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 00:56:20 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:59:42 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 201.9 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) (2019-03-18 r76245)
* 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       8.854  0.140  10.765
AnnotationFunction 7.332  0.104   7.923
* 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’ ...
** 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) (2019-03-18 r76245) -- "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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 36.273   1.112  39.542 

name	user	system	elapsed
AdditiveUnit-class	0.000	0.000	0.001
AdditiveUnit	0.000	0.001	0.000
AnnotationFunction-class	0.000	0.000	0.001
AnnotationFunction	7.332	0.104	7.923
ColorMapping-class	0.001	0.000	0.000
ColorMapping	0.019	0.001	0.021
ComplexHeatmap-package	0	0	0
Extract.AnnotationFunction	0.043	0.002	0.046
Extract.Heatmap	1.098	0.008	1.472
Extract.HeatmapAnnotation	0.083	0.003	0.086
Extract.HeatmapList	0.283	0.004	0.288
Extract.SingleAnnotation	0.037	0.002	0.039
Extract.comb_mat	0.014	0.001	0.014
Heatmap-class	0.001	0.001	0.000
Heatmap	0.000	0.000	0.001
HeatmapAnnotation-class	0	0	0
HeatmapAnnotation	0.001	0.001	0.001
HeatmapList-class	0.001	0.001	0.000
HeatmapList	0.000	0.000	0.001
Legend	0.140	0.004	0.145
Legends-class	0.013	0.001	0.013
Legends	0.001	0.000	0.001
SingleAnnotation-class	0.000	0.000	0.001
SingleAnnotation	0.169	0.005	0.175
UpSet	1.283	0.015	1.299
add.AdditiveUnit	0.000	0.000	0.001
add_heatmap-Heatmap-method	0.000	0.000	0.001
add_heatmap-HeatmapAnnotation-method	0.001	0.000	0.001
add_heatmap-HeatmapList-method	0.000	0.001	0.000
add_heatmap-dispatch	0	0	0
adjust_dend_by_x	0.050	0.004	0.055
adjust_heatmap_list-HeatmapList-method	0	0	0
anno_barplot	0.042	0.002	0.043
anno_block	0.519	0.002	0.521
anno_boxplot	0.070	0.002	0.073
anno_density	0.813	0.027	0.841
anno_empty	0.034	0.002	0.037
anno_histogram	0.185	0.003	0.189
anno_horizon	8.854	0.140	10.765
anno_image	0.000	0.000	0.001
anno_joyplot	0.831	0.029	0.875
anno_lines	0.148	0.004	0.156
anno_link	0.000	0.001	0.000
anno_mark	1.030	0.010	1.128
anno_oncoprint_barplot	0	0	0
anno_points	0.050	0.002	0.053
anno_simple	0.118	0.004	0.128
anno_summary	0.613	0.002	0.616
anno_text	0.193	0.004	0.200
anno_zoom	0.720	0.004	0.726
annotation_axis_grob	0.127	0.011	0.142
annotation_legend_size-HeatmapList-method	0	0	0
c.HeatmapAnnotation	0.079	0.001	0.081
cluster_within_group	0.037	0.001	0.038
color_mapping_legend-ColorMapping-method	0	0	0
columnAnnotation	0	0	0
column_dend-Heatmap-method	0.483	0.004	0.487
column_dend-HeatmapList-method	1.843	0.009	1.853
column_dend-dispatch	0.000	0.000	0.001
column_order-Heatmap-method	0.568	0.002	0.571
column_order-HeatmapList-method	1.949	0.009	2.308
column_order-dispatch	0	0	0
comb_degree	0.003	0.001	0.003
comb_name	0.004	0.001	0.003
comb_size	0.003	0.001	0.004
