BioC 3.5: CHECK report for ComplexHeatmap on toluca2

Package: ComplexHeatmap

Version: 1.13.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.13.2.tar.gz

StartedAt: 2017-04-23 02:12:58 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 02:15:27 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 149.3 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_1.13.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ComplexHeatmap.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.13.2’
* 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          18.968  0.087  19.431
densityHeatmap    5.241  0.026   5.312
add.AdditiveUnit  5.167  0.018   5.249
* 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	0.001	0.000	0.001
AdditiveUnit	0.001	0.001	0.000
ColorMapping-class	0	0	0
ColorMapping	0.114	0.001	0.120
ComplexHeatmap-package	0.001	0.000	0.001
Heatmap-class	0.001	0.000	0.001
Heatmap	18.968	0.087	19.431
HeatmapAnnotation-class	0.001	0.000	0.001
HeatmapAnnotation	0.201	0.001	0.202
HeatmapList-class	4.849	0.020	4.896
HeatmapList	0.001	0.000	0.000
Legend	0	0	0
SingleAnnotation-class	0.001	0.000	0.001
SingleAnnotation	0.093	0.000	0.094
add.AdditiveUnit	5.167	0.018	5.249
add_heatmap-Heatmap-method	1.318	0.004	1.333
add_heatmap-HeatmapAnnotation-method	0.496	0.001	0.503
add_heatmap-HeatmapList-method	2.281	0.006	2.293
add_heatmap-dispatch	0.001	0.000	0.001
anno_barplot	0.233	0.001	0.237
anno_boxplot	0.322	0.001	0.330
anno_density	0.480	0.003	0.490
anno_histogram	0.201	0.002	0.209
anno_link	2.142	0.029	2.182
anno_oncoprint_barplot	0.001	0.000	0.000
anno_points	0.023	0.001	0.025
anno_text	0.377	0.001	0.382
annotation_legend_size-HeatmapList-method	0.000	0.000	0.001
color_mapping_legend-ColorMapping-method	0.212	0.002	0.215
columnAnnotation	0.018	0.000	0.019
column_anno_barplot	0.001	0.000	0.000
column_anno_boxplot	0.001	0.000	0.000
column_anno_density	0.000	0.000	0.001
column_anno_histogram	0.001	0.000	0.000
column_anno_link	0.001	0.000	0.000
column_anno_points	0.000	0.000	0.001
column_anno_text	0.001	0.000	0.000
column_dend-Heatmap-method	0.109	0.001	0.110
column_dend-HeatmapList-method	0.297	0.001	0.301
column_dend-dispatch	0.001	0.000	0.000
column_order-Heatmap-method	0.102	0.001	0.103
column_order-HeatmapList-method	0.282	0.001	0.291
column_order-dispatch	0.001	0.000	0.001
component_height-Heatmap-method	0.000	0.001	0.001
component_height-HeatmapList-method	0.001	0.000	0.000
component_height-dispatch	0.001	0.000	0.000
component_width-Heatmap-method	0	0	0
component_width-HeatmapList-method	0.001	0.000	0.001
component_width-dispatch	0.001	0.000	0.001
decorate_annotation	0.753	0.002	0.761
decorate_column_dend	0.001	0.000	0.001
decorate_column_names	0.000	0.000	0.001
decorate_column_title	0.000	0.000	0.001
decorate_dend	0.368	0.001	0.372
decorate_dimnames	0.415	0.001	0.416
decorate_heatmap_body	0.381	0.002	0.383
decorate_row_dend	0.000	0.000	0.001
decorate_row_names	0.000	0.000	0.001
decorate_row_title	0.001	0.000	0.001
decorate_title	0.383	0.002	0.389
densityHeatmap	5.241	0.026	5.312
dist2	0.042	0.001	0.043
draw-Heatmap-method	0.435	0.001	0.437
draw-HeatmapAnnotation-method	0.184	0.003	0.191
draw-HeatmapList-method	1.704	0.004	1.719
draw-SingleAnnotation-method	0.149	0.003	0.166
draw-dispatch	0.001	0.001	0.001
draw_annotation-Heatmap-method	0.001	0.000	0.001
draw_annotation_legend-HeatmapList-method	0	0	0
draw_dend-Heatmap-method	0.001	0.000	0.000
draw_dimnames-Heatmap-method	0.001	0.000	0.000
draw_heatmap_body-Heatmap-method	0	0	0
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	0.000
draw_title-HeatmapList-method	0	0	0
draw_title-dispatch	0.001	0.001	0.001
enhanced_basicplot	1.403	0.004	1.433
get_color_mapping_list-HeatmapAnnotation-method	0.000	0.000	0.001
get_color_mapping_param_list-HeatmapAnnotation-method	0.001	0.000	0.001
grid.dendrogram	0.024	0.000	0.024
heatmap_legend_size-HeatmapList-method	0.000	0.001	0.000
ht_global_opt	0	0	0
is_abs_unit	0.002	0.000	0.002
make_column_cluster-Heatmap-method	0	0	0
make_layout-Heatmap-method	0.000	0.000	0.001
make_layout-HeatmapList-method	0.000	0.000	0.001
make_layout-dispatch	0	0	0
make_row_cluster-Heatmap-method	0.001	0.000	0.000
map_to_colors-ColorMapping-method	0.023	0.001	0.025
max_text_height	0.003	0.000	0.003
max_text_width	0.002	0.000	0.003
oncoPrint	0	0	0
packLegend	0.001	0.000	0.000
plotDataFrame	3.012	0.015	3.044
prepare-Heatmap-method	0.001	0.000	0.001
rowAnnotation	0.022	0.000	0.022
row_anno_barplot	0.000	0.000	0.001
row_anno_boxplot	0.001	0.000	0.001
row_anno_density	0.001	0.000	0.001
row_anno_histogram	0.000	0.000	0.001
row_anno_link	0.001	0.000	0.000
row_anno_points	0.000	0.001	0.000
row_anno_text	0	0	0
row_dend-Heatmap-method	0.097	0.000	0.098
row_dend-HeatmapList-method	0.266	0.001	0.267
row_dend-dispatch	0.000	0.000	0.001
row_order-Heatmap-method	0.093	0.001	0.094
row_order-HeatmapList-method	0.261	0.000	0.260
row_order-dispatch	0.000	0.000	0.001
selectArea	0.000	0.001	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	0.845	0.003	0.854
show-HeatmapAnnotation-method	0.000	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	0.000