BioC 3.1: CHECK report for TCC on zin2

Package: TCC

Version: 1.8.5

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings TCC_1.8.5.tar.gz

StartedAt: 2015-10-09 05:58:45 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 06:07:03 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 497.6 seconds

RetCode: 0

Status:  OK

CheckDir: TCC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings TCC_1.8.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/TCC.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.5’
* 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 ... [12s/12s] 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 ... [79s/79s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simulateReadCounts 13.173  0.000  13.182
TCC-class          10.713  0.052  10.757
calcNormFactors    10.574  0.003  10.635
calcAUCValue        9.984  0.008  10.011
plotFCPseudocolor   8.355  0.008   8.370
plot.TCC            8.264  0.008   8.286
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [311s/311s]
 [311s/312s] 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 ‘TCC’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (TCC)

name	user	system	elapsed
ROKU	0.014	0.000	0.014
TCC-class	10.713	0.052	10.757
TCC	0.009	0.000	0.008
WAD	0.182	0.000	0.182
arab	0.037	0.000	0.037
calcAUCValue	9.984	0.008	10.011
calcNormFactors	10.574	0.003	10.635
clusterSample	0.067	0.004	0.070
estimateDE	1.546	0.000	1.546
filterLowCountGenes	0.022	0.000	0.022
getNormalizedData	0.528	0.000	0.528
getResult	2.213	0.000	2.211
hypoData	3.975	0.000	3.972
hypoData_mg	4.470	0.000	4.471
hypoData_ts	0.002	0.000	0.002
nakai	0.038	0.000	0.038
plot.TCC	8.264	0.008	8.286
plotFCPseudocolor	8.355	0.008	8.370
simulateReadCounts	13.173	0.000	13.182