BioC 3.3: CHECK report for TCC on oaxaca

Package: TCC

Version: 1.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCC_1.12.1.tar.gz

StartedAt: 2016-10-13 06:47:32 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:57:52 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 620.1 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_1.12.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/TCC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.12.1’
* 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 12.263  0.075  12.345
TCC-class          10.711  0.255  10.974
calcAUCValue       10.549  0.065  10.640
plot.TCC            8.870  0.150   9.034
calcNormFactors     8.644  0.073   8.723
plotFCPseudocolor   6.339  0.035   8.749
* 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	0.028	0.004	0.032
TCC-class	10.711	0.255	10.974
TCC	0.010	0.002	0.011
WAD	0.226	0.007	0.234
arab	0.044	0.006	0.050
calcAUCValue	10.549	0.065	10.640
calcNormFactors	8.644	0.073	8.723
clusterSample	0.080	0.006	0.087
estimateDE	1.443	0.006	1.449
filterLowCountGenes	0.025	0.003	0.029
getNormalizedData	0.594	0.004	0.597
getResult	1.646	0.024	1.672
hypoData	4.059	0.024	4.086
hypoData_mg	4.422	0.018	4.444
hypoData_ts	0.002	0.001	0.003
makeFCMatrix	0.004	0.000	0.004
nakai	0.042	0.003	0.044
plot.TCC	8.870	0.150	9.034
plotFCPseudocolor	6.339	0.035	8.749
simulateReadCounts	12.263	0.075	12.345