BioC 3.2: CHECK report for TCC on oaxaca

Package: TCC

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCC_1.10.0.tar.gz

StartedAt: 2016-04-23 04:53:45 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:04:43 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 658.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TCC.Rcheck

Warnings: 1

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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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TCC.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.10.0’
* 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 ... [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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'TCC,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [88s/89s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simulateReadCounts 15.600  0.104  15.717
calcAUCValue       11.554  0.084  11.664
TCC-class           9.634  0.258   9.897
calcNormFactors     9.323  0.105   9.430
plotFCPseudocolor   9.102  0.056  10.061
plot.TCC            8.462  0.174   8.644
hypoData_mg         5.344  0.030   5.375
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [369s/369s]
 [369s/370s] 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/TCC.Rcheck/00check.log’
for details.

* 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	0.035	0.007	0.041
TCC-class	9.634	0.258	9.897
TCC	0.017	0.003	0.019
WAD	0.201	0.005	0.207
arab	0.035	0.007	0.041
calcAUCValue	11.554	0.084	11.664
calcNormFactors	9.323	0.105	9.430
clusterSample	0.061	0.004	0.065
estimateDE	1.313	0.022	1.336
filterLowCountGenes	0.031	0.003	0.034
getNormalizedData	0.284	0.005	0.290
getResult	1.817	0.020	1.840
hypoData	4.933	0.041	4.977
hypoData_mg	5.344	0.030	5.375
hypoData_ts	0.002	0.001	0.003
makeFCMatrix	0.006	0.001	0.006
nakai	0.034	0.003	0.037
plot.TCC	8.462	0.174	8.644
plotFCPseudocolor	9.102	0.056	10.061
simulateReadCounts	15.600	0.104	15.717