Package: ComplexHeatmap

Version: 2.0.0

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_2.0.0.tar.gz

StartedAt: 2019-10-16 01:44:05 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:47:20 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 195.6 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_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.0.0’
* 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       9.115  0.142   9.786
AnnotationFunction 7.147  0.121   7.280
* 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 3.6.1 (2019-07-05) -- "Action of the Toes"
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 
 33.393   0.976  34.249 

name	user	system	elapsed
AdditiveUnit-class	0.001	0.000	0.000
AdditiveUnit	0.000	0.001	0.000
AnnotationFunction-class	0	0	0
AnnotationFunction	7.147	0.121	7.280
ColorMapping-class	0.000	0.000	0.001
ColorMapping	0.016	0.001	0.018
ComplexHeatmap-package	0.000	0.001	0.000
Extract.AnnotationFunction	0.038	0.002	0.041
Extract.Heatmap	0.932	0.005	0.939
Extract.HeatmapAnnotation	0.107	0.005	0.110
Extract.HeatmapList	0.233	0.002	0.235
Extract.SingleAnnotation	0.031	0.002	0.031
Extract.comb_mat	0.006	0.001	0.007
Heatmap-class	0.001	0.000	0.000
Heatmap	0.000	0.000	0.001
HeatmapAnnotation-class	0.001	0.000	0.001
HeatmapAnnotation	0.000	0.000	0.001
HeatmapList-class	0.000	0.000	0.001
HeatmapList	0	0	0
Legend	0.153	0.004	0.158
Legends-class	0.009	0.000	0.009
Legends	0	0	0
SingleAnnotation-class	0	0	0
SingleAnnotation	0.094	0.004	0.100
UpSet	1.184	0.012	1.423
add.AdditiveUnit	0.001	0.000	0.000
add_heatmap-Heatmap-method	0	0	0
add_heatmap-HeatmapAnnotation-method	0.001	0.000	0.000
add_heatmap-HeatmapList-method	0	0	0
add_heatmap-dispatch	0.000	0.001	0.000
adjust_dend_by_x	0.056	0.004	0.060
adjust_heatmap_list-HeatmapList-method	0.000	0.000	0.001
anno_barplot	0.055	0.002	0.056
anno_block	0.553	0.002	0.556
anno_boxplot	0.075	0.002	0.079
anno_density	0.885	0.028	0.918
anno_empty	0.034	0.002	0.037
anno_histogram	0.195	0.003	0.199
anno_horizon	9.115	0.142	9.786
anno_image	0.000	0.000	0.001
anno_joyplot	0.756	0.025	0.823
anno_lines	0.148	0.004	0.155
anno_link	0.000	0.001	0.000
anno_mark	0.943	0.006	1.184
anno_oncoprint_barplot	0.001	0.000	0.000
anno_points	0.053	0.002	0.098
anno_simple	0.124	0.004	0.244
anno_summary	0.633	0.004	0.745
anno_text	0.200	0.005	0.208
anno_zoom	0.561	0.003	0.564
annotation_axis_grob	0.145	0.011	0.161
annotation_legend_size-HeatmapList-method	0	0	0
c.HeatmapAnnotation	0.061	0.002	0.063
cluster_within_group	0.044	0.001	0.045
color_mapping_legend-ColorMapping-method	0	0	0
columnAnnotation	0.001	0.001	0.000
column_dend-Heatmap-method	0.512	0.004	0.518
column_dend-HeatmapList-method	1.611	0.008	1.624
column_dend-dispatch	0.000	0.000	0.001
column_order-Heatmap-method	0.556	0.003	0.563
column_order-HeatmapList-method	1.785	0.007	1.798
column_order-dispatch	0.001	0.000	0.000
comb_degree	0.004	0.000	0.004
comb_name	0.002	0.001	0.002
