BioC 3.1: CHECK report for TCC on petty

Package: TCC

Version: 1.8.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCC_1.8.5.tar.gz

StartedAt: 2015-10-09 02:19:46 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:34:20 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 874.7 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_1.8.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.8.5’
* 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 ... [23s/24s] 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 ... [132s/133s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simulateReadCounts 21.568  0.114  21.689
calcAUCValue       17.341  0.079  17.445
TCC-class          16.289  0.302  16.600
calcNormFactors    14.542  0.071  14.622
plotFCPseudocolor  14.336  0.060  14.403
plot.TCC           12.809  0.165  12.982
hypoData_mg         8.925  0.032   8.968
hypoData            7.953  0.032   7.989
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [522s/522s]
 [522s/523s] 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	0.032	0.002	0.034
TCC-class	16.289	0.302	16.600
TCC	0.018	0.001	0.020
WAD	0.303	0.007	0.310
arab	0.047	0.006	0.054
calcAUCValue	17.341	0.079	17.445
calcNormFactors	14.542	0.071	14.622
clusterSample	0.130	0.003	0.140
estimateDE	2.155	0.004	2.159
filterLowCountGenes	0.048	0.002	0.050
getNormalizedData	0.469	0.003	0.472
getResult	3.472	0.011	3.485
hypoData	7.953	0.032	7.989
hypoData_mg	8.925	0.032	8.968
hypoData_ts	0.003	0.000	0.003
nakai	0.055	0.003	0.059
plot.TCC	12.809	0.165	12.982
plotFCPseudocolor	14.336	0.060	14.403
simulateReadCounts	21.568	0.114	21.689