BioC 3.5: CHECK report for Category on oaxaca

Package: Category

Version: 2.41.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Category_2.41.0.tar.gz

StartedAt: 2017-03-04 00:07:43 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 00:10:57 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 194.2 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_2.41.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Category.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Category/DESCRIPTION’ ... OK
* this is package ‘Category’ version ‘2.41.0’
* 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 ... 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 4.884  0.173   5.113
* 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	4.884	0.173	5.113
ChrMapHyperGParams-class	0.002	0.000	0.001
ChrMapHyperGResult-class	0.000	0.000	0.001
ChrMapLinearMParams-class	0.001	0.001	0.001
ChrMapLinearMResult-class	0.001	0.000	0.001
DatPkg-class	0.039	0.001	0.040
HyperGResult-accessors	1.001	0.050	1.310
LinearMResult-class	0.001	0.000	0.001
MAPAmat	3.080	0.160	3.242
applyByCategory	0.003	0.001	0.004
cateGOryMatrix	0.298	0.048	1.003
cb_parse_band_Hs	0	0	0
cb_parse_band_Mm	0.001	0.000	0.001
findAMstats	0.001	0.000	0.001
getPathNames	0.041	0.001	0.043
gseattperm	1.092	0.038	1.286
hyperg	0.502	0.054	0.556
makeChrBandGraph	2.056	0.049	2.106
makeEBcontr	0.125	0.003	0.184
probes2MAP	0.160	0.003	0.163
probes2Path	0.048	0.001	0.049
ttperm	0.016	0.001	0.016