BioC 3.6: CHECK report for heatmaps on veracruz1

Package: heatmaps

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings heatmaps_1.1.0.tar.gz

StartedAt: 2017-08-16 04:17:09 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:19:36 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 146.8 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/heatmaps.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 ‘heatmaps/DESCRIPTION’ ... OK
* this is package ‘heatmaps’ version ‘1.1.0’
* 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)

name	user	system	elapsed
CoverageHeatmap	0.665	0.024	0.714
Heatmap-class	0.011	0.001	0.014
Heatmap	0.010	0.002	0.012
PWMScanHeatmap	0.034	0.001	0.035
PatternHeatmap	0.120	0.002	0.128
coords	0.007	0.001	0.008
default_color	0.003	0.000	0.004
getScale	0.000	0.000	0.001
heatmapOptions	0.720	0.028	0.789
image	0.009	0.001	0.010
label	0.009	0.001	0.010
metadata	0.022	0.001	0.024
nseq	0.009	0.000	0.010
plotHeatmap	0.054	0.002	0.056
plotHeatmapList	0.183	0.002	0.192
plotHeatmapMeta	0.039	0.002	0.040
plotPatternDensityMap	0.894	0.018	0.931
plot_clusters	0.060	0.003	0.063
plot_legend	0.014	0.002	0.015
scale	0.009	0.002	0.011
smoothHeatmap	0.039	0.011	0.057
xm	0.009	0.001	0.010
ym	0.009	0.002	0.011