Package: ComplexHeatmap

Version: 1.99.7

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_1.99.7.tar.gz

StartedAt: 2019-04-09 00:05:43 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:08:41 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 178.5 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 --install=check:ComplexHeatmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ComplexHeatmap_1.99.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ComplexHeatmap.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 ‘ComplexHeatmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ComplexHeatmap’ version ‘1.99.7’
* 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 6.416  0.054   6.499
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ComplexHeatmap
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ComplexHeatmap’ ...
** 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
* DONE (ComplexHeatmap)

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)
> suppressWarnings(suppressPackageStartupMessages(library(ComplexHeatmap)))
> 
> test_check("ComplexHeatmap")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 96 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 26.237   0.513  26.829 

name	user	system	elapsed
AdditiveUnit-class	0	0	0
AdditiveUnit	0.001	0.000	0.000
AnnotationFunction-class	0	0	0
AnnotationFunction	4.761	0.043	4.834
ColorMapping-class	0.000	0.000	0.001
ColorMapping	0.014	0.001	0.015
ComplexHeatmap-package	0	0	0
Extract.AnnotationFunction	0.030	0.001	0.031
Extract.Heatmap	0.741	0.004	0.751
Extract.HeatmapAnnotation	0.062	0.001	0.064
Extract.HeatmapList	0.197	0.001	0.199
Extract.SingleAnnotation	0.028	0.000	0.029
Extract.comb_mat	0.006	0.000	0.006
Heatmap-class	0.001	0.000	0.000
Heatmap	0.001	0.000	0.000
HeatmapAnnotation-class	0	0	0
HeatmapAnnotation	0	0	0
HeatmapList-class	0.000	0.001	0.000
HeatmapList	0.000	0.000	0.001
Legend	0.108	0.002	0.111
Legends-class	0.008	0.000	0.008
Legends	0	0	0
SingleAnnotation-class	0.000	0.001	0.001
SingleAnnotation	0.100	0.002	0.103
UpSet	0.930	0.007	0.946
add.AdditiveUnit	0.000	0.000	0.001
add_heatmap-Heatmap-method	0	0	0
add_heatmap-HeatmapAnnotation-method	0.001	0.000	0.001
add_heatmap-HeatmapList-method	0	0	0
add_heatmap-dispatch	0	0	0
adjust_dend_by_x	0.034	0.003	0.036
adjust_heatmap_list-HeatmapList-method	0.000	0.000	0.001
anno_barplot	0.043	0.001	0.044
anno_block	0.438	0.001	0.443
anno_boxplot	0.060	0.001	0.062
anno_density	0.677	0.016	0.703
anno_empty	0.020	0.001	0.021
anno_histogram	0.138	0.001	0.142
anno_horizon	6.416	0.054	6.499
anno_image	0	0	0
anno_joyplot	0.625	0.012	0.643
anno_lines	0.119	0.002	0.122
anno_link	0	0	0
anno_mark	0.552	0.003	0.559
anno_oncoprint_barplot	0.000	0.001	0.000
anno_points	0.042	0.001	0.043
anno_simple	0.082	0.002	0.084
anno_summary	0.383	0.001	0.387
anno_text	0.125	0.003	0.127
anno_zoom	0.450	0.002	0.456
annotation_axis_grob	0.078	0.004	0.107
annotation_legend_size-HeatmapList-method	0.001	0.000	0.000
