Package: heatmaps

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings heatmaps_1.2.0.tar.gz

StartedAt: 2018-04-12 05:00:06 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 05:02:18 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 132.7 seconds

RetCode: 0

Status:  OK

CheckDir: heatmaps.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 heatmaps_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/heatmaps.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘heatmaps/DESCRIPTION’ ... OK
* this is package ‘heatmaps’ version ‘1.2.0’
* 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 ‘heatmaps’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   6.9Mb
* 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
makeGaussian2D: no visible binding for global variable ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘rtracklayer’
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/heatmaps.Rcheck/00check.log’
for details.

* installing *source* package ‘heatmaps’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘scale’ in package ‘heatmaps’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (heatmaps)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(heatmaps)

Attaching package: 'heatmaps'

The following object is masked from 'package:base':

    scale

> 
> test_check("heatmaps")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 22 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  5.812   0.206   6.113 

name	user	system	elapsed
CoverageHeatmap	0.583	0.023	0.619
Heatmap-class	0.010	0.002	0.011
Heatmap	0.010	0.002	0.013
PWMScanHeatmap	0.038	0.003	0.041
PatternHeatmap	0.164	0.002	0.170
coords	0.009	0.002	0.011
default_color	0.003	0.000	0.004
getScale	0.001	0.001	0.001
heatmapOptions	0.665	0.009	0.683
image	0.008	0.001	0.009
label	0.009	0.001	0.011
metadata	0.010	0.001	0.010
nseq	0.006	0.001	0.008
plotHeatmap	0.056	0.003	0.061
plotHeatmapList	0.174	0.002	0.181
plotHeatmapMeta	0.038	0.001	0.040
plotPatternDensityMap	0.767	0.014	0.803
plot_clusters	0.054	0.002	0.055
plot_legend	0.013	0.002	0.015
scale	0.008	0.001	0.010
smoothHeatmap	0.046	0.008	0.115
xm	0.010	0.002	0.011
ym	0.011	0.003	0.014