Package: ComplexHeatmap

Version: 2.3.0

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_2.3.0.tar.gz

StartedAt: 2020-01-16 03:11:39 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 03:15:29 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 230.6 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_2.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ComplexHeatmap.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.3.0’
* 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 (user + system) or elapsed time > 5s
                    user system elapsed
anno_horizon       9.464  0.171  10.140
AnnotationFunction 7.161  0.101   7.665
* 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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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 
 44.557   1.440  47.310 

name	user	system	elapsed
AdditiveUnit-class	0	0	0
AdditiveUnit	0.001	0.000	0.000
AnnotationFunction-class	0.000	0.000	0.001
AnnotationFunction	7.161	0.101	7.665
ColorMapping-class	0.001	0.000	0.000
ColorMapping	0.013	0.001	0.014
ComplexHeatmap-package	0.000	0.000	0.001
Extract.AnnotationFunction	0.046	0.003	0.048
Extract.Heatmap	1.048	0.013	1.063
Extract.HeatmapAnnotation	0.085	0.008	0.093
Extract.HeatmapList	0.271	0.005	0.276
Extract.SingleAnnotation	0.029	0.003	0.032
Extract.comb_mat	0.004	0.001	0.004
Heatmap-class	0	0	0
Heatmap	0	0	0
HeatmapAnnotation-class	0.001	0.000	0.000
HeatmapAnnotation	0.000	0.000	0.001
HeatmapList-class	0.000	0.000	0.001
HeatmapList	0.001	0.001	0.000
Legend	0.142	0.005	0.148
Legends-class	0.014	0.000	0.014
Legends	0.001	0.000	0.001
SingleAnnotation-class	0.000	0.000	0.001
SingleAnnotation	0.122	0.005	0.128
UpSet	1.152	0.010	1.168
add.AdditiveUnit	0.000	0.000	0.001
add_heatmap-Heatmap-method	0	0	0
add_heatmap-HeatmapAnnotation-method	0.000	0.001	0.000
add_heatmap-HeatmapList-method	0.000	0.000	0.001
add_heatmap-dispatch	0.001	0.000	0.001
adjust_dend_by_x	0.033	0.004	0.036
adjust_heatmap_list-HeatmapList-method	0.000	0.001	0.000
anno_barplot	0.053	0.002	0.054
anno_block	0.649	0.003	0.652
anno_boxplot	0.074	0.002	0.077
anno_density	0.947	0.028	0.981
anno_empty	0.040	0.002	0.060
anno_histogram	0.206	0.003	0.219
anno_horizon	9.464	0.171	10.140
anno_image	0.000	0.001	0.001
anno_joyplot	0.727	0.033	0.773
anno_lines	0.126	0.005	0.133
anno_link	0	0	0
anno_mark	0.909	0.021	0.933
anno_oncoprint_barplot	0.000	0.000	0.001
anno_points	0.048	0.004	0.053
anno_simple	0.115	0.004	0.124
anno_summary	0.481	0.002	0.510
anno_text	0.191	0.005	0.254
anno_zoom	0.643	0.009	0.657
annotation_axis_grob	0.151	0.012	0.285
annotation_legend_size-HeatmapList-method	0.000	0.000	0.001
c.ColorMapping	0.002	0.000	0.003
c.HeatmapAnnotation	0.098	0.002	0.100
cluster_within_group	0.041	0.001	0.051
color_mapping_legend-ColorMapping-method	0.000	0.000	0.001
columnAnnotation	0.001	0.000	0.001
column_dend-Heatmap-method	0.521	0.003	0.558
column_dend-HeatmapList-method	1.847	0.010	2.074
column_dend-dispatch	0	0	0
column_order-Heatmap-method	0.559	0.003	0.563