c.HeatmapAnnotation	0.059	0.001	0.061
cluster_within_group	0.030	0.001	0.031
color_mapping_legend-ColorMapping-method	0	0	0
columnAnnotation	0.001	0.000	0.000
column_dend-Heatmap-method	0.346	0.002	0.348
column_dend-HeatmapList-method	1.127	0.005	1.139
column_dend-dispatch	0	0	0
column_order-Heatmap-method	0.335	0.002	0.339
column_order-HeatmapList-method	1.188	0.005	1.198
column_order-dispatch	0	0	0
comb_degree	0.001	0.000	0.002
comb_name	0.001	0.000	0.002
comb_size	0.001	0.000	0.001
component_height-Heatmap-method	0	0	0
component_height-HeatmapList-method	0	0	0
component_height-dispatch	0.001	0.000	0.000
component_width-Heatmap-method	0	0	0
component_width-HeatmapList-method	0	0	0
component_width-dispatch	0.001	0.000	0.000
copy_all-AnnotationFunction-method	0.000	0.000	0.001
copy_all-SingleAnnotation-method	0.000	0.001	0.001
copy_all-dispatch	0.001	0.000	0.000
decorate_annotation	0.344	0.001	0.347
decorate_column_dend	0	0	0
decorate_column_names	0	0	0
decorate_column_title	0.000	0.000	0.001
decorate_dend	0.209	0.001	0.210
decorate_dimnames	0.236	0.001	0.238
decorate_heatmap_body	0.159	0.001	0.161
decorate_row_dend	0.000	0.001	0.001
decorate_row_names	0	0	0
decorate_row_title	0	0	0
decorate_title	0.178	0.001	0.179
default_axis_param	0.001	0.001	0.001
default_get_type	0.001	0.000	0.001
dend_heights	0.000	0.000	0.001
dend_xy	0.023	0.000	0.024
dendrogramGrob	0	0	0
densityHeatmap	1.637	0.010	1.657
dim.Heatmap	0.000	0.001	0.001
dist2	0.013	0.000	0.014
draw-AnnotationFunction-method	0.000	0.001	0.000
draw-Heatmap-method	0.000	0.000	0.001
draw-HeatmapAnnotation-method	0	0	0
draw-HeatmapList-method	0.001	0.001	0.000
draw-Legends-method	0.026	0.000	0.026
draw-SingleAnnotation-method	0.000	0.000	0.001
draw-dispatch	0	0	0
draw_annotation-Heatmap-method	0	0	0
draw_annotation_legend-HeatmapList-method	0.000	0.000	0.001
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	0.001
draw_heatmap_list-HeatmapList-method	0	0	0
draw_title-Heatmap-method	0	0	0
draw_title-HeatmapList-method	0	0	0
draw_title-dispatch	0	0	0
extract_comb	0.002	0.000	0.002
getXY_in_parent_vp	0.023	0.001	0.024
get_color_mapping_list-HeatmapAnnotation-method	0.001	0.000	0.000
get_legend_param_list-HeatmapAnnotation-method	0	0	0
grid.annotation_axis	0	0	0
grid.boxplot	0.013	0.000	0.014
grid.dendrogram	1.818	0.078	1.902
grid.draw.Legends	0.012	0.000	0.012
heatmap_legend_size-HeatmapList-method	0.000	0.001	0.000
height.AnnotationFunction	0.009	0.000	0.008
height.Heatmap	0	0	0
height.HeatmapAnnotation	0	0	0
height.HeatmapList	0.000	0.001	0.000
height.Legends	0.012	0.000	0.013
height.SingleAnnotation	0	0	0
heightAssign.AnnotationFunction	0.000	0.000	0.001
heightAssign.HeatmapAnnotation	0.001	0.001	0.001
heightAssign.SingleAnnotation	0.000	0.000	0.001
heightDetails.annotation_axis	0	0	0
heightDetails.legend	0	0	0
heightDetails.legend_body	0	0	0
heightDetails.packed_legends	0.000	0.000	0.001
ht_global_opt	0	0	0
ht_opt	0.010	0.001	0.010
is_abs_unit	0.001	0.000	0.001
length.HeatmapAnnotation	0	0	0
