BioC 3.5: CHECK report for TCC on toluca2

Package: TCC

Version: 1.15.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCC_1.15.1.tar.gz

StartedAt: 2017-04-23 10:38:36 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 10:51:55 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 799.1 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 TCC_1.15.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TCC.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.15.1’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simulateReadCounts 16.116  0.089  19.506
calcAUCValue       13.448  0.120  19.146
TCC-class          12.215  0.282  18.928
plotFCPseudocolor  10.548  0.057  13.436
calcNormFactors    10.025  0.103  14.697
plot.TCC            8.506  0.168  12.250
hypoData_mg         5.399  0.032   8.299
hypoData            5.210  0.030   7.928
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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	0.115	0.017	0.220
TCC-class	12.215	0.282	18.928
TCC	0.013	0.001	0.023
WAD	0.247	0.008	0.389
arab	0.047	0.014	0.091
calcAUCValue	13.448	0.120	19.146
calcNormFactors	10.025	0.103	14.697
clusterSample	0.107	0.005	0.169
estimateDE	1.886	0.016	3.029
filterLowCountGenes	0.083	0.003	0.131
getNormalizedData	0.304	0.005	0.466
getResult	1.843	0.011	2.814
hypoData	5.210	0.030	7.928
hypoData_mg	5.399	0.032	8.299
hypoData_ts	0.002	0.002	0.003
makeFCMatrix	0.004	0.000	0.004
nakai	0.038	0.003	0.050
plot.TCC	8.506	0.168	12.250
plotFCPseudocolor	10.548	0.057	13.436
simulateReadCounts	16.116	0.089	19.506