comb_size	0.003	0.000	0.004
component_height-Heatmap-method	0.000	0.000	0.001
component_height-HeatmapList-method	0	0	0
component_height-dispatch	0.000	0.000	0.001
component_width-Heatmap-method	0.001	0.000	0.001
component_width-HeatmapList-method	0.000	0.000	0.001
component_width-dispatch	0.001	0.000	0.000
copy_all-AnnotationFunction-method	0.000	0.001	0.000
copy_all-SingleAnnotation-method	0.000	0.000	0.001
copy_all-dispatch	0.000	0.000	0.001
decorate_annotation	0.528	0.003	0.532
decorate_column_dend	0.001	0.000	0.001
decorate_column_names	0	0	0
decorate_column_title	0	0	0
decorate_dend	0.321	0.002	0.325
decorate_dimnames	0.372	0.002	0.375
decorate_heatmap_body	0.216	0.001	0.218
decorate_row_dend	0.001	0.000	0.000
decorate_row_names	0	0	0
decorate_row_title	0.001	0.000	0.000
decorate_title	0.315	0.001	0.318
default_axis_param	0.002	0.001	0.002
default_get_type	0.000	0.001	0.001
dend_heights	0.000	0.000	0.001
dend_xy	0.037	0.001	0.037
dendrogramGrob	0.001	0.001	0.001
densityHeatmap	2.289	0.019	2.912
dim.Heatmap	0.000	0.000	0.001
dist2	0.021	0.002	0.030
draw-AnnotationFunction-method	0.001	0.001	0.001
draw-Heatmap-method	0	0	0
draw-HeatmapAnnotation-method	0.000	0.000	0.001
draw-HeatmapList-method	0	0	0
draw-Legends-method	0.029	0.001	0.032
draw-SingleAnnotation-method	0.000	0.001	0.001
draw-dispatch	0.000	0.000	0.001
draw_annotation-Heatmap-method	0	0	0
draw_annotation_legend-HeatmapList-method	0.001	0.001	0.000
draw_dend-Heatmap-method	0	0	0
draw_dimnames-Heatmap-method	0.000	0.000	0.001
draw_heatmap_body-Heatmap-method	0.000	0.001	0.001
draw_heatmap_legend-HeatmapList-method	0.001	0.000	0.001
draw_heatmap_list-HeatmapList-method	0.000	0.001	0.001
draw_title-Heatmap-method	0.000	0.000	0.001
draw_title-HeatmapList-method	0.001	0.000	0.001
draw_title-dispatch	0.000	0.000	0.001
extract_comb	0.013	0.000	0.014
getXY_in_parent_vp	0.027	0.001	0.030
get_color_mapping_list-HeatmapAnnotation-method	0	0	0
get_legend_param_list-HeatmapAnnotation-method	0.001	0.001	0.001
grid.annotation_axis	0	0	0
grid.boxplot	0.024	0.001	0.026
grid.dendrogram	1.055	0.075	1.132
grid.draw.Legends	0.023	0.000	0.023
heatmap_legend_size-HeatmapList-method	0.001	0.000	0.001
height.AnnotationFunction	0.020	0.002	0.023
height.Heatmap	0	0	0
height.HeatmapAnnotation	0	0	0
height.HeatmapList	0.000	0.001	0.001
height.Legends	0.031	0.006	0.036
height.SingleAnnotation	0	0	0
heightAssign.AnnotationFunction	0.001	0.001	0.001
heightAssign.HeatmapAnnotation	0.000	0.001	0.000
heightAssign.SingleAnnotation	0.000	0.000	0.001
heightDetails.annotation_axis	0.001	0.000	0.001
heightDetails.legend	0	0	0
heightDetails.legend_body	0.000	0.000	0.001
heightDetails.packed_legends	0	0	0
ht_global_opt	0.001	0.000	0.001
ht_opt	0.010	0.003	0.013
is_abs_unit	0.002	0.001	0.002
length.HeatmapAnnotation	0	0	0
length.HeatmapList	0.000	0.000	0.001
list_components	0.000	0.001	0.001
list_to_matrix	0.003	0.002	0.005
make_column_cluster-Heatmap-method	0.001	0.000	0.001
