Package: ComplexHeatmap

Version: 2.0.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ComplexHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ComplexHeatmap_2.0.0.tar.gz

StartedAt: 2019-10-16 00:45:21 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:47:37 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 135.9 seconds

RetCode: 0

Status:  OK

CheckDir: ComplexHeatmap.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ComplexHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ComplexHeatmap_2.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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       6.232  0.036   6.353
AnnotationFunction 5.041  0.028   5.070
* 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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ComplexHeatmap
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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 
 26.536   0.308  26.758 

name	user	system	elapsed
AdditiveUnit-class	0	0	0
AdditiveUnit	0	0	0
AnnotationFunction-class	0	0	0
AnnotationFunction	5.041	0.028	5.070
ColorMapping-class	0.000	0.000	0.001
ColorMapping	0.009	0.000	0.008
ComplexHeatmap-package	0	0	0
Extract.AnnotationFunction	0.019	0.000	0.020
Extract.Heatmap	0.519	0.000	0.520
Extract.HeatmapAnnotation	0.048	0.000	0.048
Extract.HeatmapList	0.112	0.000	0.112
Extract.SingleAnnotation	0.014	0.000	0.015
Extract.comb_mat	0.002	0.000	0.003
Heatmap-class	0	0	0
Heatmap	0	0	0
HeatmapAnnotation-class	0	0	0
HeatmapAnnotation	0	0	0
HeatmapList-class	0	0	0
HeatmapList	0	0	0
Legend	0.069	0.000	0.069
Legends-class	0.006	0.000	0.006
Legends	0	0	0
SingleAnnotation-class	0	0	0
SingleAnnotation	0.076	0.000	0.076
UpSet	0.578	0.000	0.577
add.AdditiveUnit	0	0	0
add_heatmap-Heatmap-method	0	0	0
add_heatmap-HeatmapAnnotation-method	0	0	0
add_heatmap-HeatmapList-method	0.000	0.000	0.001
add_heatmap-dispatch	0.001	0.000	0.000
adjust_dend_by_x	0.015	0.004	0.019
adjust_heatmap_list-HeatmapList-method	0.000	0.000	0.001
anno_barplot	0.034	0.000	0.033
anno_block	0.332	0.000	0.331
anno_boxplot	0.041	0.000	0.040
anno_density	0.535	0.004	0.539
anno_empty	0.018	0.000	0.017
anno_histogram	0.094	0.000	0.093
anno_horizon	6.232	0.036	6.353
anno_image	0	0	0
anno_joyplot	0.758	0.000	0.758
anno_lines	0.112	0.008	0.121
anno_link	0	0	0
anno_mark	0.732	0.000	0.731
anno_oncoprint_barplot	0	0	0
anno_points	0.044	0.000	0.044
anno_simple	0.087	0.000	0.087
anno_summary	0.474	0.000	0.475
anno_text	0.154	0.000	0.154
anno_zoom	0.542	0.000	0.542
annotation_axis_grob	0.122	0.000	0.122
annotation_legend_size-HeatmapList-method	0	0	0
c.HeatmapAnnotation	0.057	0.003	0.061
cluster_within_group	0.025	0.003	0.029
color_mapping_legend-ColorMapping-method	0	0	0
columnAnnotation	0	0	0
column_dend-Heatmap-method	0.411	0.000	0.412
column_dend-HeatmapList-method	1.500	0.000	1.503
column_dend-dispatch	0	0	0
column_order-Heatmap-method	0.416	0.003	0.420
column_order-HeatmapList-method	1.325	0.000	1.324
column_order-dispatch	0	0	0
comb_degree	0.001	0.000	0.002
comb_name	0.000	0.001	0.001
comb_size	0.000	0.001	0.001
component_height-Heatmap-method	0	0	0
component_height-HeatmapList-method	0	0	0
component_height-dispatch	0	0	0
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	0	0
copy_all-SingleAnnotation-method	0	0	0
copy_all-dispatch	0.000	0.000	0.001
decorate_annotation	0.244	0.004	0.248
decorate_column_dend	0	0	0
decorate_column_names	0	0	0
decorate_column_title	0	0	0
decorate_dend	0.152	0.000	0.152
decorate_dimnames	0.190	0.000	0.189
decorate_heatmap_body	0.161	0.001	0.161
decorate_row_dend	0	0	0
decorate_row_names	0	0	0
decorate_row_title	0	0	0
decorate_title	0.158	0.000	0.158
default_axis_param	0.001	0.000	0.000
default_get_type	0	0	0
dend_heights	0	0	0
dend_xy	0.014	0.000	0.014
dendrogramGrob	0	0	0
densityHeatmap	1.360	0.004	1.364
dim.Heatmap	0	0	0
dist2	0.016	0.000	0.016
draw-AnnotationFunction-method	0	0	0
draw-Heatmap-method	0	0	0
draw-HeatmapAnnotation-method	0	0	0