component_height-Heatmap-method	0.001	0.001	0.000
component_height-HeatmapList-method	0	0	0
component_height-dispatch	0	0	0
component_width-Heatmap-method	0.001	0.001	0.001
component_width-HeatmapList-method	0.000	0.000	0.001
component_width-dispatch	0	0	0
copy_all-AnnotationFunction-method	0.001	0.000	0.000
copy_all-SingleAnnotation-method	0.000	0.001	0.001
copy_all-dispatch	0	0	0
decorate_annotation	0.547	0.002	0.549
decorate_column_dend	0.000	0.000	0.001
decorate_column_names	0.000	0.001	0.001
decorate_column_title	0.001	0.000	0.001
decorate_dend	0.288	0.001	0.291
decorate_dimnames	0.367	0.001	0.370
decorate_heatmap_body	0.225	0.001	0.227
decorate_row_dend	0.001	0.000	0.000
decorate_row_names	0.001	0.000	0.001
decorate_row_title	0.001	0.000	0.000
decorate_title	0.349	0.002	0.351
default_axis_param	0.001	0.001	0.003
default_get_type	0.000	0.000	0.001
dend_heights	0.000	0.000	0.001
dend_xy	0.030	0.001	0.030
dendrogramGrob	0.001	0.000	0.000
densityHeatmap	2.362	0.018	2.388
dim.Heatmap	0.000	0.001	0.001
dist2	0.021	0.002	0.049
draw-AnnotationFunction-method	0.001	0.000	0.001
draw-Heatmap-method	0.001	0.001	0.000
draw-HeatmapAnnotation-method	0.000	0.000	0.001
draw-HeatmapList-method	0	0	0
draw-Legends-method	0.027	0.000	0.030
draw-SingleAnnotation-method	0.000	0.000	0.001
draw-dispatch	0.001	0.000	0.000
draw_annotation-Heatmap-method	0	0	0
draw_annotation_legend-HeatmapList-method	0.001	0.000	0.001
draw_dend-Heatmap-method	0	0	0
draw_dimnames-Heatmap-method	0.001	0.000	0.001
draw_heatmap_body-Heatmap-method	0.000	0.000	0.001
draw_heatmap_legend-HeatmapList-method	0	0	0
draw_heatmap_list-HeatmapList-method	0	0	0
draw_title-Heatmap-method	0	0	0
draw_title-HeatmapList-method	0.000	0.000	0.001
draw_title-dispatch	0.001	0.001	0.001
extract_comb	0.003	0.001	0.004
getXY_in_parent_vp	0.028	0.002	0.030
get_color_mapping_list-HeatmapAnnotation-method	0.001	0.000	0.000
get_legend_param_list-HeatmapAnnotation-method	0	0	0
grid.annotation_axis	0.001	0.000	0.000
grid.boxplot	0.026	0.001	0.027
grid.dendrogram	2.725	0.147	2.889
grid.draw.Legends	0.027	0.001	0.027
heatmap_legend_size-HeatmapList-method	0.000	0.000	0.001
height.AnnotationFunction	0.018	0.000	0.019
height.Heatmap	0.000	0.000	0.001
height.HeatmapAnnotation	0.001	0.000	0.001
height.HeatmapList	0	0	0
height.Legends	0.027	0.001	0.028
height.SingleAnnotation	0.000	0.001	0.001
heightAssign.AnnotationFunction	0.001	0.001	0.000
heightAssign.HeatmapAnnotation	0.000	0.000	0.001
heightAssign.SingleAnnotation	0.000	0.000	0.001
heightDetails.annotation_axis	0	0	0
heightDetails.legend	0.000	0.001	0.001
heightDetails.legend_body	0.001	0.000	0.000
heightDetails.packed_legends	0	0	0
ht_global_opt	0.001	0.000	0.000
ht_opt	0.011	0.001	0.012
is_abs_unit	0.002	0.001	0.002
length.HeatmapAnnotation	0.000	0.000	0.001
length.HeatmapList	0	0	0
list_components	0.001	0.000	0.001
list_to_matrix	0.003	0.002	0.006
make_column_cluster-Heatmap-method	0.001	0.001	0.000
make_comb_mat	0.009	0.003	0.011
