BioC 3.1: CHECK report for TIN on petty

Package: TIN

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TIN_1.0.0.tar.gz

StartedAt: 2015-10-09 02:21:51 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:27:24 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 332.7 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 --no-vignettes --timings TIN_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/TIN.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.0.0’
* 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 ... [19s/19s] 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 loading without being on the library search path ... 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [54s/54s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
geneSetCorrelation 27.904  0.396  28.313
posNegCorrPlot      6.372  0.289   6.670
correlationPlot     5.897  0.201   6.102
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [79s/79s]
 [79s/79s] 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: OK

* installing *source* package ‘TIN’ ...
** R
** data
** inst
** preparing package for lazy loading
The following object is masked _by_ package:aroma.affymetrix:

    writeCdf

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

    findFiles

Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** 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

Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (TIN)

name	user	system	elapsed
aberrantExonUsage	0.445	0.018	0.463
clusterPlot	0.675	0.038	0.784
correlation	0.247	0.042	0.288
correlationPlot	5.897	0.201	6.102
firmaAnalysis	0.018	0.002	0.020
geneSetCorrelation	27.904	0.396	28.313
posNegCorrPlot	6.372	0.289	6.670
probesetPermutations	0.492	0.015	0.506
readGeneSummaries	0.048	0.005	0.053
scatterPlot	0.818	0.042	0.862