length.HeatmapList	0	0	0
list_components	0.000	0.000	0.001
list_to_matrix	0.001	0.001	0.002
make_column_cluster-Heatmap-method	0.001	0.000	0.000
make_comb_mat	0.005	0.001	0.005
make_layout-Heatmap-method	0.000	0.000	0.001
make_layout-HeatmapList-method	0	0	0
make_layout-dispatch	0.000	0.000	0.001
make_row_cluster-Heatmap-method	0	0	0
map_to_colors-ColorMapping-method	0.015	0.001	0.014
max_text_height	0.002	0.000	0.002
max_text_width	0.003	0.000	0.003
merge_dendrogram	0.112	0.002	0.116
names.HeatmapAnnotation	0.031	0.001	0.032
names.HeatmapList	0.000	0.000	0.001
namesAssign.HeatmapAnnotation	0.027	0.001	0.028
ncol.Heatmap	0.001	0.000	0.000
nobs.AnnotationFunction	0.007	0.000	0.007
nobs.HeatmapAnnotation	0	0	0
nobs.SingleAnnotation	0.001	0.000	0.000
normalize_comb_mat	0	0	0
nrow.Heatmap	0	0	0
oncoPrint	0.000	0.000	0.001
order.comb_mat	0.000	0.001	0.000
packLegend	0.080	0.001	0.083
pct_v_pct	0	0	0
pindex	0.004	0.000	0.005
prepare-Heatmap-method	0	0	0
print.comb_mat	0.001	0.000	0.000
re_size-HeatmapAnnotation-method	0	0	0
restore_matrix	0.556	0.003	0.562
rowAnnotation	0	0	0
row_anno_barplot	0	0	0
row_anno_boxplot	0	0	0
row_anno_density	0	0	0
row_anno_histogram	0.001	0.000	0.001
row_anno_link	0.000	0.000	0.001
row_anno_points	0.000	0.000	0.001
row_anno_text	0.000	0.000	0.001
row_dend-Heatmap-method	0.354	0.002	0.356
row_dend-HeatmapList-method	0.910	0.004	0.918
row_dend-dispatch	0	0	0
row_order-Heatmap-method	0.376	0.001	0.378
row_order-HeatmapList-method	0.877	0.005	0.890
row_order-dispatch	0	0	0
set_component_height-Heatmap-method	0.000	0.000	0.001
set_component_width-Heatmap-method	0.000	0.000	0.001
set_name	0.002	0.000	0.002
set_size	0.001	0.000	0.001
show-AnnotationFunction-method	0.000	0.000	0.001
show-ColorMapping-method	0	0	0
show-Heatmap-method	0.000	0.001	0.000
show-HeatmapAnnotation-method	0.001	0.000	0.000
show-HeatmapList-method	0.001	0.000	0.000
show-SingleAnnotation-method	0	0	0
show-dispatch	0.000	0.000	0.001
size.AnnotationFunction	0.013	0.001	0.013
size.HeatmapAnnotation	0.000	0.000	0.001
size.SingleAnnotation	0	0	0
sizeAssign.AnnotationFunction	0.007	0.000	0.007
sizeAssign.HeatmapAnnotation	0	0	0
sizeAssign.SingleAnnotation	0	0	0
smartAlign2	0.102	0.003	0.106
str.comb_mat	0	0	0
subset_gp	0.001	0.000	0.000
subset_matrix_by_row	0.000	0.000	0.001
subset_vector	0	0	0
summary.Heatmap	0	0	0
summary.HeatmapList	0	0	0
t.comb_mat	0.002	0.000	0.002
test_alter_fun	0.082	0.001	0.082
unify_mat_list	0	0	0
upset_right_annotation	0.000	0.001	0.001
upset_top_annotation	0	0	0
width.AnnotationFunction	0.017	0.000	0.018
width.Heatmap	0	0	0
width.HeatmapAnnotation	0.000	0.000	0.001
width.HeatmapList	0	0	0
width.Legends	0.02	0.00	0.02
width.SingleAnnotation	0	0	0
widthAssign.AnnotationFunction	0.001	0.000	0.000
widthAssign.HeatmapAnnotation	0.001	0.000	0.000
widthAssign.SingleAnnotation	0	0	0
widthDetails.annotation_axis	0.000	0.001	0.000
widthDetails.legend	0	0	0
widthDetails.legend_body	0	0	0
widthDetails.packed_legends	0.000	0.000	0.001