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CHECK report for TIN on tokay2

This page was generated on 2019-10-16 12:32:46 -0400 (Wed, 16 Oct 2019).

Package 1649/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TIN 1.16.0
Bjarne Johannessen
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/TIN
Branch: RELEASE_3_9
Last Commit: ae1c373
Last Changed Date: 2019-05-02 11:53:53 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TIN
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TIN.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TIN_1.16.0.tar.gz
StartedAt: 2019-10-16 07:34:13 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:39:30 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 316.9 seconds
RetCode: 0
Status:  OK  
CheckDir: TIN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TIN.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TIN_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/TIN.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TIN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TIN' version '1.16.0'
* 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 '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
* 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 ... OK
** checking whether the namespace can be unloaded cleanly ... 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
geneSetCorrelation 13.58   0.17   13.76
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
geneSetCorrelation 15.47   0.11   15.58
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/TIN.Rcheck/00check.log'
for details.



Installation output

TIN.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/TIN_1.16.0.tar.gz && rm -rf TIN.buildbin-libdir && mkdir TIN.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TIN.buildbin-libdir TIN_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL TIN_1.16.0.zip && rm TIN_1.16.0.tar.gz TIN_1.16.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4578k  100 4578k    0     0  43.1M      0 --:--:-- --:--:-- --:--:-- 46.5M

install for i386

* 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
  converting help for package 'TIN'
    finding HTML links ... done
    aberrantExonUsage                       html  
    clusterPlot                             html  
    correlation                             html  
    correlationPlot                         html  
    firmaAnalysis                           html  
    geneAnnotation                          html  
    geneSetCorrelation                      html  
    geneSets                                html  
    posNegCorrPlot                          html  
    probesetPermutations                    html  
    readGeneSummaries                       html  
    sampleSetFirmaScores                    html  
    sampleSetGeneSummaries                  html  
    scatterPlot                             html  
    splicingFactors                         html  
** 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

install for x64

* installing *source* package 'TIN' ...
** 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

* MD5 sums
packaged installation of 'TIN' as TIN_1.16.0.zip
* DONE (TIN)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'TIN' successfully unpacked and MD5 sums checked

Tests output

TIN.Rcheck/tests_i386/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, nullfile, 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 v3.14.0 (2018-09-04) 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 16 07:38:46 2019 
*********************************************** 
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 
  39.28    1.26   40.78 

TIN.Rcheck/tests_x64/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, nullfile, 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 v3.14.0 (2018-09-04) 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 16 07:39:24 2019 
*********************************************** 
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 
  36.85    0.82   37.67 

Example timings

TIN.Rcheck/examples_i386/TIN-Ex.timings

nameusersystemelapsed
aberrantExonUsage0.550.020.56
clusterPlot0.160.110.26
correlation0.160.030.19
correlationPlot3.300.143.43
firmaAnalysis0.030.000.04
geneSetCorrelation13.58 0.1713.76
posNegCorrPlot3.920.094.02
probesetPermutations0.500.020.51
readGeneSummaries0.030.020.05
scatterPlot0.550.030.58

TIN.Rcheck/examples_x64/TIN-Ex.timings

nameusersystemelapsed
aberrantExonUsage0.550.030.58
clusterPlot0.610.050.65
correlation0.140.030.17
correlationPlot4.360.034.39
firmaAnalysis0.020.000.02
geneSetCorrelation15.47 0.1115.58
posNegCorrPlot4.600.084.68
probesetPermutations0.310.000.31
readGeneSummaries0.050.000.05
scatterPlot0.500.030.53