BioC 3.5: CHECK report for ComplexHeatmap on veracruz2

Package: ComplexHeatmap

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.14.0.tar.gz

StartedAt: 2017-10-18 02:05:15 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:07:26 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 130.6 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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.14.0’
* 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 16.678  0.139  17.515
* 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-3.5-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	0	0
AdditiveUnit	0.001	0.000	0.001
ColorMapping-class	0	0	0
ColorMapping	0.094	0.002	0.102
ComplexHeatmap-package	0.001	0.000	0.000
Heatmap-class	0.001	0.000	0.001
Heatmap	16.678	0.139	17.515
HeatmapAnnotation-class	0.001	0.000	0.000
HeatmapAnnotation	0.194	0.002	0.198
HeatmapList-class	4.092	0.024	4.261
HeatmapList	0.000	0.001	0.000
Legend	0.001	0.000	0.000
SingleAnnotation-class	0.000	0.000	0.001
SingleAnnotation	0.090	0.002	0.092
add.AdditiveUnit	4.609	0.033	4.813
add_heatmap-Heatmap-method	0.987	0.005	1.031
add_heatmap-HeatmapAnnotation-method	0.404	0.002	0.421
add_heatmap-HeatmapList-method	1.808	0.011	1.885
add_heatmap-dispatch	0.000	0.000	0.001
anno_barplot	0.155	0.002	0.164
anno_boxplot	0.241	0.002	0.249
anno_density	0.364	0.005	0.394
anno_histogram	0.166	0.002	0.172
anno_link	1.807	0.033	1.899
anno_oncoprint_barplot	0.001	0.000	0.000
anno_points	0.022	0.002	0.024
anno_text	0.309	0.002	0.321
annotation_legend_size-HeatmapList-method	0.000	0.000	0.001
color_mapping_legend-ColorMapping-method	0.198	0.003	0.209
columnAnnotation	0.017	0.000	0.017
column_anno_barplot	0.001	0.000	0.000
column_anno_boxplot	0.000	0.000	0.001
column_anno_density	0.001	0.000	0.001
column_anno_histogram	0	0	0
column_anno_link	0.001	0.000	0.001
column_anno_points	0.001	0.000	0.001
column_anno_text	0.000	0.000	0.001
column_dend-Heatmap-method	0.092	0.001	0.094
column_dend-HeatmapList-method	0.256	0.001	0.261
column_dend-dispatch	0.000	0.000	0.001
column_order-Heatmap-method	0.084	0.000	0.086
column_order-HeatmapList-method	0.239	0.002	0.244
column_order-dispatch	0.001	0.000	0.000
component_height-Heatmap-method	0	0	0
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	0.001	0.000	0.001
component_width-dispatch	0.001	0.000	0.001
decorate_annotation	0.657	0.005	0.681
decorate_column_dend	0.001	0.000	0.000
decorate_column_names	0.001	0.000	0.000
decorate_column_title	0.000	0.000	0.001
decorate_dend	0.328	0.002	0.334
decorate_dimnames	0.360	0.003	0.371
decorate_heatmap_body	0.313	0.002	0.335
decorate_row_dend	0.001	0.000	0.000
decorate_row_names	0.001	0.000	0.001
decorate_row_title	0.000	0.000	0.001
decorate_title	0.318	0.002	0.328
densityHeatmap	4.571	0.031	4.727
dist2	0.041	0.001	0.042
draw-Heatmap-method	0.357	0.002	0.367
draw-HeatmapAnnotation-method	0.150	0.004	0.161
draw-HeatmapList-method	1.373	0.006	1.413
draw-SingleAnnotation-method	0.140	0.004	0.148
draw-dispatch	0.001	0.000	0.000
draw_annotation-Heatmap-method	0.001	0.000	0.001
draw_annotation_legend-HeatmapList-method	0.000	0.000	0.001
draw_dend-Heatmap-method	0.001	0.000	0.001
draw_dimnames-Heatmap-method	0	0	0
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	0.001	0.000	0.000
draw_title-Heatmap-method	0.001	0.000	0.001
draw_title-HeatmapList-method	0.001	0.000	0.001
draw_title-dispatch	0.000	0.000	0.001
enhanced_basicplot	1.094	0.006	1.155
get_color_mapping_list-HeatmapAnnotation-method	0.001	0.000	0.001
get_color_mapping_param_list-HeatmapAnnotation-method	0.000	0.000	0.001
grid.dendrogram	0.025	0.001	0.026
heatmap_legend_size-HeatmapList-method	0.001	0.000	0.000
ht_global_opt	0	0	0
is_abs_unit	0.002	0.000	0.002
make_column_cluster-Heatmap-method	0.001	0.000	0.001
make_layout-Heatmap-method	0	0	0
make_layout-HeatmapList-method	0.000	0.001	0.001
make_layout-dispatch	0.001	0.000	0.000
make_row_cluster-Heatmap-method	0.001	0.000	0.001
map_to_colors-ColorMapping-method	0.023	0.001	0.024
max_text_height	0.002	0.000	0.003
max_text_width	0.002	0.000	0.002
oncoPrint	0.000	0.000	0.001
packLegend	0.000	0.000	0.001
plotDataFrame	2.658	0.012	2.835
prepare-Heatmap-method	0.001	0.000	0.000
rowAnnotation	0.021	0.000	0.021
row_anno_barplot	0.001	0.000	0.000
row_anno_boxplot	0.001	0.000	0.001
row_anno_density	0.001	0.000	0.001
row_anno_histogram	0.001	0.000	0.000
row_anno_link	0.001	0.000	0.001
row_anno_points	0.001	0.000	0.001
row_anno_text	0.000	0.000	0.001
row_dend-Heatmap-method	0.100	0.000	0.102
row_dend-HeatmapList-method	0.263	0.001	0.271
row_dend-dispatch	0.000	0.000	0.001
row_order-Heatmap-method	0.097	0.000	0.100
row_order-HeatmapList-method	0.259	0.002	0.277
row_order-dispatch	0.001	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	0.001	0.000	0.001
show-Heatmap-method	0.820	0.005	0.848
show-HeatmapAnnotation-method	0.001	0.000	0.001
show-HeatmapList-method	0	0	0
show-SingleAnnotation-method	0.000	0.000	0.001
show-dispatch	0.001	0.000	0.001
unify_mat_list	0.001	0.000	0.001