make_layout-Heatmap-method	0	0	0
make_layout-HeatmapList-method	0.001	0.000	0.000
make_layout-dispatch	0.000	0.001	0.001
make_row_cluster-Heatmap-method	0.001	0.000	0.000
map_to_colors-ColorMapping-method	0.029	0.001	0.031
max_text_height	0.006	0.000	0.006
max_text_width	0.005	0.000	0.005
merge_dendrogram	0.412	0.006	0.418
names.HeatmapAnnotation	0.039	0.000	0.039
names.HeatmapList	0.000	0.001	0.000
namesAssign.HeatmapAnnotation	0.034	0.001	0.035
ncol.Heatmap	0	0	0
nobs.AnnotationFunction	0.009	0.000	0.009
nobs.HeatmapAnnotation	0.000	0.000	0.001
nobs.SingleAnnotation	0.000	0.000	0.001
normalize_comb_mat	0.000	0.000	0.001
nrow.Heatmap	0	0	0
oncoPrint	0.000	0.001	0.000
order.comb_mat	0.000	0.000	0.001
packLegend	0.136	0.003	0.140
pct_v_pct	0	0	0
pindex	0.008	0.001	0.009
prepare-Heatmap-method	0.000	0.000	0.001
print.comb_mat	0.000	0.001	0.001
re_size-HeatmapAnnotation-method	0	0	0
restore_matrix	0.866	0.047	0.914
rowAnnotation	0.000	0.000	0.001
row_anno_barplot	0	0	0
row_anno_boxplot	0.000	0.000	0.001
row_anno_density	0.000	0.000	0.001
row_anno_histogram	0.001	0.001	0.001
row_anno_link	0.000	0.001	0.001
row_anno_points	0.000	0.001	0.001
row_anno_text	0	0	0
row_dend-Heatmap-method	0.603	0.004	0.656
row_dend-HeatmapList-method	1.388	0.009	1.400
row_dend-dispatch	0.001	0.000	0.001
row_order-Heatmap-method	0.569	0.003	0.573
row_order-HeatmapList-method	1.340	0.009	1.350
row_order-dispatch	0	0	0
set_component_height-Heatmap-method	0.001	0.000	0.000
set_component_width-Heatmap-method	0.000	0.001	0.001
set_name	0.002	0.001	0.003
set_size	0.001	0.000	0.002
show-AnnotationFunction-method	0.000	0.000	0.001
show-ColorMapping-method	0	0	0
show-Heatmap-method	0.000	0.000	0.001
show-HeatmapAnnotation-method	0.000	0.000	0.001
show-HeatmapList-method	0	0	0
show-SingleAnnotation-method	0.001	0.001	0.000
show-dispatch	0.000	0.000	0.001
size.AnnotationFunction	0.017	0.001	0.018
size.HeatmapAnnotation	0.000	0.001	0.000
size.SingleAnnotation	0.001	0.000	0.001
sizeAssign.AnnotationFunction	0.010	0.000	0.011
sizeAssign.HeatmapAnnotation	0	0	0
sizeAssign.SingleAnnotation	0.000	0.001	0.001
smartAlign2	0.139	0.006	0.148
str.comb_mat	0.001	0.000	0.001
subset_gp	0.001	0.000	0.002
subset_matrix_by_row	0.000	0.000	0.001
subset_vector	0.001	0.000	0.001
summary.Heatmap	0.000	0.000	0.001
summary.HeatmapList	0.001	0.000	0.000
t.comb_mat	0.002	0.000	0.003
test_alter_fun	0.135	0.002	0.137
unify_mat_list	0.000	0.001	0.001
upset_right_annotation	0	0	0
upset_top_annotation	0.001	0.000	0.001
width.AnnotationFunction	0.012	0.000	0.013
width.Heatmap	0.001	0.000	0.001
width.HeatmapAnnotation	0.000	0.001	0.001
width.HeatmapList	0	0	0
width.Legends	0.027	0.000	0.027
width.SingleAnnotation	0.000	0.001	0.001
widthAssign.AnnotationFunction	0	0	0
widthAssign.HeatmapAnnotation	0	0	0
widthAssign.SingleAnnotation	0	0	0
widthDetails.annotation_axis	0	0	0
widthDetails.legend	0.001	0.001	0.000
widthDetails.legend_body	0	0	0
widthDetails.packed_legends	0.001	0.000	0.001