column_order-HeatmapList-method	1.759	0.008	1.770
column_order-dispatch	0	0	0
comb_degree	0.003	0.000	0.003
comb_name	0.003	0.001	0.004
comb_size	0.003	0.000	0.004
component_height-Heatmap-method	0.000	0.001	0.000
component_height-HeatmapList-method	0	0	0
component_height-dispatch	0.001	0.000	0.000
component_width-Heatmap-method	0.000	0.001	0.001
component_width-HeatmapList-method	0.001	0.000	0.001
component_width-dispatch	0.000	0.000	0.001
copy_all-AnnotationFunction-method	0.001	0.001	0.000
copy_all-SingleAnnotation-method	0	0	0
copy_all-dispatch	0.001	0.000	0.001
decorate_annotation	0.544	0.002	0.547
decorate_column_dend	0.000	0.001	0.001
decorate_column_names	0.001	0.000	0.000
decorate_column_title	0	0	0
decorate_dend	0.316	0.002	0.319
decorate_dimnames	0.361	0.002	0.363
decorate_heatmap_body	0.222	0.001	0.224
decorate_row_dend	0	0	0
decorate_row_names	0.001	0.000	0.001
decorate_row_title	0.000	0.001	0.000
decorate_title	0.312	0.002	0.313
default_axis_param	0.002	0.001	0.002
default_get_type	0.000	0.001	0.000
dend_heights	0.001	0.000	0.000
dend_xy	0.037	0.001	0.038
dendrogramGrob	0	0	0
densityHeatmap	2.319	0.028	2.873
dim.Heatmap	0	0	0
dist2	0.022	0.002	0.029
draw-AnnotationFunction-method	0.000	0.000	0.001
draw-Heatmap-method	0.000	0.001	0.000
draw-HeatmapAnnotation-method	0.001	0.000	0.000
draw-HeatmapList-method	0.000	0.000	0.001
draw-Legends-method	0.025	0.001	0.026
draw-SingleAnnotation-method	0.000	0.001	0.001
draw-dispatch	0.000	0.000	0.001
draw_annotation-Heatmap-method	0.001	0.000	0.000
draw_annotation_legend-HeatmapList-method	0.001	0.000	0.001
draw_dend-Heatmap-method	0.000	0.001	0.001
draw_dimnames-Heatmap-method	0.000	0.000	0.001
draw_heatmap_body-Heatmap-method	0.001	0.000	0.000
draw_heatmap_legend-HeatmapList-method	0.000	0.001	0.000
draw_heatmap_list-HeatmapList-method	0.000	0.001	0.001
draw_title-Heatmap-method	0.001	0.000	0.000
draw_title-HeatmapList-method	0	0	0
draw_title-dispatch	0.000	0.001	0.001
extract_comb	0.004	0.000	0.004
getXY_in_parent_vp	0.026	0.002	0.040
get_color_mapping_list-HeatmapAnnotation-method	0.001	0.000	0.001
get_legend_param_list-HeatmapAnnotation-method	0.000	0.000	0.001
grid.annotation_axis	0.000	0.000	0.001
grid.boxplot	0.017	0.001	0.018
grid.dendrogram	1.011	0.051	1.063
grid.draw.Legends	0.024	0.000	0.025
heatmap_legend_size-HeatmapList-method	0	0	0
height.AnnotationFunction	0.019	0.000	0.020
height.Heatmap	0.000	0.000	0.001
height.HeatmapAnnotation	0	0	0
height.HeatmapList	0.001	0.000	0.001
height.Legends	0.021	0.001	0.020
height.SingleAnnotation	0	0	0
heightAssign.AnnotationFunction	0	0	0
heightAssign.HeatmapAnnotation	0.000	0.000	0.001
heightAssign.SingleAnnotation	0.000	0.001	0.000
heightDetails.annotation_axis	0.000	0.000	0.001
heightDetails.legend	0	0	0
heightDetails.legend_body	0.000	0.001	0.001
heightDetails.packed_legends	0.001	0.000	0.000
ht_global_opt	0.000	0.000	0.001
ht_opt	0.010	0.001	0.012
is_abs_unit	0.002	0.001	0.003
length.HeatmapAnnotation	0.001	0.000	0.000
length.HeatmapList	0.000	0.001	0.001
list_components	0	0	0
list_to_matrix	0.003	0.003	0.005
