BioC 3.0: CHECK report for TCC on perceval

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 06:56:55 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 07:10:20 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 805.1 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-darwin10.8.0 (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 ... [31s/32s] 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 ... [126s/127s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simulateReadCounts 20.916  0.125  21.049
TCC-class          16.388  0.301  16.691
calcAUCValue       15.187  0.065  15.268
calcNormFactors    13.485  0.068  13.556
plotFCPseudocolor  13.000  0.064  13.102
plot.TCC           12.620  0.182  13.041
hypoData_mg         6.918  0.045   7.008
hypoData            6.193  0.030   6.227
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [402s/403s]
 [403s/403s] 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	0.017	0.001	0.019
TCC-class	16.388	0.301	16.691
TCC	0.012	0.001	0.013
WAD	0.346	0.010	0.356
arab	0.045	0.006	0.052
calcAUCValue	15.187	0.065	15.268
calcNormFactors	13.485	0.068	13.556
clusterSample	0.112	0.007	0.324
estimateDE	1.812	0.007	1.821
filterLowCountGenes	0.030	0.002	0.032
getNormalizedData	0.406	0.002	0.408
getResult	2.881	0.014	2.897
hypoData	6.193	0.030	6.227
hypoData_mg	6.918	0.045	7.008
hypoData_ts	0.002	0.001	0.003
nakai	0.044	0.004	0.047
plot.TCC	12.620	0.182	13.041
plotFCPseudocolor	13.000	0.064	13.102
simulateReadCounts	20.916	0.125	21.049