BioC 3.3: CHECK report for ComplexHeatmap on morelia

Package: ComplexHeatmap

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.7.1.tar.gz

StartedAt: 2015-10-22 04:51:31 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 04:52:41 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 69.6 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_1.7.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ComplexHeatmap.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.7.1’
* 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 ... [3s/3s] OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
* 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 ... [26s/27s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
Heatmap 8.502  0.052   8.588
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [1s/1s]
 [1s/1s] 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-3.3-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	0.001	0.000	0.000
ColorMapping-class	0.001	0.000	0.001
ColorMapping	0.026	0.002	0.027
ComplexHeatmap-package	0.001	0.000	0.001
Heatmap-class	0.001	0.000	0.001
Heatmap	8.502	0.052	8.588
HeatmapAnnotation-class	0	0	0
HeatmapAnnotation	0.049	0.000	0.050
HeatmapList-class	2.442	0.012	2.461
HeatmapList	0.000	0.000	0.001
SingleAnnotation-class	0	0	0
SingleAnnotation	0.049	0.001	0.050
add.AdditiveUnit	2.733	0.007	2.751
add_heatmap-Heatmap-method	0.806	0.004	0.813
add_heatmap-HeatmapAnnotation-method	0.244	0.001	0.244
add_heatmap-HeatmapList-method	1.147	0.001	1.152
add_heatmap-dispatch	0.001	0.000	0.000
anno_barplot	0.011	0.001	0.012
anno_boxplot	0.027	0.001	0.028
anno_density	0.194	0.004	0.200
anno_histogram	0.046	0.002	0.048
anno_points	0.004	0.000	0.005
anno_text	0.256	0.000	0.257
annotation_legend_size-HeatmapList-method	0	0	0
color_mapping_legend-ColorMapping-method	0.159	0.002	0.162
columnAnnotation	0.008	0.001	0.008
column_anno_barplot	0	0	0
column_anno_boxplot	0.000	0.000	0.001
column_anno_density	0.000	0.000	0.001
column_anno_histogram	0	0	0
column_anno_points	0	0	0
column_anno_text	0	0	0
column_dend-Heatmap-method	0.000	0.000	0.001
column_dend-HeatmapList-method	0.000	0.000	0.001
column_dend-dispatch	0.001	0.000	0.000
column_order-Heatmap-method	0.001	0.000	0.000
column_order-HeatmapList-method	0.001	0.000	0.000
column_order-dispatch	0.001	0.000	0.001
component_height-Heatmap-method	0.001	0.000	0.000
component_height-HeatmapList-method	0	0	0
component_height-dispatch	0	0	0
component_width-Heatmap-method	0	0	0
component_width-HeatmapList-method	0.000	0.000	0.001
component_width-dispatch	0.000	0.000	0.001
decorate_annotation	0.519	0.003	0.522
decorate_column_dend	0	0	0
decorate_column_names	0.000	0.000	0.001
decorate_column_title	0.000	0.000	0.001
decorate_dend	0.229	0.000	0.229
decorate_dimnames	0.271	0.001	0.272
decorate_heatmap_body	0.234	0.001	0.236
decorate_row_dend	0	0	0
decorate_row_names	0.001	0.000	0.001
decorate_row_title	0.001	0.000	0.001
decorate_title	0.248	0.001	0.249
densityHeatmap	2.242	0.010	2.257
dist2	0.001	0.000	0.002
draw-Heatmap-method	0.201	0.000	0.201
draw-HeatmapAnnotation-method	0.088	0.002	0.091
draw-HeatmapList-method	0.807	0.002	0.809
draw-SingleAnnotation-method	0.087	0.004	0.092
draw-dispatch	0.000	0.000	0.001
draw_annotation-Heatmap-method	0	0	0
draw_annotation_legend-HeatmapList-method	0.000	0.000	0.001
draw_dend-Heatmap-method	0.001	0.000	0.000
draw_dimnames-Heatmap-method	0.001	0.001	0.000
draw_heatmap_body-Heatmap-method	0.000	0.000	0.001
draw_heatmap_legend-HeatmapList-method	0	0	0
draw_heatmap_list-HeatmapList-method	0.000	0.000	0.001
draw_title-Heatmap-method	0.001	0.000	0.000
draw_title-HeatmapList-method	0.000	0.000	0.001
draw_title-dispatch	0.001	0.000	0.000
enhanced_basicplot	1.066	0.004	1.071
get_color_mapping_list-HeatmapAnnotation-method	0.000	0.000	0.001
get_color_mapping_param_list-HeatmapAnnotation-method	0.000	0.000	0.001
grid.dendrogram	0.016	0.001	0.018
heatmap_legend_size-HeatmapList-method	0	0	0
ht_global_opt	0.001	0.000	0.001
is_abs_unit	0.001	0.000	0.001
make_column_cluster-Heatmap-method	0.000	0.000	0.001
make_layout-Heatmap-method	0.001	0.000	0.000
make_layout-HeatmapList-method	0	0	0
make_layout-dispatch	0.001	0.000	0.001
make_row_cluster-Heatmap-method	0.001	0.000	0.000
map_to_colors-ColorMapping-method	0.027	0.001	0.028
max_text_height	0.012	0.000	0.012
max_text_width	0.012	0.001	0.014
oncoPrint	0.001	0.000	0.001
plotDataFrame	2.307	0.008	2.315
prepare-Heatmap-method	0.001	0.000	0.001
rowAnnotation	0.01	0.00	0.01
row_anno_barplot	0.001	0.000	0.000
row_anno_boxplot	0.000	0.000	0.001
row_anno_density	0	0	0
row_anno_histogram	0.000	0.000	0.001
row_anno_points	0.001	0.000	0.000
row_anno_text	0.001	0.000	0.000
row_dend-Heatmap-method	0.000	0.000	0.001
row_dend-HeatmapList-method	0	0	0
row_dend-dispatch	0.000	0.000	0.001
row_order-Heatmap-method	0.001	0.000	0.000
row_order-HeatmapList-method	0	0	0
row_order-dispatch	0	0	0
selectArea	0	0	0
set_component_height-Heatmap-method	0.000	0.000	0.001
show-ColorMapping-method	0.001	0.000	0.000
show-Heatmap-method	0.488	0.001	0.491
show-HeatmapAnnotation-method	0.001	0.000	0.000
show-HeatmapList-method	0	0	0
show-SingleAnnotation-method	0.000	0.000	0.001
show-dispatch	0	0	0
unify_mat_list	0	0	0