Package: ComplexHeatmap

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ComplexHeatmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ComplexHeatmap_2.2.0.tar.gz

StartedAt: 2020-04-15 01:24:55 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:27:26 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 150.7 seconds

RetCode: 0

Status:  OK

CheckDir: ComplexHeatmap.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ComplexHeatmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ComplexHeatmap_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.2.0’
* 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 ‘ComplexHeatmap’ can be installed ... OK
* checking installed package size ... OK
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
anno_horizon 7.38  0.073   7.547
* 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: OK

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ComplexHeatmap’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ComplexHeatmap)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 96 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 28.597   0.535  29.256 

name	user	system	elapsed
AdditiveUnit-class	0.000	0.001	0.000
AdditiveUnit	0.000	0.000	0.001
AnnotationFunction-class	0.001	0.000	0.001
AnnotationFunction	4.815	0.052	4.894
ColorMapping-class	0.000	0.000	0.001
ColorMapping	0.013	0.001	0.013
ComplexHeatmap-package	0.001	0.000	0.001
Extract.AnnotationFunction	0.035	0.001	0.037
Extract.Heatmap	0.749	0.004	0.762
Extract.HeatmapAnnotation	0.055	0.002	0.056
Extract.HeatmapList	0.192	0.002	0.196
Extract.SingleAnnotation	0.023	0.001	0.023
Extract.comb_mat	0.005	0.000	0.006
Heatmap-class	0	0	0
Heatmap	0.001	0.000	0.000
HeatmapAnnotation-class	0.001	0.000	0.000
HeatmapAnnotation	0.000	0.000	0.001
HeatmapList-class	0.000	0.000	0.001
HeatmapList	0.000	0.000	0.001
Legend	0.098	0.003	0.101
Legends-class	0.008	0.000	0.008
Legends	0	0	0
SingleAnnotation-class	0	0	0
SingleAnnotation	0.071	0.002	0.073
UpSet	0.975	0.006	0.989
add.AdditiveUnit	0.001	0.001	0.000
add_heatmap-Heatmap-method	0.000	0.000	0.001
add_heatmap-HeatmapAnnotation-method	0	0	0
add_heatmap-HeatmapList-method	0	0	0
add_heatmap-dispatch	0.000	0.000	0.001
adjust_dend_by_x	0.027	0.003	0.030
adjust_heatmap_list-HeatmapList-method	0	0	0
anno_barplot	0.044	0.002	0.047
anno_block	0.496	0.003	0.503
anno_boxplot	0.054	0.001	0.056
anno_density	0.674	0.013	0.710
anno_empty	0.033	0.002	0.034
anno_histogram	0.164	0.002	0.167
anno_horizon	7.380	0.073	7.547
anno_image	0	0	0
anno_joyplot	0.678	0.015	0.707
anno_lines	0.130	0.003	0.134
anno_link	0.001	0.000	0.000
anno_mark	0.841	0.004	0.851
anno_oncoprint_barplot	0	0	0
anno_points	0.040	0.002	0.042
anno_simple	0.088	0.002	0.091
anno_summary	0.414	0.002	0.418
anno_text	0.144	0.003	0.146
anno_zoom	0.515	0.002	0.518
annotation_axis_grob	0.119	0.007	0.126
annotation_legend_size-HeatmapList-method	0	0	0
c.ColorMapping	0.002	0.001	0.002
c.HeatmapAnnotation	0.060	0.001	0.061
cluster_within_group	0.042	0.001	0.043
color_mapping_legend-ColorMapping-method	0.000	0.000	0.001
