BioC 3.1: CHECK report for ComplexHeatmap on petty

Package: ComplexHeatmap

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.0.0.tar.gz

StartedAt: 2015-10-08 22:16:49 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:18:25 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 95.4 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.0.0’
* 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 ... 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 ... 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 ... [38s/38s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
Heatmap           14.471  0.065  14.557
add.AdditiveUnit   6.474  0.017   6.505
HeatmapList-class  5.771  0.014   5.792
* 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: OK

* 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	0.000	0.000	0.001
AdditiveUnit	0.001	0.000	0.001
ColorMapping-class	0.001	0.000	0.001
ColorMapping	0.069	0.001	0.070
Heatmap-class	0.001	0.000	0.001
Heatmap	14.471	0.065	14.557
HeatmapAnnotation-class	0.001	0.000	0.002
HeatmapAnnotation	0.030	0.001	0.031
HeatmapList-class	5.771	0.014	5.792
HeatmapList	0.001	0.000	0.001
SingleAnnotation-class	0.000	0.000	0.001
SingleAnnotation	0.077	0.002	0.079
add.AdditiveUnit	6.474	0.017	6.505
add_heatmap-Heatmap-method	1.574	0.005	1.581
add_heatmap-HeatmapAnnotation-method	0.577	0.002	0.580
add_heatmap-HeatmapList-method	2.556	0.006	2.570
add_heatmap-dispatch	0.001	0.000	0.002
anno_barplot	0.019	0.002	0.034
anno_boxplot	0.050	0.002	0.052
anno_density	0.442	0.006	0.450
anno_histogram	0.097	0.002	0.100
anno_points	0.01	0.00	0.01
annotation_legend_size-HeatmapList-method	0.001	0.000	0.001
color_mapping_legend-ColorMapping-method	0.122	0.003	0.125
component_height-Heatmap-method	0.001	0.000	0.001
component_height-HeatmapList-method	0	0	0
component_height-dispatch	0.001	0.000	0.001
component_width-Heatmap-method	0.001	0.000	0.001
component_width-HeatmapList-method	0	0	0
component_width-dispatch	0.000	0.000	0.001
dist2	0.003	0.000	0.004
draw-Heatmap-method	0.593	0.001	0.596
draw-HeatmapAnnotation-method	0.109	0.005	0.114
draw-HeatmapList-method	2.151	0.004	2.161
draw-SingleAnnotation-method	0.141	0.005	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	0.001	0.001	0.001
draw_dimnames-Heatmap-method	0.001	0.000	0.001
draw_hclust-Heatmap-method	0.001	0.000	0.001
draw_heatmap_body-Heatmap-method	0.000	0.001	0.001
draw_heatmap_legend-HeatmapList-method	0.001	0.000	0.000
draw_heatmap_list-HeatmapList-method	0.001	0.000	0.001
draw_title-Heatmap-method	0.001	0.001	0.001
draw_title-HeatmapList-method	0.001	0.000	0.001
draw_title-dispatch	0.001	0.000	0.001
get_color_mapping_list-HeatmapAnnotation-method	0.001	0.000	0.001
grid.dendrogram	0.052	0.001	0.053
heatmap_legend_size-HeatmapList-method	0.001	0.000	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	0.000	0.001
make_layout-dispatch	0.001	0.001	0.001
make_row_cluster-Heatmap-method	0.001	0.000	0.000
map_to_colors-ColorMapping-method	0.081	0.001	0.082
prepare-Heatmap-method	0.000	0.000	0.001
set_component_height-Heatmap-method	0.000	0.000	0.001
show-Heatmap-method	1.108	0.003	1.113
show-dispatch	0.000	0.000	0.001