draw-HeatmapList-method	0	0	0
draw-Legends-method	0.023	0.000	0.023
draw-SingleAnnotation-method	0	0	0
draw-dispatch	0	0	0
draw_annotation-Heatmap-method	0.001	0.000	0.001
draw_annotation_legend-HeatmapList-method	0.001	0.000	0.001
draw_dend-Heatmap-method	0	0	0
draw_dimnames-Heatmap-method	0	0	0
draw_heatmap_body-Heatmap-method	0	0	0
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	0	0
draw_title-dispatch	0	0	0
extract_comb	0.01	0.00	0.01
getXY_in_parent_vp	0.024	0.000	0.024
get_color_mapping_list-HeatmapAnnotation-method	0	0	0
get_legend_param_list-HeatmapAnnotation-method	0	0	0
grid.annotation_axis	0	0	0
grid.boxplot	0.018	0.000	0.018
grid.dendrogram	0.788	0.060	0.849
grid.draw.Legends	0.011	0.000	0.011
heatmap_legend_size-HeatmapList-method	0	0	0
height.AnnotationFunction	0.008	0.000	0.008
height.Heatmap	0	0	0
height.HeatmapAnnotation	0	0	0
height.HeatmapList	0	0	0
height.Legends	0.011	0.000	0.012
height.SingleAnnotation	0	0	0
heightAssign.AnnotationFunction	0	0	0
heightAssign.HeatmapAnnotation	0	0	0
heightAssign.SingleAnnotation	0.001	0.000	0.000
heightDetails.annotation_axis	0	0	0
heightDetails.legend	0	0	0
heightDetails.legend_body	0	0	0
heightDetails.packed_legends	0	0	0
ht_global_opt	0	0	0
ht_opt	0.004	0.000	0.005
is_abs_unit	0.000	0.000	0.001
length.HeatmapAnnotation	0	0	0
length.HeatmapList	0	0	0
list_components	0	0	0
list_to_matrix	0.001	0.000	0.001
make_column_cluster-Heatmap-method	0	0	0
make_comb_mat	0.004	0.000	0.004
make_layout-Heatmap-method	0	0	0
make_layout-HeatmapList-method	0.000	0.000	0.001
make_layout-dispatch	0	0	0
make_row_cluster-Heatmap-method	0	0	0
map_to_colors-ColorMapping-method	0.013	0.000	0.013
max_text_height	0.000	0.002	0.003
max_text_width	0.002	0.001	0.003
merge_dendrogram	0.07	0.00	0.07
names.HeatmapAnnotation	0.016	0.000	0.016
names.HeatmapList	0	0	0
namesAssign.HeatmapAnnotation	0.016	0.000	0.016
ncol.Heatmap	0	0	0
nobs.AnnotationFunction	0.005	0.000	0.004
nobs.HeatmapAnnotation	0	0	0
nobs.SingleAnnotation	0.000	0.000	0.001
normalize_comb_mat	0	0	0
nrow.Heatmap	0	0	0
oncoPrint	0.001	0.000	0.000
order.comb_mat	0	0	0
packLegend	0.071	0.000	0.072
pct_v_pct	0	0	0
pindex	0.004	0.000	0.004
prepare-Heatmap-method	0.001	0.000	0.000
print.comb_mat	0	0	0
re_size-HeatmapAnnotation-method	0	0	0
restore_matrix	0.341	0.004	0.343
rowAnnotation	0	0	0
row_anno_barplot	0.000	0.000	0.001
row_anno_boxplot	0	0	0
row_anno_density	0	0	0
row_anno_histogram	0	0	0
row_anno_link	0	0	0
row_anno_points	0	0	0
row_anno_text	0	0	0
row_dend-Heatmap-method	0.263	0.000	0.263
row_dend-HeatmapList-method	0.744	0.000	0.744
row_dend-dispatch	0	0	0
row_order-Heatmap-method	0.279	0.000	0.279
row_order-HeatmapList-method	0.744	0.003	0.749
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	0.001
set_size	0.001	0.000	0.002
show-AnnotationFunction-method	0	0	0
show-ColorMapping-method	0	0	0
show-Heatmap-method	0	0	0
show-HeatmapAnnotation-method	0	0	0
show-HeatmapList-method	0	0	0
show-SingleAnnotation-method	0	0	0
show-dispatch	0.000	0.000	0.001
size.AnnotationFunction	0.013	0.000	0.014
size.HeatmapAnnotation	0	0	0
size.SingleAnnotation	0.000	0.000	0.001
sizeAssign.AnnotationFunction	0.007	0.000	0.007
sizeAssign.HeatmapAnnotation	0.000	0.000	0.001
sizeAssign.SingleAnnotation	0.000	0.000	0.001
smartAlign2	0.115	0.004	0.120
str.comb_mat	0	0	0
subset_gp	0.000	0.001	0.000
subset_matrix_by_row	0	0	0
subset_vector	0.000	0.001	0.000
summary.Heatmap	0	0	0
summary.HeatmapList	0	0	0
t.comb_mat	0.002	0.000	0.002
test_alter_fun	0.108	0.000	0.109
unify_mat_list	0.001	0.000	0.000
upset_right_annotation	0.001	0.000	0.000
upset_top_annotation	0	0	0
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	0.019	0.000	0.019
width.SingleAnnotation	0	0	0
widthAssign.AnnotationFunction	0	0	0
widthAssign.HeatmapAnnotation	0.001	0.000	0.000
widthAssign.SingleAnnotation	0	0	0
widthDetails.annotation_axis	0	0	0
widthDetails.legend	0	0	0
widthDetails.legend_body	0	0	0
widthDetails.packed_legends	0.000	0.000	0.001