BioC 3.3: CHECK report for HilbertCurve on oaxaca

Package: HilbertCurve

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HilbertCurve_1.2.2.tar.gz

StartedAt: 2016-10-13 02:42:49 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:45:17 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 148.1 seconds

RetCode: 0

Status:  OK

CheckDir: HilbertCurve.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 HilbertCurve_1.2.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/HilbertCurve.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HilbertCurve/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HilbertCurve’ version ‘1.2.2’
* 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 ‘HilbertCurve’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc   8.5Mb
* 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 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
hc_centered_text,HilbertCurve : <anonymous>: no visible global function
  definition for ‘hist’
hc_segmented_points,HilbertCurve: no visible global function definition
  for ‘rgb’
Undefined global functions or variables:
  hist rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "hist")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
hc_layer-HilbertCurve-method        21.860  0.674  22.700
hc_layer-GenomicHilbertCurve-method  7.895  0.143   8.066
hc_png-HilbertCurve-method           7.191  0.200   7.646
* 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-3.3-bioc/meat/HilbertCurve.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
GenomicHilbertCurve-class	0	0	0
GenomicHilbertCurve	4.507	0.088	4.973
HilbertCurve-class	0.000	0.001	0.001
HilbertCurve	2.014	0.031	2.609
default_overlay	0.000	0.000	0.001
hc_centered_text-HilbertCurve-method	0.087	0.001	0.089
hc_layer-GenomicHilbertCurve-method	7.895	0.143	8.066
hc_layer-HilbertCurve-method	21.860	0.674	22.700
hc_layer-dispatch	0.001	0.000	0.000
hc_level-HilbertCurve-method	0.037	0.002	0.039
hc_map-GenomicHilbertCurve-method	3.345	0.028	3.555
hc_normal_points-HilbertCurve-method	0	0	0
hc_offset-HilbertCurve-method	0.025	0.001	0.029
hc_png-HilbertCurve-method	7.191	0.200	7.646
hc_points-GenomicHilbertCurve-method	0.356	0.006	0.396
hc_points-HilbertCurve-method	0.699	0.013	0.786
hc_points-dispatch	0	0	0
hc_polygon-GenomicHilbertCurve-method	0.678	0.004	0.700
hc_polygon-HilbertCurve-method	0.071	0.001	0.072
hc_polygon-dispatch	0.001	0.000	0.001
hc_rect-GenomicHilbertCurve-method	0.181	0.002	0.182
hc_rect-HilbertCurve-method	0.044	0.001	0.045
hc_rect-dispatch	0.001	0.000	0.001
hc_segmented_points-HilbertCurve-method	0.001	0.000	0.000
hc_segments-GenomicHilbertCurve-method	0.800	0.003	0.818
hc_segments-HilbertCurve-method	0.085	0.001	0.086
hc_segments-dispatch	0.001	0.000	0.000
hc_text-GenomicHilbertCurve-method	0.164	0.002	0.166
hc_text-HilbertCurve-method	0.029	0.001	0.029
hc_text-dispatch	0.001	0.000	0.001
show-HilbertCurve-method	0.013	0.001	0.014
unzoom-HilbertCurve-method	0.011	0.000	0.012
zoom-HilbertCurve-method	0.012	0.000	0.013