --no-vignettes --timings AgiMicroRna_2.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/AgiMicroRna.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AgiMicroRna/DESCRIPTION' ... OK
* this is package 'AgiMicroRna' version '2.22.0'
* 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 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
* 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 ... 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
* 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 ... 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
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
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 '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 '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'
esetMicroRna: no visible global function definition for 'dev.new'
esetMicroRna: no visible global function definition for 'exprs'
filter.wellaboveNEG.miRNA: no visible binding for global variable 'sd'
filterMicroRna: no visible global function definition for 'dev.new'
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 'dev.new'
read.agiMicroRna: no visible global function definition for
  'read.columns'
readTargets: no visible global function definition for 'read.table'
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 'exprs'
significantMicroRna: no visible global function definition for
  'p.adjust'
tgsMicroRna: no visible global function definition for 'dev.new'
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
  'write.table'
write.control.out.miRNA: no visible global function definition for
  'write.table'
write.filt.out.miRNA: no visible global function definition for
  'write.table'
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'
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
  legend lines lmFit loess maPalette median na.omit
  normalizeBetweenArrays p.adjust par plot plotPCA points rainbow
  read.columns read.table rma.background.correct sd title var
  write.table
Consider adding
  importFrom("grDevices", "dev.new", "rainbow")
  importFrom("graphics", "abline", "boxplot", "hist", "legend", "lines",
             "par", "plot", "points", "title")
  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.
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mvaMicroRna     16.22   0.02   16.24
rmaMicroRna      7.58   0.02    7.60
HeatMapMicroRna  0.36   0.00   29.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
mvaMicroRna 18.3   0.04   18.35
rmaMicroRna  8.6   0.03    8.62
* 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: 6 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/AgiMicroRna.Rcheck/00check.log'
for details.


AgiMicroRna.Rcheck/00install.out:


install for i386

* installing *source* package 'AgiMicroRna' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'

install for x64

* installing *source* package 'AgiMicroRna' ...
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
* MD5 sums
packaged installation of 'AgiMicroRna' as AgiMicroRna_2.22.0.zip
* DONE (AgiMicroRna)

AgiMicroRna.Rcheck/examples_i386/AgiMicroRna-Ex.timings:

nameusersystemelapsed
HeatMapMicroRna 0.36 0.0029.64
PCAplotMicroRna0.210.010.34
RleMicroRna1.740.021.76
basicLimma000
boxplotMicroRna0.790.000.79
cvArray000
filterMicroRna0.630.112.02
getDecideTests0.010.000.01
hierclusMicroRna0.020.000.49
mvaBASIC1.780.011.79
mvaMicroRna16.22 0.0216.24
plotDensityMicroRna0.270.010.28
pvalHistogram000
qcPlots000
readMicroRnaAFE000
rmaMicroRna7.580.027.60
significantMicroRna0.610.093.63
tgsMicroRna0.280.000.28
tgsNormalization000
uRNAList000
writeEset000

AgiMicroRna.Rcheck/examples_x64/AgiMicroRna-Ex.timings:

nameusersystemelapsed
HeatMapMicroRna0.530.001.18
PCAplotMicroRna0.220.010.31
RleMicroRna1.930.051.98
basicLimma000
boxplotMicroRna0.820.020.83
cvArray000
filterMicroRna0.680.101.17
getDecideTests000
hierclusMicroRna0.020.020.03
mvaBASIC1.670.021.81
mvaMicroRna18.30 0.0418.35
plotDensityMicroRna0.240.020.25
pvalHistogram000
qcPlots0.010.000.02
readMicroRnaAFE000
rmaMicroRna8.600.038.62
significantMicroRna0.670.090.77
tgsMicroRna0.180.020.20
tgsNormalization000
uRNAList000
writeEset000