Package: ComplexHeatmap

Version: 1.18.1

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_1.18.1.tar.gz

StartedAt: 2018-10-16 20:38:30 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:40:23 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 112.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ComplexHeatmap.Rcheck

Warnings: 1

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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_1.18.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.18.1’
* 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 ... WARNING
Codoc mismatches from documentation object 'ht_global_opt':
ht_global_opt
  Code: function(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE,
                 ADD = FALSE)
  Docs: function(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE)
  Argument names in code not in docs:
    ADD

* 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
Heatmap 18.889   0.12  19.227
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/ComplexHeatmap.Rcheck/00check.log’
for details.

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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/3.5/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 version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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: 17 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  1.485   0.138   1.952 

name	user	system	elapsed
AdditiveUnit-class	0.001	0.000	0.001
AdditiveUnit	0.000	0.000	0.001
ColorMapping-class	0.001	0.000	0.001
ColorMapping	0.078	0.001	0.080
ComplexHeatmap-package	0.001	0.000	0.001
Heatmap-class	0.001	0.000	0.001
Heatmap	18.889	0.120	19.227
HeatmapAnnotation-class	0.001	0.000	0.001
HeatmapAnnotation	0.034	0.000	0.035
HeatmapList-class	3.455	0.011	3.509
HeatmapList	0.001	0.000	0.001
Legend	0.325	0.004	0.334
SingleAnnotation-class	0.001	0.000	0.001
SingleAnnotation	0.027	0.001	0.027
add.AdditiveUnit	4.444	0.011	4.485
add_heatmap-Heatmap-method	1.148	0.003	1.161
add_heatmap-HeatmapAnnotation-method	0.675	0.002	0.683
add_heatmap-HeatmapList-method	1.486	0.006	1.501
add_heatmap-dispatch	0.001	0.001	0.002
adjust_dend_by_leaf_width	1.696	0.057	1.781
anno_barplot	0.013	0.001	0.014
anno_boxplot	0.037	0.001	0.040
anno_density	0.244	0.004	0.249
anno_histogram	0.062	0.001	0.064
anno_link	2.032	0.018	2.076
anno_oncoprint_barplot	0.001	0.000	0.001
anno_points	0.030	0.001	0.033
anno_text	0.463	0.002	0.468
annotation_legend_size-HeatmapList-method	0.001	0.000	0.001
color_mapping_legend-ColorMapping-method	0.386	0.003	0.391
columnAnnotation	0.009	0.000	0.009
column_anno_barplot	0.001	0.001	0.001
column_anno_boxplot	0.001	0.000	0.001
column_anno_density	0.000	0.000	0.001
column_anno_histogram	0.001	0.000	0.001
column_anno_link	0.001	0.001	0.001
column_anno_points	0.001	0.000	0.001
column_anno_text	0.002	0.000	0.001
column_dend-Heatmap-method	0.057	0.005	0.062
column_dend-HeatmapList-method	0.236	0.001	0.239
column_dend-dispatch	0.001	0.000	0.002
column_order-Heatmap-method	0.058	0.000	0.058
column_order-HeatmapList-method	0.204	0.001	0.207
column_order-dispatch	0.001	0.000	0.001
component_height-Heatmap-method	0.000	0.000	0.001
component_height-HeatmapList-method	0.001	0.000	0.001
component_height-dispatch	0.001	0.000	0.001
component_width-Heatmap-method	0.001	0.000	0.001
component_width-HeatmapList-method	0.001	0.000	0.001
component_width-dispatch	0.001	0.000	0.001
decorate_annotation	0.686	0.004	0.699
decorate_column_dend	0.001	0.000	0.002
decorate_column_names	0.002	0.000	0.002
decorate_column_title	0.002	0.000	0.002
decorate_dend	0.349	0.002	0.357
decorate_dimnames	0.484	0.003	0.490
decorate_heatmap_body	0.332	0.002	0.341
decorate_row_dend	0.002	0.000	0.001
decorate_row_names	0.001	0.001	0.001
decorate_row_title	0.001	0.000	0.002
decorate_title	0.348	0.002	0.349
densityHeatmap	3.654	0.025	3.716
dist2	0.032	0.000	0.032
draw-Heatmap-method	0.489	0.002	0.495
draw-HeatmapAnnotation-method	0.116	0.004	0.132
draw-HeatmapList-method	1.207	0.004	1.215
draw-SingleAnnotation-method	0.083	0.004	0.087
draw-dispatch	0.001	0.000	0.002
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	0.001	0.000	0.002
draw_dimnames-Heatmap-method	0.001	0.001	0.001
draw_heatmap_body-Heatmap-method	0.001	0.000	0.001
draw_heatmap_legend-HeatmapList-method	0.001	0.000	0.001
draw_heatmap_list-HeatmapList-method	0.002	0.000	0.001
draw_title-Heatmap-method	0.001	0.000	0.002
draw_title-HeatmapList-method	0.002	0.000	0.002
draw_title-dispatch	0.002	0.000	0.002
enhanced_basicplot	1.214	0.004	1.226
get_color_mapping_list-HeatmapAnnotation-method	0.002	0.000	0.002
get_color_mapping_param_list-HeatmapAnnotation-method	0.001	0.000	0.002
grid.dendrogram	0.019	0.001	0.020
grid.dendrogram2	0.019	0.001	0.020
heatmap_legend_size-HeatmapList-method	0.001	0.000	0.001
ht_global_opt	0.001	0.000	0.001
is_abs_unit	0.003	0.001	0.003
make_column_cluster-Heatmap-method	0.000	0.000	0.001
make_layout-Heatmap-method	0.001	0.000	0.002
make_layout-HeatmapList-method	0.002	0.000	0.001
make_layout-dispatch	0.001	0.000	0.001
make_row_cluster-Heatmap-method	0.001	0.000	0.001
map_to_colors-ColorMapping-method	0.027	0.001	0.028
max_text_height	0.005	0.000	0.004
max_text_width	0.003	0.000	0.004
oncoPrint	0.001	0.000	0.001
packLegend	1.280	0.003	1.297
plotDataFrame	3.694	0.007	3.919
prepare-Heatmap-method	0.001	0.000	0.002
rowAnnotation	0.011	0.000	0.012
row_anno_barplot	0.001	0.000	0.002
row_anno_boxplot	0.001	0.000	0.001
row_anno_density	0.001	0.000	0.002
row_anno_histogram	0.001	0.000	0.001
row_anno_link	0.002	0.001	0.001
row_anno_points	0.002	0.000	0.002
row_anno_text	0.001	0.001	0.002
row_dend-Heatmap-method	0.068	0.000	0.069
row_dend-HeatmapList-method	0.459	0.001	0.533
row_dend-dispatch	0.002	0.001	0.001
row_order-Heatmap-method	0.075	0.000	0.121
row_order-HeatmapList-method	0.257	0.012	0.280
row_order-dispatch	0.001	0.000	0.001
selectArea	0.002	0.000	0.001
set_component_height-Heatmap-method	0.002	0.000	0.002
show-ColorMapping-method	0.001	0.000	0.002
show-Heatmap-method	1.124	0.016	1.160
show-HeatmapAnnotation-method	0.001	0.000	0.001
show-HeatmapList-method	0.002	0.000	0.001
show-SingleAnnotation-method	0.001	0.000	0.002
show-dispatch	0.001	0.000	0.001
unify_mat_list	0.001	0.000	0.002