BioC 3.2: CHECK report for TCC on perceval

Package: TCC

Version: 1.9.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCC_1.9.2.tar.gz

StartedAt: 2015-08-24 05:43:20 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 05:55:07 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 707.3 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 TCC_1.9.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TCC.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 ‘TCC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCC’ version ‘1.9.2’
* 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 ... [22s/22s] 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 ... [110s/110s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simulateReadCounts 20.345  0.125  20.485
calcAUCValue       13.733  0.083  13.839
TCC-class          13.423  0.318  13.746
plotFCPseudocolor  12.295  0.086  12.481
calcNormFactors    12.123  0.093  12.263
plot.TCC           10.579  0.184  10.795
hypoData_mg         6.154  0.033   6.191
hypoData            5.920  0.026   5.947
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [397s/398s]
 [398s/398s] 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 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	0.000	0.018
TCC-class	13.423	0.318	13.746
TCC	0.011	0.002	0.012
WAD	0.27	0.01	0.28
arab	0.056	0.015	0.071
calcAUCValue	13.733	0.083	13.839
calcNormFactors	12.123	0.093	12.263
clusterSample	0.094	0.005	0.099
estimateDE	1.708	0.008	1.717
filterLowCountGenes	0.027	0.001	0.028
getNormalizedData	0.343	0.002	0.346
getResult	2.311	0.008	2.318
hypoData	5.920	0.026	5.947
hypoData_mg	6.154	0.033	6.191
hypoData_ts	0.002	0.001	0.003
nakai	0.038	0.004	0.042
plot.TCC	10.579	0.184	10.795
plotFCPseudocolor	12.295	0.086	12.481
simulateReadCounts	20.345	0.125	20.485