columnAnnotation	0.001	0.001	0.000
column_dend-Heatmap-method	0.441	0.002	0.445
column_dend-HeatmapList-method	1.408	0.006	1.424
column_dend-dispatch	0	0	0
column_order-Heatmap-method	0.373	0.002	0.379
column_order-HeatmapList-method	1.395	0.005	1.414
column_order-dispatch	0	0	0
comb_degree	0.002	0.000	0.003
comb_name	0.003	0.000	0.003
comb_size	0.002	0.000	0.002
component_height-Heatmap-method	0.000	0.000	0.001
component_height-HeatmapList-method	0.000	0.001	0.000
component_height-dispatch	0.000	0.000	0.001
component_width-Heatmap-method	0	0	0
component_width-HeatmapList-method	0	0	0
component_width-dispatch	0	0	0
copy_all-AnnotationFunction-method	0.001	0.000	0.000
copy_all-SingleAnnotation-method	0.001	0.000	0.000
copy_all-dispatch	0.000	0.000	0.001
decorate_annotation	0.381	0.001	0.388
decorate_column_dend	0.000	0.001	0.001
decorate_column_names	0	0	0
decorate_column_title	0	0	0
decorate_dend	0.245	0.001	0.250
decorate_dimnames	0.283	0.001	0.286
decorate_heatmap_body	0.185	0.001	0.186
decorate_row_dend	0.000	0.000	0.001
decorate_row_names	0	0	0
decorate_row_title	0	0	0
decorate_title	0.215	0.001	0.216
default_axis_param	0.001	0.001	0.001
default_get_type	0.000	0.000	0.001
dend_heights	0.001	0.000	0.000
dend_xy	0.035	0.000	0.036
dendrogramGrob	0	0	0
densityHeatmap	1.731	0.010	1.758
dim.Heatmap	0.000	0.000	0.001
dist2	0.019	0.001	0.020
draw-AnnotationFunction-method	0	0	0
draw-Heatmap-method	0	0	0
draw-HeatmapAnnotation-method	0.000	0.000	0.001
draw-HeatmapList-method	0	0	0
draw-Legends-method	0.023	0.000	0.023
draw-SingleAnnotation-method	0.000	0.000	0.001
draw-dispatch	0.000	0.001	0.000
draw_annotation-Heatmap-method	0.000	0.000	0.001
draw_annotation_legend-HeatmapList-method	0	0	0
draw_dend-Heatmap-method	0	0	0
draw_dimnames-Heatmap-method	0.000	0.000	0.001
draw_heatmap_body-Heatmap-method	0	0	0
draw_heatmap_legend-HeatmapList-method	0.001	0.000	0.000
draw_heatmap_list-HeatmapList-method	0.001	0.000	0.001
draw_title-Heatmap-method	0	0	0
draw_title-HeatmapList-method	0.000	0.000	0.001
draw_title-dispatch	0.000	0.001	0.000
extract_comb	0.003	0.000	0.003
getXY_in_parent_vp	0.022	0.001	0.023
get_color_mapping_list-HeatmapAnnotation-method	0	0	0
get_legend_param_list-HeatmapAnnotation-method	0	0	0
grid.annotation_axis	0.001	0.000	0.000
grid.boxplot	0.018	0.001	0.019
grid.dendrogram	1.016	0.041	1.063
grid.draw.Legends	0.022	0.002	0.024
heatmap_legend_size-HeatmapList-method	0	0	0
height.AnnotationFunction	0.017	0.001	0.018
height.Heatmap	0	0	0
height.HeatmapAnnotation	0.001	0.000	0.001
height.HeatmapList	0	0	0
height.Legends	0.020	0.001	0.022
height.SingleAnnotation	0.001	0.000	0.001
heightAssign.AnnotationFunction	0	0	0
heightAssign.HeatmapAnnotation	0	0	0
heightAssign.SingleAnnotation	0.000	0.000	0.001
heightDetails.annotation_axis	0.000	0.000	0.001
heightDetails.legend	0	0	0
heightDetails.legend_body	0.000	0.001	0.000
heightDetails.packed_legends	0.001	0.000	0.001
ht_global_opt	0.000	0.000	0.001
ht_opt	0.007	0.001	0.008
is_abs_unit	0.002	0.000	0.002
length.HeatmapAnnotation	0	0	0
