BioC 3.5: CHECK report for EnrichedHeatmap on oaxaca

Package: EnrichedHeatmap

Version: 1.5.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EnrichedHeatmap_1.5.1.tar.gz

StartedAt: 2017-03-04 02:19:48 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 02:22:34 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 165.9 seconds

RetCode: 0

Status:  OK

CheckDir: EnrichedHeatmap.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 EnrichedHeatmap_1.5.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/EnrichedHeatmap.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 ‘EnrichedHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EnrichedHeatmap’ version ‘1.5.1’
* 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 ‘EnrichedHeatmap’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   2.5Mb
* 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 loading without being on the library search path ... 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
+.AdditiveUnit: no visible global function definition for ‘new’
EnrichedHeatmapList: no visible global function definition for ‘new’
anno_enriched : <anonymous>: no visible global function definition for
  ‘col2rgb’
anno_enriched : <anonymous>: no visible global function definition for
  ‘rgb’
changeClassName: no visible global function definition for ‘new’
changeClassName: no visible global function definition for ‘slotNames’
changeClassName: no visible global function definition for ‘slot<-’
changeClassName: no visible global function definition for ‘slot’
default_smooth_fun: no visible global function definition for ‘predict’
default_smooth_fun: no visible global function definition for
  ‘loess.control’
draw,EnrichedHeatmap: no visible global function definition for ‘new’
draw,EnrichedHeatmapList: no visible global function definition for
  ‘selectMethod’
Undefined global functions or variables:
  col2rgb loess.control new predict rgb selectMethod slot slot<-
  slotNames
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("methods", "new", "selectMethod", "slot", "slot<-",
             "slotNames")
  importFrom("stats", "loess.control", "predict")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
EnrichedHeatmap 12.782  0.316  19.144
anno_enriched    6.228  0.152   6.408
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/EnrichedHeatmap.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
EnrichedHeatmap-class	0.001	0.000	0.001
EnrichedHeatmap	12.782	0.316	19.144
EnrichedHeatmapList-class	0.000	0.000	0.001
EnrichedHeatmapList	0.000	0.000	0.001
Extract.normalizedMatrix	0	0	0
add.AdditiveUnit	0	0	0
anno_enriched	6.228	0.152	6.408
copyAttr	0.000	0.000	0.001
default_smooth_fun	0.000	0.000	0.001
draw-EnrichedHeatmap-method	0	0	0
draw-EnrichedHeatmapList-method	0	0	0
draw-dispatch	0.001	0.000	0.001
enriched_score	0.001	0.000	0.001
getSignalsFromList	0.001	0.000	0.001
makeWindows	0.369	0.003	0.372
normalizeToMatrix	2.460	0.009	2.469
print.normalizedMatrix	0	0	0
show-EnrichedHeatmap-method	0	0	0
show-EnrichedHeatmapList-method	0.000	0.000	0.001
show-dispatch	0.000	0.000	0.001