BioC 3.6: CHECK report for ComplexHeatmap on veracruz1

Package: ComplexHeatmap

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.15.0.tar.gz

StartedAt: 2017-08-16 01:33:21 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:35:30 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 129.1 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 --no-vignettes --timings ComplexHeatmap_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.15.0’
* 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 ... NOTE
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
Heatmap 15.699  0.071   16.25
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/ComplexHeatmap.Rcheck/00check.log’
for details.

* installing *source* package ‘ComplexHeatmap’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ComplexHeatmap)

name	user	system	elapsed
AdditiveUnit-class	0.001	0.000	0.001
AdditiveUnit	0.001	0.000	0.000
ColorMapping-class	0.000	0.000	0.001
ColorMapping	0.101	0.002	0.109
ComplexHeatmap-package	0	0	0
Heatmap-class	0.001	0.000	0.000
Heatmap	15.699	0.071	16.250
HeatmapAnnotation-class	0.001	0.000	0.000
HeatmapAnnotation	0.208	0.002	0.213
HeatmapList-class	4.015	0.012	4.089
HeatmapList	0.001	0.000	0.001
Legend	0	0	0
SingleAnnotation-class	0	0	0
SingleAnnotation	0.087	0.001	0.089
add.AdditiveUnit	4.704	0.017	4.786
add_heatmap-Heatmap-method	1.280	0.006	1.336
add_heatmap-HeatmapAnnotation-method	0.471	0.003	0.496
add_heatmap-HeatmapList-method	1.860	0.006	1.918
add_heatmap-dispatch	0	0	0
anno_barplot	0.166	0.001	0.177
anno_boxplot	0.264	0.002	0.271
anno_density	0.408	0.004	0.428
anno_histogram	0.186	0.002	0.197
anno_link	1.992	0.021	2.106
anno_oncoprint_barplot	0.000	0.000	0.001
anno_points	0.023	0.001	0.024
anno_text	0.348	0.001	0.360
annotation_legend_size-HeatmapList-method	0.001	0.001	0.001
color_mapping_legend-ColorMapping-method	0.200	0.002	0.207
columnAnnotation	0.017	0.000	0.017
column_anno_barplot	0.000	0.000	0.001
column_anno_boxplot	0.000	0.000	0.001
column_anno_density	0.001	0.000	0.001
column_anno_histogram	0.000	0.000	0.001
column_anno_link	0.000	0.000	0.001
column_anno_points	0.001	0.000	0.001
column_anno_text	0.001	0.000	0.001
column_dend-Heatmap-method	0.087	0.000	0.087
column_dend-HeatmapList-method	0.352	0.001	0.378
column_dend-dispatch	0.000	0.001	0.001
column_order-Heatmap-method	0.089	0.000	0.094
column_order-HeatmapList-method	0.252	0.001	0.254
column_order-dispatch	0.001	0.000	0.000
component_height-Heatmap-method	0	0	0
component_height-HeatmapList-method	0.001	0.000	0.001
component_height-dispatch	0.001	0.000	0.001
component_width-Heatmap-method	0.000	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	0.625	0.002	0.643
decorate_column_dend	0.000	0.000	0.001
decorate_column_names	0.001	0.000	0.001
decorate_column_title	0.001	0.000	0.001
decorate_dend	0.298	0.001	0.305
decorate_dimnames	0.337	0.001	0.346
decorate_heatmap_body	0.277	0.001	0.284
decorate_row_dend	0.001	0.000	0.001
decorate_row_names	0	0	0
decorate_row_title	0.001	0.000	0.000
decorate_title	0.301	0.000	0.307
densityHeatmap	4.370	0.015	4.483
dist2	0.037	0.000	0.038
draw-Heatmap-method	0.376	0.001	0.380
draw-HeatmapAnnotation-method	0.167	0.004	0.171
draw-HeatmapList-method	1.399	0.003	1.445
draw-SingleAnnotation-method	0.109	0.004	0.117
draw-dispatch	0.001	0.000	0.000
draw_annotation-Heatmap-method	0.001	0.000	0.000
draw_annotation_legend-HeatmapList-method	0.000	0.001	0.000
draw_dend-Heatmap-method	0.001	0.000	0.001
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	0.000	0.000	0.001
draw_heatmap_list-HeatmapList-method	0.000	0.001	0.000
draw_title-Heatmap-method	0.001	0.000	0.001
draw_title-HeatmapList-method	0.000	0.000	0.001
draw_title-dispatch	0.000	0.000	0.001
enhanced_basicplot	1.076	0.003	1.098
get_color_mapping_list-HeatmapAnnotation-method	0.000	0.000	0.001
get_color_mapping_param_list-HeatmapAnnotation-method	0.000	0.001	0.001
grid.dendrogram	0.023	0.000	0.023
heatmap_legend_size-HeatmapList-method	0.001	0.000	0.000
ht_global_opt	0.001	0.000	0.001
is_abs_unit	0.002	0.000	0.002
make_column_cluster-Heatmap-method	0.001	0.001	0.001
make_layout-Heatmap-method	0	0	0
make_layout-HeatmapList-method	0	0	0
make_layout-dispatch	0.001	0.000	0.000
make_row_cluster-Heatmap-method	0.001	0.001	0.000
map_to_colors-ColorMapping-method	0.024	0.000	0.027
max_text_height	0.003	0.000	0.002
max_text_width	0.003	0.000	0.002
oncoPrint	0	0	0
packLegend	0	0	0
plotDataFrame	2.426	0.007	2.484
prepare-Heatmap-method	0.000	0.001	0.000
rowAnnotation	0.019	0.000	0.019
row_anno_barplot	0	0	0
row_anno_boxplot	0.001	0.000	0.000
row_anno_density	0.000	0.000	0.001
row_anno_histogram	0	0	0
row_anno_link	0.001	0.000	0.001
row_anno_points	0.000	0.000	0.001
row_anno_text	0.001	0.000	0.000
row_dend-Heatmap-method	0.086	0.000	0.086
row_dend-HeatmapList-method	0.217	0.001	0.218
row_dend-dispatch	0.001	0.000	0.001
row_order-Heatmap-method	0.083	0.000	0.084
row_order-HeatmapList-method	0.265	0.000	0.271
row_order-dispatch	0.000	0.000	0.001
selectArea	0.000	0.000	0.001
set_component_height-Heatmap-method	0.001	0.000	0.001
show-ColorMapping-method	0.000	0.000	0.001
show-Heatmap-method	0.686	0.002	0.696
show-HeatmapAnnotation-method	0.001	0.000	0.001
show-HeatmapList-method	0.000	0.000	0.001
show-SingleAnnotation-method	0.001	0.000	0.001
show-dispatch	0.001	0.000	0.001
unify_mat_list	0.001	0.000	0.001