make_column_cluster-Heatmap-method	0.000	0.000	0.001
make_comb_mat	0.011	0.001	0.013
make_layout-Heatmap-method	0	0	0
make_layout-HeatmapList-method	0.000	0.001	0.001
make_layout-dispatch	0.000	0.000	0.001
make_row_cluster-Heatmap-method	0	0	0
map_to_colors-ColorMapping-method	0.026	0.001	0.028
max_text_height	0.006	0.001	0.006
max_text_width	0.003	0.001	0.003
merge_dendrogram	0.152	0.004	0.156
names.HeatmapAnnotation	0.028	0.001	0.028
names.HeatmapList	0	0	0
namesAssign.HeatmapAnnotation	0.021	0.001	0.022
ncol.Heatmap	0.001	0.001	0.001
nobs.AnnotationFunction	0.008	0.000	0.008
nobs.HeatmapAnnotation	0.001	0.000	0.001
nobs.SingleAnnotation	0.000	0.000	0.001
normalize_comb_mat	0	0	0
nrow.Heatmap	0	0	0
oncoPrint	0.000	0.001	0.000
order.comb_mat	0.000	0.000	0.001
packLegend	0.152	0.005	0.157
pct_v_pct	0.000	0.000	0.001
pindex	0.010	0.002	0.012
prepare-Heatmap-method	0.001	0.000	0.000
print.comb_mat	0.000	0.000	0.001
re_size-HeatmapAnnotation-method	0	0	0
restore_matrix	0.730	0.007	0.743
rowAnnotation	0.001	0.000	0.000
row_anno_barplot	0.000	0.000	0.001
row_anno_boxplot	0.000	0.000	0.001
row_anno_density	0	0	0
row_anno_histogram	0.000	0.000	0.001
row_anno_link	0.001	0.001	0.001
row_anno_points	0.001	0.001	0.000
row_anno_text	0.000	0.000	0.001
row_dend-Heatmap-method	0.605	0.004	0.635
row_dend-HeatmapList-method	1.580	0.017	1.630
row_dend-dispatch	0.001	0.000	0.000
row_order-Heatmap-method	0.646	0.004	0.658
row_order-HeatmapList-method	1.504	0.013	1.576
row_order-dispatch	0.000	0.000	0.001
set_component_height-Heatmap-method	0.000	0.000	0.001
set_component_width-Heatmap-method	0	0	0
set_name	0.002	0.000	0.002
set_size	0.003	0.001	0.003
show-AnnotationFunction-method	0.000	0.001	0.001
show-ColorMapping-method	0.001	0.000	0.000
show-Heatmap-method	0.000	0.000	0.001
show-HeatmapAnnotation-method	0	0	0
show-HeatmapList-method	0.000	0.001	0.001
show-SingleAnnotation-method	0	0	0
show-dispatch	0	0	0
size.AnnotationFunction	0.018	0.000	0.019
size.HeatmapAnnotation	0.000	0.000	0.001
size.SingleAnnotation	0.000	0.001	0.000
sizeAssign.AnnotationFunction	0.009	0.000	0.016
sizeAssign.HeatmapAnnotation	0	0	0
sizeAssign.SingleAnnotation	0	0	0
smartAlign2	0.215	0.007	0.404
str.comb_mat	0.000	0.000	0.001
subset_gp	0.001	0.001	0.001
subset_matrix_by_row	0.001	0.000	0.000
subset_vector	0.001	0.000	0.000
summary.Heatmap	0.000	0.000	0.001
summary.HeatmapList	0.001	0.001	0.000
t.comb_mat	0.003	0.001	0.004
test_alter_fun	0.148	0.002	0.260
unify_mat_list	0	0	0
upset_right_annotation	0.000	0.001	0.001
upset_top_annotation	0.001	0.001	0.001
width.AnnotationFunction	0.019	0.001	0.029
width.Heatmap	0.000	0.001	0.000
width.HeatmapAnnotation	0	0	0
width.HeatmapList	0	0	0
width.Legends	0.023	0.000	0.034
width.SingleAnnotation	0.001	0.001	0.000
widthAssign.AnnotationFunction	0.000	0.000	0.001
widthAssign.HeatmapAnnotation	0.000	0.000	0.001
widthAssign.SingleAnnotation	0	0	0
widthDetails.annotation_axis	0.000	0.001	0.001
widthDetails.legend	0.000	0.001	0.001
widthDetails.legend_body	0.000	0.000	0.001
widthDetails.packed_legends	0	0	0