BioC 3.4: CHECK report for TCC on morelia

Package: TCC

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCC_1.14.0.tar.gz

StartedAt: 2017-04-15 08:46:37 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:56:54 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 617.5 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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/TCC.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.14.0’
* 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 15.000  0.107  16.222
calcAUCValue       12.414  0.108  14.717
TCC-class          11.493  0.305  13.026
calcNormFactors    11.332  0.111  13.768
plotFCPseudocolor  10.686  0.072  12.344
plot.TCC            9.070  0.173  10.272
hypoData_mg         5.310  0.026   5.736
hypoData            4.659  0.023   5.066
* 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	0.016	0.002	0.018
TCC-class	11.493	0.305	13.026
TCC	0.014	0.002	0.022
WAD	0.272	0.008	0.348
arab	0.053	0.007	0.068
calcAUCValue	12.414	0.108	14.717
calcNormFactors	11.332	0.111	13.768
clusterSample	0.082	0.005	0.105
estimateDE	1.671	0.012	2.001
filterLowCountGenes	0.036	0.003	0.050
getNormalizedData	0.352	0.004	0.434
getResult	2.112	0.012	2.392
hypoData	4.659	0.023	5.066
hypoData_mg	5.310	0.026	5.736
hypoData_ts	0.002	0.001	0.002
makeFCMatrix	0.004	0.000	0.004
nakai	0.043	0.003	0.046
plot.TCC	9.070	0.173	10.272
plotFCPseudocolor	10.686	0.072	12.344
simulateReadCounts	15.000	0.107	16.222