BioC 2.13: CHECK report for Category on zin1

Package: Category

Version: 2.28.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings Category_2.28.0.tar.gz

StartedAt: 2014-04-05 00:02:47 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:06:57 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 250.0 seconds

RetCode: 0

Status:  OK

CheckDir: Category.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/Category.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 ‘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 ... [16s/18s] 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 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 ... [39s/39s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ChrBandTree-class 11.873  0.076  11.977
MAPAmat            7.480  0.032   7.547
makeChrBandGraph   7.321  0.000   7.330
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [48s/48s]
 [48s/48s] 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
  ‘/home/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	11.873	0.076	11.977
ChrMapHyperGParams-class	0.000	0.000	0.002
ChrMapHyperGResult-class	0.004	0.000	0.002
ChrMapLinearMParams-class	0.008	0.000	0.006
ChrMapLinearMResult-class	0.004	0.000	0.002
DatPkg-class	0.064	0.004	0.067
HyperGResult-accessors	0.632	0.008	0.653
LinearMResult-class	0.024	0.000	0.024
MAPAmat	7.480	0.032	7.547
applyByCategory	0.004	0.004	0.009
cateGOryMatrix	0.248	0.004	0.262
cb_parse_band_Hs	0.000	0.000	0.001
cb_parse_band_Mm	0.004	0.000	0.001
findAMstats	0.004	0.000	0.007
getPathNames	0.304	0.008	0.312
gseattperm	1.268	0.032	1.535
hyperg	0.676	0.012	0.701
makeChrBandGraph	7.321	0.000	7.330
makeEBcontr	0.268	0.008	0.278
probes2MAP	0.236	0.004	0.239
probes2Path	0.092	0.004	0.094
ttperm	0.024	0.000	0.026