BioC 2.13: CHECK report for Category on perceval

Package: Category

Version: 2.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Category_2.28.0.tar.gz

StartedAt: 2014-04-05 00:01:24 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:08:43 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 438.4 seconds

RetCode: 0

Status:  OK

CheckDir: Category.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/Category.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Category/DESCRIPTION’ ... OK
* this is package ‘Category’ version ‘2.28.0’
* 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 ‘Category’ can be installed ... [28s/28s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘methods’ ‘Biobase’ ‘AnnotationDbi’ ‘graph’ ‘genefilter’
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
  ‘GO.db’ ‘Matrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘DatPkgFactory’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Category.Rnw’, ‘ChromBand.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [72s/72s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ChrBandTree-class 23.479  0.387  23.887
MAPAmat           13.573  0.470  14.072
makeChrBandGraph  13.498  0.274  13.827
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [87s/87s]
 [87s/88s] 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/Category.Rcheck/00check.log’
for details.

* installing *source* package ‘Category’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Category)

name	user	system	elapsed
ChrBandTree-class	23.479	0.387	23.887
ChrMapHyperGParams-class	0.004	0.004	0.007
ChrMapHyperGResult-class	0.004	0.004	0.009
ChrMapLinearMParams-class	0.015	0.005	0.019
ChrMapLinearMResult-class	0.004	0.004	0.008
DatPkg-class	0.129	0.012	0.141
HyperGResult-accessors	1.018	0.067	1.085
LinearMResult-class	0.004	0.004	0.007
MAPAmat	13.573	0.470	14.072
applyByCategory	0.009	0.005	0.014
cateGOryMatrix	0.391	0.059	0.450
cb_parse_band_Hs	0.033	0.004	0.037
cb_parse_band_Mm	0.014	0.003	0.018
findAMstats	0.543	0.028	0.572
getPathNames	0.122	0.011	0.134
gseattperm	1.349	0.139	1.491
hyperg	1.089	0.167	1.271
makeChrBandGraph	13.498	0.274	13.827
makeEBcontr	0.387	0.014	0.400
probes2MAP	0.419	0.020	0.439
probes2Path	0.174	0.012	0.187
ttperm	0.040	0.008	0.048