BioC 3.2: CHECK report for ComplexHeatmap on perceval

Package: ComplexHeatmap

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.6.0.tar.gz

StartedAt: 2015-10-27 06:46:25 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:47:59 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 94.1 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.6.0’
* 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 ... [4s/4s] OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
* 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 ... [41s/41s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
Heatmap 12.577  0.067  12.653
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [1s/1s]
 [2s/2s] 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-3.2-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	0.000
AdditiveUnit	0	0	0
ColorMapping-class	0.001	0.000	0.000
ColorMapping	0.049	0.002	0.051
ComplexHeatmap-package	0.000	0.000	0.001
Heatmap-class	0	0	0
Heatmap	12.577	0.067	12.653
HeatmapAnnotation-class	0.000	0.000	0.001
HeatmapAnnotation	0.108	0.001	0.108
HeatmapList-class	3.965	0.008	3.975
HeatmapList	0.000	0.001	0.000
SingleAnnotation-class	0.001	0.000	0.000
SingleAnnotation	0.106	0.001	0.107
add.AdditiveUnit	4.422	0.014	4.439
add_heatmap-Heatmap-method	1.134	0.003	1.138
add_heatmap-HeatmapAnnotation-method	0.417	0.001	0.419
add_heatmap-HeatmapList-method	1.937	0.005	1.942
add_heatmap-dispatch	0.001	0.000	0.001
anno_barplot	0.013	0.002	0.016
anno_boxplot	0.036	0.002	0.045
anno_density	0.271	0.005	0.277
anno_histogram	0.052	0.002	0.055
anno_points	0.006	0.001	0.006
anno_text	0.375	0.001	0.376
annotation_legend_size-HeatmapList-method	0.000	0.000	0.001
color_mapping_legend-ColorMapping-method	0.267	0.003	0.271
columnAnnotation	0.018	0.000	0.018
column_anno_barplot	0.001	0.001	0.001
column_anno_boxplot	0.001	0.000	0.000
column_anno_density	0.001	0.000	0.000
column_anno_histogram	0	0	0
column_anno_points	0.001	0.000	0.000
column_anno_text	0.001	0.000	0.002
column_dend-Heatmap-method	0.000	0.000	0.001
column_dend-HeatmapList-method	0.001	0.000	0.001
column_dend-dispatch	0.001	0.000	0.001
column_order-Heatmap-method	0.001	0.000	0.001
column_order-HeatmapList-method	0.001	0.000	0.000
column_order-dispatch	0.001	0.000	0.000
component_height-Heatmap-method	0.001	0.000	0.001
component_height-HeatmapList-method	0.000	0.000	0.001
component_height-dispatch	0.000	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	0.000	0.001	0.001
decorate_annotation	0.783	0.002	0.785
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	0.399	0.001	0.401
decorate_dimnames	0.426	0.001	0.427
decorate_heatmap_body	0.359	0.001	0.360
decorate_row_dend	0.001	0.000	0.000
decorate_row_names	0.000	0.000	0.001
decorate_row_title	0.000	0.000	0.001
decorate_title	0.409	0.001	0.410
densityHeatmap	3.774	0.021	3.799
dist2	0.003	0.001	0.003
draw-Heatmap-method	0.345	0.001	0.347
draw-HeatmapAnnotation-method	0.176	0.006	0.183
draw-HeatmapList-method	1.331	0.003	1.335
draw-SingleAnnotation-method	0.157	0.005	0.169
draw-dispatch	0.001	0.000	0.001
draw_annotation-Heatmap-method	0.000	0.000	0.001
draw_annotation_legend-HeatmapList-method	0.000	0.001	0.000
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	0.000	0.000	0.001
draw_heatmap_legend-HeatmapList-method	0.000	0.000	0.001
draw_heatmap_list-HeatmapList-method	0.001	0.000	0.001
draw_title-Heatmap-method	0.001	0.000	0.001
draw_title-HeatmapList-method	0.000	0.000	0.001
draw_title-dispatch	0	0	0
enhanced_basicplot	1.210	0.003	1.213
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	0.026	0.001	0.028
heatmap_legend_size-HeatmapList-method	0.000	0.000	0.001
ht_global_opt	0	0	0
is_abs_unit	0.002	0.001	0.001
make_column_cluster-Heatmap-method	0.001	0.000	0.001
make_layout-Heatmap-method	0.001	0.000	0.001
make_layout-HeatmapList-method	0.001	0.001	0.001
make_layout-dispatch	0.000	0.000	0.001
make_row_cluster-Heatmap-method	0.000	0.000	0.001
map_to_colors-ColorMapping-method	0.051	0.001	0.052
max_text_height	0.013	0.000	0.013
max_text_width	0.013	0.000	0.013
oncoPrint	0	0	0
plotDataFrame	3.396	0.006	3.403
prepare-Heatmap-method	0.001	0.000	0.000
rowAnnotation	0.014	0.000	0.014
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	0.001	0.000	0.001
row_anno_points	0.001	0.000	0.001
row_anno_text	0.001	0.001	0.001
row_dend-Heatmap-method	0.001	0.000	0.001
row_dend-HeatmapList-method	0.001	0.000	0.001
row_dend-dispatch	0.001	0.000	0.001
row_order-Heatmap-method	0	0	0
row_order-HeatmapList-method	0.000	0.000	0.001
row_order-dispatch	0.001	0.000	0.001
select	0.001	0.000	0.001
set_component_height-Heatmap-method	0.000	0.000	0.001
show-ColorMapping-method	0.000	0.000	0.001
show-Heatmap-method	0.692	0.004	0.698
show-HeatmapAnnotation-method	0.000	0.000	0.001
show-HeatmapList-method	0.000	0.001	0.000
show-SingleAnnotation-method	0.001	0.000	0.001
show-dispatch	0.001	0.001	0.001
unify_mat_list	0.001	0.000	0.001