Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:56 -0400 (Fri, 15 Oct 2021).

CHECK results for TIN on machv2

To the developers/maintainers of the TIN package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TIN.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1923/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TIN 1.24.0  (landing page)
Bjarne Johannessen
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/TIN
git_branch: RELEASE_3_13
git_last_commit: 4ee1fa2
git_last_commit_date: 2021-05-19 12:12:06 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TIN
Version: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2021-10-15 00:45:44 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 00:50:10 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 266.8 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_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/TIN.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ‘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 ‘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 ‘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 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", "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 (user + system) or elapsed time > 5s
                     user system elapsed
geneSetCorrelation 16.029  0.138  16.176
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-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/4.1/Resources/library’
* installing *source* package ‘TIN’ ...
** using staged installation
** 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 from temporary location
The following object is masked _by_ package:aroma.affymetrix:

    writeCdf

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

    findFiles

** testing if installed package can be loaded from final location
The following object is masked _by_ package:aroma.affymetrix:

    writeCdf

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

    findFiles

** testing if installed package keeps a record of temporary installation path
* DONE (TIN)

Tests output

TIN.Rcheck/tests/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 object is masked from 'package:R.methodsS3':

    throw

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

    getClasses, getMethods

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

    attach, detach, 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, nullfile, parse,
    warnings


Attaching package: 'R.filesets'

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

    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 v3.22.0 (2021-10-14) 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 -- Fri Oct 15 00:50:03 2021 
*********************************************** 
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 
 52.188   0.973  53.175 

Example timings

TIN.Rcheck/TIN-Ex.timings

nameusersystemelapsed
aberrantExonUsage0.1030.0190.122
clusterPlot0.7240.0410.774
correlation0.1280.0290.157
correlationPlot3.4590.1673.631
firmaAnalysis0.0170.0020.021
geneSetCorrelation16.029 0.13816.176
posNegCorrPlot3.5280.1983.728
probesetPermutations0.4570.0220.479
readGeneSummaries0.0370.0050.042
scatterPlot0.5420.0470.590