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CHECK report for heatmaps on merida2

This page was generated on 2019-04-09 13:35:01 -0400 (Tue, 09 Apr 2019).

Package 734/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
heatmaps 1.7.0
Malcolm Perry
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/heatmaps
Branch: master
Last Commit: 5a637bc
Last Changed Date: 2018-10-30 11:54:37 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: heatmaps
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:heatmaps.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings heatmaps_1.7.0.tar.gz
StartedAt: 2019-04-09 01:27:28 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:29:50 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 142.4 seconds
RetCode: 0
Status:  OK 
CheckDir: heatmaps.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:heatmaps.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings heatmaps_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/heatmaps.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.7.0’
* 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  7.4Mb
  sub-directories of 1Mb or more:
    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 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 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 ... 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-3.9-bioc/meat/heatmaps.Rcheck/00check.log’
for details.



Installation output

heatmaps.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL heatmaps
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘heatmaps’ ...
** R
** data
** inst
** byte-compile and prepare 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)

Tests output

heatmaps.Rcheck/tests/testthat.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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 
  6.910   0.445   7.395 

Example timings

heatmaps.Rcheck/heatmaps-Ex.timings

nameusersystemelapsed
CoverageHeatmap0.5070.0120.524
Heatmap-class0.0130.0020.015
Heatmap0.0120.0010.014
PWMScanHeatmap0.0480.0030.052
PatternHeatmap0.0600.0030.065
coords0.0120.0020.013
default_color0.0070.0010.008
getScale0.0000.0010.001
heatmapOptions0.0010.0000.001
image0.0130.0020.016
label0.0100.0020.012
metadata0.0100.0020.012
nseq0.0110.0020.013
plotHeatmap0.3820.0120.398
plotHeatmapList0.0950.0130.110
plotHeatmapMeta0.0410.0030.044
plotPatternDensityMap0.2700.0320.305
plot_clusters0.0690.0040.074
plot_legend0.0160.0020.019
scale0.0110.0020.013
smoothHeatmap0.0500.0150.064
xm0.0080.0010.009
ym0.0100.0030.013