length.HeatmapList	0.001	0.000	0.001
list_components	0.000	0.001	0.001
list_to_matrix	0.002	0.001	0.003
make_column_cluster-Heatmap-method	0.000	0.000	0.001
make_comb_mat	0.008	0.000	0.009
make_layout-Heatmap-method	0	0	0
make_layout-HeatmapList-method	0	0	0
make_layout-dispatch	0.001	0.000	0.000
make_row_cluster-Heatmap-method	0.000	0.000	0.001
map_to_colors-ColorMapping-method	0.014	0.001	0.015
max_text_height	0.004	0.001	0.005
max_text_width	0.004	0.000	0.004
merge_dendrogram	0.094	0.002	0.098
names.HeatmapAnnotation	0.024	0.000	0.025
names.HeatmapList	0	0	0
namesAssign.HeatmapAnnotation	0.021	0.000	0.021
ncol.Heatmap	0.001	0.000	0.000
nobs.AnnotationFunction	0.007	0.000	0.007
nobs.HeatmapAnnotation	0.000	0.000	0.001
nobs.SingleAnnotation	0	0	0
normalize_comb_mat	0.000	0.000	0.001
nrow.Heatmap	0.001	0.000	0.001
oncoPrint	0.000	0.000	0.001
order.comb_mat	0.000	0.000	0.001
packLegend	0.098	0.002	0.102
pct_v_pct	0.000	0.000	0.001
pindex	0.007	0.001	0.008
prepare-Heatmap-method	0.000	0.001	0.000
print.comb_mat	0.001	0.000	0.001
re_size-HeatmapAnnotation-method	0	0	0
restore_matrix	0.562	0.003	0.567
rowAnnotation	0	0	0
row_anno_barplot	0.001	0.001	0.000
row_anno_boxplot	0.001	0.000	0.000
row_anno_density	0	0	0
row_anno_histogram	0.000	0.001	0.000
row_anno_link	0.001	0.000	0.001
row_anno_points	0	0	0
row_anno_text	0.000	0.000	0.001
row_dend-Heatmap-method	0.384	0.002	0.388
row_dend-HeatmapList-method	1.004	0.004	1.012
row_dend-dispatch	0	0	0
row_order-Heatmap-method	0.432	0.003	0.436
row_order-HeatmapList-method	1.076	0.004	1.083
row_order-dispatch	0	0	0
set_component_height-Heatmap-method	0	0	0
set_component_width-Heatmap-method	0	0	0
set_name	0.002	0.000	0.002
set_size	0.002	0.000	0.002
show-AnnotationFunction-method	0.000	0.001	0.000
show-ColorMapping-method	0.001	0.000	0.001
show-Heatmap-method	0.001	0.000	0.000
show-HeatmapAnnotation-method	0.001	0.001	0.000
show-HeatmapList-method	0.000	0.000	0.001
show-SingleAnnotation-method	0	0	0
show-dispatch	0.000	0.001	0.001
size.AnnotationFunction	0.013	0.000	0.013
size.HeatmapAnnotation	0.000	0.000	0.001
size.SingleAnnotation	0.001	0.000	0.000
sizeAssign.AnnotationFunction	0.007	0.000	0.008
sizeAssign.HeatmapAnnotation	0.000	0.001	0.000
sizeAssign.SingleAnnotation	0	0	0
smartAlign2	0.122	0.004	0.128
str.comb_mat	0	0	0
subset_gp	0.001	0.000	0.000
subset_matrix_by_row	0	0	0
subset_vector	0	0	0
summary.Heatmap	0.001	0.000	0.000
summary.HeatmapList	0.001	0.000	0.000
t.comb_mat	0.003	0.001	0.002
test_alter_fun	0.094	0.001	0.098
unify_mat_list	0.000	0.000	0.001
upset_right_annotation	0	0	0
upset_top_annotation	0.000	0.001	0.000
width.AnnotationFunction	0.013	0.000	0.013
width.Heatmap	0	0	0
width.HeatmapAnnotation	0	0	0
width.HeatmapList	0	0	0
width.Legends	0.015	0.000	0.016
width.SingleAnnotation	0.000	0.001	0.000
widthAssign.AnnotationFunction	0.000	0.000	0.001
widthAssign.HeatmapAnnotation	0	0	0
widthAssign.SingleAnnotation	0.000	0.001	0.000
widthDetails.annotation_axis	0	0	0
widthDetails.legend	0	0	0
widthDetails.legend_body	0.000	0.001	0.000
widthDetails.packed_legends	0	0	0