BioC 3.5: CHECK report for Category on veracruz2

Package: Category

Version: 2.42.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Category_2.42.1.tar.gz

StartedAt: 2017-08-16 00:38:28 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:41:29 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 181.5 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 Category_2.42.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Category.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Category/DESCRIPTION’ ... OK
* this is package ‘Category’ version ‘2.42.1’
* 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 ... 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 ... NOTE
.linearMTestInternal: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ChrBandTree-class 4.777  0.148   5.057
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-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	4.777	0.148	5.057
ChrMapHyperGParams-class	0.002	0.000	0.002
ChrMapHyperGResult-class	0.001	0.000	0.000
ChrMapLinearMParams-class	0.001	0.000	0.000
ChrMapLinearMResult-class	0.001	0.000	0.001
DatPkg-class	0.042	0.001	0.042
HyperGResult-accessors	0.999	0.044	1.131
LinearMResult-class	0.002	0.001	0.002
MAPAmat	3.090	0.147	3.297
applyByCategory	0.005	0.001	0.006
cateGOryMatrix	0.318	0.019	0.339
cb_parse_band_Hs	0.001	0.001	0.001
cb_parse_band_Mm	0.000	0.000	0.001
findAMstats	0.002	0.000	0.002
getPathNames	0.039	0.001	0.041
gseattperm	1.039	0.041	1.083
hyperg	0.596	0.049	0.652
makeChrBandGraph	2.093	0.044	2.164
makeEBcontr	0.136	0.002	0.142
probes2MAP	0.203	0.004	0.208
probes2Path	0.047	0.001	0.048
ttperm	0.013	0.000	0.013