make_comb_mat	0.020	0.002	0.022
make_layout-Heatmap-method	0	0	0
make_layout-HeatmapList-method	0.001	0.000	0.000
make_layout-dispatch	0.000	0.000	0.001
make_row_cluster-Heatmap-method	0.001	0.001	0.001
map_to_colors-ColorMapping-method	0.029	0.002	0.030
max_text_height	0.006	0.000	0.006
max_text_width	0.006	0.000	0.006
merge_dendrogram	0.161	0.004	0.166
names.HeatmapAnnotation	0.033	0.001	0.034
names.HeatmapList	0.000	0.001	0.001
namesAssign.HeatmapAnnotation	0.03	0.00	0.03
ncol.Heatmap	0.001	0.000	0.001
nobs.AnnotationFunction	0.008	0.000	0.008
nobs.HeatmapAnnotation	0.001	0.001	0.000
nobs.SingleAnnotation	0	0	0
normalize_comb_mat	0.001	0.000	0.000
nrow.Heatmap	0	0	0
oncoPrint	0.001	0.000	0.001
order.comb_mat	0.000	0.000	0.001
packLegend	0.103	0.002	0.107
pct_v_pct	0	0	0
pindex	0.009	0.001	0.011
prepare-Heatmap-method	0.000	0.000	0.001
print.comb_mat	0	0	0
re_size-HeatmapAnnotation-method	0.000	0.001	0.001
restore_matrix	0.710	0.005	0.717
rowAnnotation	0.000	0.001	0.000
row_anno_barplot	0.001	0.000	0.001
row_anno_boxplot	0	0	0
row_anno_density	0	0	0
row_anno_histogram	0.000	0.001	0.000
row_anno_link	0.000	0.000	0.001
row_anno_points	0.000	0.001	0.000
row_anno_text	0	0	0
row_dend-Heatmap-method	0.418	0.003	0.423
row_dend-HeatmapList-method	1.114	0.007	1.124
row_dend-dispatch	0.000	0.000	0.001
row_order-Heatmap-method	0.480	0.004	0.486
row_order-HeatmapList-method	1.368	0.006	1.377
row_order-dispatch	0.001	0.000	0.001
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	0.003
set_size	0.003	0.000	0.003
show-AnnotationFunction-method	0.001	0.000	0.001
show-ColorMapping-method	0.000	0.001	0.000
show-Heatmap-method	0.000	0.001	0.001
show-HeatmapAnnotation-method	0.001	0.000	0.001
show-HeatmapList-method	0.000	0.000	0.001
show-SingleAnnotation-method	0.000	0.001	0.001
show-dispatch	0	0	0
size.AnnotationFunction	0.018	0.000	0.018
size.HeatmapAnnotation	0	0	0
size.SingleAnnotation	0.000	0.001	0.001
sizeAssign.AnnotationFunction	0.007	0.000	0.007
sizeAssign.HeatmapAnnotation	0	0	0
sizeAssign.SingleAnnotation	0.000	0.000	0.001
smartAlign2	0.160	0.006	0.171
str.comb_mat	0.001	0.000	0.001
subset_gp	0.000	0.001	0.000
subset_matrix_by_row	0.001	0.000	0.001
subset_vector	0.000	0.000	0.001
summary.Heatmap	0	0	0
summary.HeatmapList	0	0	0
t.comb_mat	0.001	0.000	0.002
test_alter_fun	0.123	0.001	0.124
unify_mat_list	0.000	0.000	0.001
upset_right_annotation	0.001	0.001	0.000
upset_top_annotation	0	0	0
width.AnnotationFunction	0.019	0.000	0.019
width.Heatmap	0.001	0.000	0.001
width.HeatmapAnnotation	0.001	0.001	0.000
width.HeatmapList	0.000	0.000	0.001
width.Legends	0.025	0.000	0.025
width.SingleAnnotation	0.001	0.000	0.000
widthAssign.AnnotationFunction	0.000	0.001	0.001
widthAssign.HeatmapAnnotation	0	0	0
widthAssign.SingleAnnotation	0	0	0
widthDetails.annotation_axis	0.000	0.001	0.001
widthDetails.legend	0.001	0.001	0.000
widthDetails.legend_body	0.000	0.000	0.001
widthDetails.packed_legends	0	0	0