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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:55:15 -0400 (Wed, 16 Oct 2019).
| Package 1649/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TIN 1.16.0 Bjarne Johannessen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: TIN |
| Version: 1.16.0 |
| 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_1.16.0.tar.gz |
| StartedAt: 2019-10-16 07:23:14 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:28:22 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 307.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TIN.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TIN.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.16.0’
* 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 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 21.877 0.378 22.252
posNegCorrPlot 6.307 0.511 6.811
* 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-3.9-bioc/meat/TIN.Rcheck/00check.log’
for details.
TIN.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TIN
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)
TIN.Rcheck/tests/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-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, 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 07:28:15 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
62.969 1.990 64.918
TIN.Rcheck/TIN-Ex.timings
| name | user | system | elapsed | |
| aberrantExonUsage | 0.114 | 0.026 | 0.141 | |
| clusterPlot | 0.758 | 0.079 | 0.851 | |
| correlation | 0.153 | 0.033 | 0.187 | |
| correlationPlot | 4.272 | 0.371 | 4.642 | |
| firmaAnalysis | 0.014 | 0.006 | 0.021 | |
| geneSetCorrelation | 21.877 | 0.378 | 22.252 | |
| posNegCorrPlot | 6.307 | 0.511 | 6.811 | |
| probesetPermutations | 0.455 | 0.066 | 0.520 | |
| readGeneSummaries | 0.034 | 0.016 | 0.050 | |
| scatterPlot | 0.567 | 0.133 | 0.694 | |