BioC 2.14: CHECK report for Category on petty

Package: Category

Version: 2.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Category_2.30.0.tar.gz

StartedAt: 2014-10-07 21:04:08 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:12:53 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 525.0 seconds

RetCode: 0

Status:  OK

CheckDir: Category.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 --no-multiarch Category_2.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Category.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘2.30.0’
* 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 ... [35s/36s] 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 files in ‘vignettes’ ... OK
* checking examples ... [56s/56s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ChrBandTree-class 12.658  0.222  12.928
MAPAmat           10.539  0.289  10.860
makeChrBandGraph   7.760  0.086   7.869
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [114s/116s]
 [114s/117s] 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
  ‘/Users/biocbuild/bbs-2.14-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	12.658	0.222	12.928
ChrMapHyperGParams-class	0.005	0.000	0.005
ChrMapHyperGResult-class	0.002	0.000	0.003
ChrMapLinearMParams-class	0.004	0.001	0.003
ChrMapLinearMResult-class	0.003	0.001	0.004
DatPkg-class	0.172	0.008	0.186
HyperGResult-accessors	1.444	0.047	1.497
LinearMResult-class	0.003	0.000	0.003
MAPAmat	10.539	0.289	10.860
applyByCategory	0.008	0.001	0.008
cateGOryMatrix	0.578	0.059	0.638
cb_parse_band_Hs	0.001	0.000	0.001
cb_parse_band_Mm	0.002	0.000	0.002
findAMstats	0.002	0.000	0.003
getPathNames	0.183	0.007	0.201
gseattperm	2.396	0.113	2.527
hyperg	1.284	0.119	1.602
makeChrBandGraph	7.760	0.086	7.869
makeEBcontr	0.563	0.013	0.578
probes2MAP	0.536	0.009	0.554
probes2Path	0.193	0.008	0.202
ttperm	0.038	0.002	0.040