BioC 2.13: CHECK report for TCC on zin1

Package: TCC

Version: 1.2.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings TCC_1.2.0.tar.gz

StartedAt: 2014-04-05 04:18:19 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:30:52 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 752.2 seconds

RetCode: 0

Status:  OK

CheckDir: TCC.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/TCC.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.2.0’
* 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 ... [14s/14s] 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 ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘TCC.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [110s/110s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simulateReadCounts 20.109  0.000  20.176
calcAUCValue       14.693  0.008  14.725
TCC-class          14.365  0.040  14.429
plotFCPseudocolor  13.009  0.004  13.036
calcNormFactors    12.368  0.004  12.394
plot.TCC           11.100  0.008  11.129
hypoData_mg         6.565  0.004   6.611
hypoData            6.244  0.000   6.256
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [516s/517s]
 [516s/517s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-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
MAplot	0.152	0.004	0.156
NB	0.148	0.004	0.151
ROKU	0.036	0.000	0.035
TCC-class	14.365	0.040	14.429
TCC	0.016	0.000	0.015
WAD	0.268	0.004	0.273
arab	0.212	0.000	0.210
calcAUCValue	14.693	0.008	14.725
calcNormFactors	12.368	0.004	12.394
do_TbT	0.004	0.000	0.005
estimateDE	1.949	0.000	1.949
exactTestafterTbT	0.004	0.000	0.003
filterLowCountGenes	0.028	0.004	0.030
getNormalizedData	0.404	0.000	0.405
getResult	2.392	0.004	2.400
hypoData	6.244	0.000	6.256
hypoData_mg	6.565	0.004	6.611
hypoData_ts	0.008	0.000	0.007
nakai	0.040	0.000	0.037
plot.TCC	11.100	0.008	11.129
plotFCPseudocolor	13.009	0.004	13.036
simulateReadCounts	20.109	0.000	20.176