Package: ComplexHeatmap

Version: 1.17.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.17.1.tar.gz

StartedAt: 2018-04-12 02:06:42 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:08:33 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 110.7 seconds

RetCode: 0

Status:  OK

CheckDir: ComplexHeatmap.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 ComplexHeatmap_1.17.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ComplexHeatmap.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 ‘ComplexHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ComplexHeatmap’ version ‘1.17.1’
* 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 ‘ComplexHeatmap’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* 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 ... OK
* 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
Heatmap 19.569  0.113  20.198
* 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-3.6-bioc/meat/ComplexHeatmap.Rcheck/00check.log’
for details.

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

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)
> suppressWarnings(suppressPackageStartupMessages(library(ComplexHeatmap)))
> 
> test_check("ComplexHeatmap")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 17 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  1.942   0.084   2.073 

name	user	system	elapsed
AdditiveUnit-class	0	0	0
AdditiveUnit	0.001	0.000	0.001
ColorMapping-class	0	0	0
ColorMapping	0.130	0.006	0.139
ComplexHeatmap-package	0	0	0
Heatmap-class	0	0	0
Heatmap	19.569	0.113	20.198
HeatmapAnnotation-class	0.001	0.000	0.001
HeatmapAnnotation	0.188	0.002	0.192
HeatmapList-class	3.113	0.013	3.183
HeatmapList	0.001	0.000	0.000
Legend	0.304	0.003	0.320
SingleAnnotation-class	0.001	0.001	0.001
SingleAnnotation	0.092	0.001	0.094
add.AdditiveUnit	3.634	0.014	3.746
add_heatmap-Heatmap-method	1.045	0.006	1.073
add_heatmap-HeatmapAnnotation-method	0.516	0.003	0.526
add_heatmap-HeatmapList-method	1.482	0.009	1.510
add_heatmap-dispatch	0.000	0.000	0.001
adjust_dend_by_leaf_width	1.252	0.023	1.314
anno_barplot	0.160	0.001	0.167
anno_boxplot	0.262	0.002	0.272
anno_density	0.383	0.004	0.398
anno_histogram	0.165	0.001	0.172
anno_link	1.893	0.021	1.951
anno_oncoprint_barplot	0.000	0.000	0.001
anno_points	0.022	0.002	0.027
anno_text	0.375	0.002	0.399
annotation_legend_size-HeatmapList-method	0.001	0.001	0.001
color_mapping_legend-ColorMapping-method	0.226	0.002	0.242
columnAnnotation	0.017	0.001	0.017
column_anno_barplot	0	0	0
column_anno_boxplot	0.000	0.000	0.001
column_anno_density	0.000	0.001	0.001
column_anno_histogram	0.001	0.000	0.000
column_anno_link	0.000	0.000	0.001
column_anno_points	0.001	0.000	0.000
column_anno_text	0.001	0.000	0.001
column_dend-Heatmap-method	0.082	0.000	0.083
column_dend-HeatmapList-method	0.290	0.001	0.301
column_dend-dispatch	0.001	0.000	0.000
column_order-Heatmap-method	0.094	0.001	0.095
column_order-HeatmapList-method	0.278	0.001	0.285
column_order-dispatch	0.000	0.000	0.001
component_height-Heatmap-method	0.001	0.000	0.000
component_height-HeatmapList-method	0.001	0.000	0.000
component_height-dispatch	0.000	0.000	0.001
component_width-Heatmap-method	0.000	0.000	0.001
component_width-HeatmapList-method	0.000	0.000	0.001
component_width-dispatch	0	0	0
decorate_annotation	0.663	0.004	0.678
decorate_column_dend	0.000	0.000	0.001
decorate_column_names	0.000	0.000	0.001
decorate_column_title	0.001	0.000	0.001
decorate_dend	0.373	0.002	0.377
decorate_dimnames	0.449	0.002	0.453
decorate_heatmap_body	0.331	0.001	0.337
decorate_row_dend	0.000	0.001	0.000
decorate_row_names	0	0	0
decorate_row_title	0.001	0.000	0.000
decorate_title	0.377	0.002	0.387
densityHeatmap	4.379	0.025	4.492
dist2	0.034	0.000	0.033
draw-Heatmap-method	0.476	0.002	0.495
draw-HeatmapAnnotation-method	0.159	0.003	0.166
draw-HeatmapList-method	1.226	0.004	1.273
draw-SingleAnnotation-method	0.141	0.004	0.159
draw-dispatch	0.000	0.000	0.001
draw_annotation-Heatmap-method	0.000	0.000	0.001
draw_annotation_legend-HeatmapList-method	0.001	0.000	0.001
draw_dend-Heatmap-method	0.001	0.000	0.000
draw_dimnames-Heatmap-method	0.001	0.000	0.001
draw_heatmap_body-Heatmap-method	0.001	0.000	0.001
draw_heatmap_legend-HeatmapList-method	0.001	0.000	0.001
draw_heatmap_list-HeatmapList-method	0.001	0.000	0.000
draw_title-Heatmap-method	0	0	0
draw_title-HeatmapList-method	0.000	0.000	0.001
draw_title-dispatch	0.001	0.000	0.001
enhanced_basicplot	1.200	0.005	1.253
get_color_mapping_list-HeatmapAnnotation-method	0.001	0.000	0.002
get_color_mapping_param_list-HeatmapAnnotation-method	0	0	0
grid.dendrogram	0.024	0.001	0.028
grid.dendrogram2	0.243	0.001	0.252
heatmap_legend_size-HeatmapList-method	0.001	0.000	0.001
ht_global_opt	0.000	0.001	0.001
is_abs_unit	0.002	0.000	0.002
make_column_cluster-Heatmap-method	0.000	0.000	0.001
make_layout-Heatmap-method	0.000	0.000	0.001
make_layout-HeatmapList-method	0.000	0.000	0.001
make_layout-dispatch	0.001	0.000	0.000
make_row_cluster-Heatmap-method	0.001	0.001	0.000
map_to_colors-ColorMapping-method	0.025	0.001	0.026
max_text_height	0.002	0.000	0.002
max_text_width	0.001	0.000	0.002
oncoPrint	0.000	0.000	0.001
packLegend	1.201	0.004	1.237
plotDataFrame	3.416	0.016	3.492
prepare-Heatmap-method	0	0	0
rowAnnotation	0.020	0.000	0.019
row_anno_barplot	0.001	0.000	0.000
row_anno_boxplot	0.001	0.000	0.001
row_anno_density	0.001	0.000	0.001
row_anno_histogram	0.000	0.000	0.001
row_anno_link	0	0	0
row_anno_points	0.000	0.000	0.001
row_anno_text	0.000	0.001	0.001
row_dend-Heatmap-method	0.107	0.000	0.108
row_dend-HeatmapList-method	0.273	0.000	0.277
row_dend-dispatch	0.001	0.000	0.001
row_order-Heatmap-method	0.094	0.000	0.097
row_order-HeatmapList-method	0.277	0.001	0.285
row_order-dispatch	0.001	0.000	0.001
selectArea	0.001	0.000	0.001
set_component_height-Heatmap-method	0.001	0.000	0.001
show-ColorMapping-method	0.000	0.000	0.001
show-Heatmap-method	0.929	0.005	0.951
show-HeatmapAnnotation-method	0.001	0.000	0.000
show-HeatmapList-method	0.000	0.001	0.001
show-SingleAnnotation-method	0.000	0.000	0.001
show-dispatch	0.000	0.000	0.001
unify_mat_list	0.001	0.001	0.001