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CHECK report for heatmaps on malbec1

This page was generated on 2018-04-12 13:16:14 -0400 (Thu, 12 Apr 2018).

Package 643/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
heatmaps 1.2.0
Malcolm Perry
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/heatmaps
Branch: RELEASE_3_6
Last Commit: 8e0f6f1
Last Changed Date: 2017-10-30 12:41:27 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: heatmaps
Version: 1.2.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings heatmaps_1.2.0.tar.gz
StartedAt: 2018-04-12 00:14:38 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:16:33 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 115.7 seconds
RetCode: 0
Status:  OK 
CheckDir: heatmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings heatmaps_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/heatmaps.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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  9.8Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/heatmaps.Rcheck/00check.log’
for details.



Installation output

heatmaps.Rcheck/00install.out

* 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)

Tests output

heatmaps.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  4.960   0.100   5.058 

Example timings

heatmaps.Rcheck/heatmaps-Ex.timings

nameusersystemelapsed
CoverageHeatmap0.5440.0000.546
Heatmap-class0.0080.0000.010
Heatmap0.0120.0000.009
PWMScanHeatmap0.0280.0000.029
PatternHeatmap0.1240.0000.121
coords0.0080.0000.009
default_color0.0040.0000.003
getScale000
heatmapOptions0.4840.0080.489
image0.0080.0040.012
label0.0080.0000.008
metadata0.0080.0000.009
nseq0.0080.0000.011
plotHeatmap0.0400.0000.041
plotHeatmapList0.3640.0000.363
plotHeatmapMeta0.0320.0000.030
plotPatternDensityMap0.7960.0160.815
plot_clusters0.0600.0040.063
plot_legend0.0120.0040.013
scale0.0040.0040.010
smoothHeatmap0.0480.0000.293
xm0.0120.0000.012
ym0.0120.0000.014