BioC 3.0: CHECK report for TCC on oaxaca

Package: TCC

Version: 1.6.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch TCC_1.6.5.tar.gz

StartedAt: 2015-04-10 03:48:12 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:59:29 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 677.9 seconds

RetCode: 0

Status:  OK

CheckDir: TCC.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 --no-multiarch TCC_1.6.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/TCC.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCC’ version ‘1.6.5’
* 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 ‘TCC’ can be installed ... [24s/25s] 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 ... 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 ... [95s/96s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simulateReadCounts 15.537  0.080  15.759
calcAUCValue       12.236  0.069  12.363
TCC-class          11.827  0.177  12.023
calcNormFactors    10.275  0.067  10.350
plotFCPseudocolor  10.128  0.047  10.186
plot.TCC            8.988  0.094   9.094
hypoData_mg         5.131  0.020   5.156
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [362s/367s]
 [363s/367s] 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

* installing *source* package ‘TCC’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘calcNormFactors’ in package ‘TCC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TCC)

name	user	system	elapsed
ROKU	0.015	0.001	0.015
TCC-class	11.827	0.177	12.023
TCC	0.009	0.001	0.010
WAD	0.273	0.005	0.279
arab	0.051	0.010	0.060
calcAUCValue	12.236	0.069	12.363
calcNormFactors	10.275	0.067	10.350
clusterSample	0.077	0.002	0.081
estimateDE	1.707	0.019	1.727
filterLowCountGenes	0.024	0.001	0.025
getNormalizedData	0.306	0.004	0.311
getResult	1.851	0.018	1.871
hypoData	4.858	0.020	4.882
hypoData_mg	5.131	0.020	5.156
hypoData_ts	0.002	0.000	0.002
nakai	0.040	0.002	0.042
plot.TCC	8.988	0.094	9.094
plotFCPseudocolor	10.128	0.047	10.186
simulateReadCounts	15.537	0.080	15.759