BioC 3.2: CHECK report for ComplexHeatmap on perceval

Package: ComplexHeatmap

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.3.1.tar.gz

StartedAt: 2015-08-23 23:32:50 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:34:20 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 90.1 seconds

RetCode: 0

Status:  OK

CheckDir: ComplexHeatmap.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-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 ‘1.3.1’
* 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  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
* 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 ... [37s/38s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
Heatmap 12.145  0.114  12.364
* 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	0.001
AdditiveUnit	0.001	0.000	0.000
ColorMapping-class	0.001	0.001	0.001
ColorMapping	0.051	0.001	0.053
Heatmap-class	0	0	0
Heatmap	12.145	0.114	12.364
HeatmapAnnotation-class	0.000	0.000	0.001
HeatmapAnnotation	0.071	0.000	0.072
HeatmapList-class	3.920	0.014	3.960
HeatmapList	0.001	0.000	0.001
SingleAnnotation-class	0.000	0.000	0.001
SingleAnnotation	0.099	0.001	0.100
add.AdditiveUnit	4.448	0.020	4.503
add_heatmap-Heatmap-method	1.048	0.004	1.059
add_heatmap-HeatmapAnnotation-method	0.380	0.002	0.383
add_heatmap-HeatmapList-method	1.888	0.009	1.903
add_heatmap-dispatch	0.000	0.000	0.001
anno_barplot	0.013	0.002	0.015
anno_boxplot	0.031	0.003	0.033
anno_density	0.253	0.009	0.264
anno_histogram	0.057	0.003	0.063
anno_points	0.007	0.001	0.008
anno_text	0.372	0.003	0.381
annotation_legend_size-HeatmapList-method	0.000	0.000	0.001
color_mapping_legend-ColorMapping-method	0.235	0.004	0.239
columnAnnotation	0.012	0.000	0.012
component_height-Heatmap-method	0.001	0.000	0.000
component_height-HeatmapList-method	0	0	0
component_height-dispatch	0.001	0.000	0.000
component_width-Heatmap-method	0.001	0.000	0.000
component_width-HeatmapList-method	0.000	0.000	0.001
component_width-dispatch	0.001	0.000	0.001
decorate_annotation	0.593	0.005	0.603
decorate_dimnames	0.359	0.002	0.362
decorate_hclust	0.331	0.002	0.336
decorate_heatmap_body	0.335	0.003	0.339
decorate_title	0.349	0.001	0.352
densityHeatmap	3.044	0.024	3.089
dist2	0.002	0.000	0.003
draw-Heatmap-method	0.308	0.002	0.313
draw-HeatmapAnnotation-method	0.144	0.006	0.152
draw-HeatmapList-method	1.282	0.006	1.296
draw-SingleAnnotation-method	0.167	0.008	0.177
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	0.000	0.001
draw_dimnames-Heatmap-method	0.001	0.000	0.000
draw_hclust-Heatmap-method	0.001	0.000	0.001
draw_heatmap_body-Heatmap-method	0.001	0.000	0.001
draw_heatmap_legend-HeatmapList-method	0.001	0.000	0.000
draw_heatmap_list-HeatmapList-method	0.001	0.000	0.000
draw_title-Heatmap-method	0.000	0.000	0.001
draw_title-HeatmapList-method	0.000	0.000	0.001
draw_title-dispatch	0.000	0.000	0.001
get_color_mapping_list-HeatmapAnnotation-method	0.001	0.000	0.000
grid.dendrogram	0.026	0.002	0.028
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	0.000	0.000	0.001
make_layout-HeatmapList-method	0.001	0.000	0.001
make_layout-dispatch	0.001	0.000	0.001
make_row_cluster-Heatmap-method	0	0	0
map_to_colors-ColorMapping-method	0.051	0.001	0.052
plotDataFrame	3.226	0.025	3.267
prepare-Heatmap-method	0.000	0.000	0.001
rowAnnotation	0.016	0.001	0.017
set_component_height-Heatmap-method	0.001	0.000	0.001
show-Heatmap-method	0.714	0.005	0.721
show-dispatch	0.001	0.000	0.001