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CHECK report for TIN on merida2

This page was generated on 2018-10-17 08:54:28 -0400 (Wed, 17 Oct 2018).

Package 1484/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TIN 1.12.0
Bjarne Johannessen
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/TIN
Branch: RELEASE_3_7
Last Commit: 470f4c0
Last Changed Date: 2018-04-30 10:35:36 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: TIN
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TIN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TIN_1.12.0.tar.gz
StartedAt: 2018-10-17 00:25:41 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:29:21 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 220.0 seconds
RetCode: 0
Status:  OK 
CheckDir: TIN.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TIN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TIN_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/TIN.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TIN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TIN’ version ‘1.12.0’
* 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 ‘TIN’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aberrantExonUsage: no visible global function definition for ‘quantile’
aberrantExonUsage: no visible global function definition for ‘ave’
clusterPlot: no visible global function definition for ‘dist’
clusterPlot: no visible global function definition for ‘hclust’
clusterPlot: no visible global function definition for
  ‘colorRampPalette’
clusterPlot: no visible global function definition for ‘par’
clusterPlot: no visible global function definition for ‘png’
clusterPlot: no visible global function definition for ‘jpeg’
clusterPlot: no visible global function definition for ‘postscript’
clusterPlot: no visible global function definition for ‘pdf’
clusterPlot: no visible global function definition for ‘bmp’
clusterPlot: no visible global function definition for ‘dev.off’
correlationPlot: no visible global function definition for ‘png’
correlationPlot: no visible global function definition for ‘jpeg’
correlationPlot: no visible global function definition for ‘postscript’
correlationPlot: no visible global function definition for ‘pdf’
correlationPlot: no visible global function definition for ‘bmp’
correlationPlot: no visible global function definition for ‘hist’
correlationPlot: no visible global function definition for ‘plot’
correlationPlot: no visible global function definition for ‘axis’
correlationPlot: no visible global function definition for ‘points’
correlationPlot: no visible global function definition for ‘dev.off’
firmaAnalysis: no visible global function definition for ‘data’
geneSetCorrelation: no visible global function definition for ‘median’
posNegCorrPlot: no visible global function definition for ‘png’
posNegCorrPlot: no visible global function definition for ‘jpeg’
posNegCorrPlot: no visible global function definition for ‘postscript’
posNegCorrPlot: no visible global function definition for ‘pdf’
posNegCorrPlot: no visible global function definition for ‘bmp’
posNegCorrPlot: no visible global function definition for ‘plot’
posNegCorrPlot: no visible global function definition for ‘axis’
posNegCorrPlot: no visible global function definition for ‘points’
posNegCorrPlot: no visible global function definition for ‘dev.off’
readGeneSummaries: no visible global function definition for ‘data’
readGeneSummaries: no visible global function definition for
  ‘read.table’
scatterPlot: no visible global function definition for ‘png’
scatterPlot: no visible global function definition for ‘jpeg’
scatterPlot: no visible global function definition for ‘postscript’
scatterPlot: no visible global function definition for ‘pdf’
scatterPlot: no visible global function definition for ‘bmp’
scatterPlot: no visible global function definition for ‘plot’
scatterPlot: no visible global function definition for ‘ave’
scatterPlot: no visible global function definition for ‘axis’
scatterPlot: no visible global function definition for ‘text’
scatterPlot: no visible global function definition for ‘mtext’
scatterPlot: no visible global function definition for ‘points’
scatterPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  ave axis bmp colorRampPalette data dev.off dist hclust hist jpeg
  median mtext par pdf plot png points postscript quantile read.table
  text
Consider adding
  importFrom("grDevices", "bmp", "colorRampPalette", "dev.off", "jpeg",
             "pdf", "png", "postscript")
  importFrom("graphics", "axis", "hist", "mtext", "par", "plot",
             "points", "text")
  importFrom("stats", "ave", "dist", "hclust", "median", "quantile")
  importFrom("utils", "data", "read.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 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
geneSetCorrelation 15.762  0.151  16.058
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/TIN.Rcheck/00check.log’
for details.



Installation output

TIN.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TIN
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘TIN’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
The following object is masked _by_ package:aroma.affymetrix:

    writeCdf

The following object is masked from package:R.utils:

    findFiles

** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
The following object is masked _by_ package:aroma.affymetrix:

    writeCdf

The following object is masked from package:R.utils:

    findFiles

* DONE (TIN)

Tests output

TIN.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("TIN")

Attaching package: 'R.oo'

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, gc, load, save


Attaching package: 'R.utils'

The following object is masked from 'package:utils':

    timestamp

The following objects are masked from 'package:base':

    cat, commandArgs, getOption, inherits, isOpen, parse, warnings


Attaching package: 'R.filesets'

The following objects are masked from 'package:R.utils':

    extract, validate

The following objects are masked from 'package:base':

    append, readLines


Attaching package: 'aroma.core'

The following objects are masked from 'package:base':

    .Machine, colMeans, colSums, library, require, write

Loading required package: aroma.light
aroma.light v3.10.0 (2017-12-19) successfully loaded. See ?aroma.light for help.

Attaching package: 'aroma.light'

The following objects are masked from 'package:aroma.affymetrix':

    averageQuantile, normalizeQuantile, plotDensity, plotMvsA,
    plotXYCurve

The following objects are masked from 'package:aroma.core':

    callNaiveGenotypes, normalizeTumorBoost

Loading required package: affxparser

Attaching package: 'affxparser'

The following object is masked from 'package:aroma.affymetrix':

    writeCdf

The following object is masked from 'package:R.utils':

    findFiles

The following object is masked _by_ package:aroma.affymetrix:

    writeCdf

The following object is masked from package:R.utils:

    findFiles


Attaching package: 'aroma.affymetrix'

The following objects are masked _by_ 'package:aroma.light':

    averageQuantile, normalizeQuantile, plotDensity, plotMvsA,
    plotXYCurve

The following object is masked from 'package:affxparser':

    writeCdf




RUNIT TEST PROTOCOL -- Wed Oct 17 00:29:16 2018 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TIN RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 45.562   0.903  46.910 

Example timings

TIN.Rcheck/TIN-Ex.timings

nameusersystemelapsed
aberrantExonUsage0.4430.0160.473
clusterPlot0.2340.0310.278
correlation0.1140.0140.129
correlationPlot3.5440.1533.733
firmaAnalysis0.0110.0020.013
geneSetCorrelation15.762 0.15116.058
posNegCorrPlot3.9960.1754.195
probesetPermutations0.3400.0250.367
readGeneSummaries0.0260.0030.030
scatterPlot0.4000.0490.450