BioC 3.4: CHECK report for ComplexHeatmap on morelia

Package: ComplexHeatmap

Version: 1.11.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.11.6.tar.gz

StartedAt: 2016-09-20 04:57:06 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:59:05 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 118.7 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_1.11.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.11.6’
* 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  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
* 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 ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
Heatmap 12.452  0.069  12.605
* 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-3.4-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	0	0
ColorMapping	0.025	0.002	0.026
ComplexHeatmap-package	0.001	0.000	0.000
Heatmap-class	0	0	0
Heatmap	12.452	0.069	12.605
HeatmapAnnotation-class	0.001	0.000	0.000
HeatmapAnnotation	0.106	0.000	0.107
HeatmapList-class	4.279	0.020	4.306
HeatmapList	0.000	0.000	0.001
Legend	0.001	0.000	0.000
SingleAnnotation-class	0.001	0.000	0.000
SingleAnnotation	0.059	0.001	0.059
add.AdditiveUnit	4.195	0.012	4.232
add_heatmap-Heatmap-method	1.278	0.009	1.288
add_heatmap-HeatmapAnnotation-method	0.431	0.001	0.433
add_heatmap-HeatmapList-method	2.039	0.003	2.046
add_heatmap-dispatch	0.001	0.000	0.001
anno_barplot	0.017	0.001	0.018
anno_boxplot	0.032	0.001	0.033
anno_density	0.252	0.003	0.256
anno_histogram	0.064	0.003	0.067
anno_link	2.020	0.020	2.042
anno_oncoprint_barplot	0.001	0.000	0.001
anno_points	0.026	0.001	0.030
anno_text	0.306	0.001	0.308
annotation_legend_size-HeatmapList-method	0.001	0.000	0.000
color_mapping_legend-ColorMapping-method	0.225	0.002	0.228
columnAnnotation	0.018	0.000	0.018
column_anno_barplot	0.001	0.000	0.001
column_anno_boxplot	0.001	0.000	0.001
column_anno_density	0.001	0.000	0.001
column_anno_histogram	0.001	0.000	0.001
column_anno_link	0.000	0.000	0.001
column_anno_points	0	0	0
column_anno_text	0.000	0.000	0.001
column_dend-Heatmap-method	0.116	0.001	0.115
column_dend-HeatmapList-method	0.237	0.000	0.238
column_dend-dispatch	0	0	0
column_order-Heatmap-method	0.108	0.000	0.109
column_order-HeatmapList-method	0.249	0.001	0.249
column_order-dispatch	0.000	0.000	0.001
component_height-Heatmap-method	0	0	0
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	0	0
component_width-dispatch	0.000	0.000	0.001
decorate_annotation	0.701	0.001	0.704
decorate_column_dend	0.001	0.001	0.000
decorate_column_names	0.001	0.000	0.000
decorate_column_title	0.000	0.000	0.001
decorate_dend	0.359	0.001	0.361
decorate_dimnames	0.463	0.001	0.465
decorate_heatmap_body	0.419	0.001	0.423
decorate_row_dend	0.000	0.001	0.000
decorate_row_names	0.000	0.000	0.001
decorate_row_title	0.000	0.000	0.001
decorate_title	0.411	0.002	0.413
densityHeatmap	3.663	0.013	3.696
dist2	0.008	0.000	0.008
draw-Heatmap-method	0.442	0.002	0.445
draw-HeatmapAnnotation-method	0.166	0.003	0.379
draw-HeatmapList-method	1.580	0.008	1.590
draw-SingleAnnotation-method	0.117	0.004	0.123
draw-dispatch	0.001	0.000	0.001
draw_annotation-Heatmap-method	0.001	0.000	0.001
draw_annotation_legend-HeatmapList-method	0.001	0.001	0.001
draw_dend-Heatmap-method	0.000	0.000	0.001
draw_dimnames-Heatmap-method	0	0	0
draw_heatmap_body-Heatmap-method	0.001	0.000	0.000
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	0	0
draw_title-HeatmapList-method	0.000	0.000	0.001
draw_title-dispatch	0.001	0.000	0.001
enhanced_basicplot	0.885	0.002	0.887
get_color_mapping_list-HeatmapAnnotation-method	0.000	0.000	0.001
get_color_mapping_param_list-HeatmapAnnotation-method	0	0	0
grid.dendrogram	0.016	0.001	0.017
heatmap_legend_size-HeatmapList-method	0	0	0
ht_global_opt	0.000	0.000	0.001
is_abs_unit	0.001	0.000	0.002
make_column_cluster-Heatmap-method	0.000	0.000	0.001
make_layout-Heatmap-method	0	0	0
make_layout-HeatmapList-method	0	0	0
make_layout-dispatch	0	0	0
make_row_cluster-Heatmap-method	0.001	0.000	0.001
map_to_colors-ColorMapping-method	0.017	0.000	0.017
max_text_height	0.002	0.000	0.002
max_text_width	0.002	0.001	0.002
oncoPrint	0	0	0
plotDataFrame	2.628	0.005	2.634
prepare-Heatmap-method	0.001	0.000	0.000
rowAnnotation	0.011	0.000	0.011
row_anno_barplot	0	0	0
row_anno_boxplot	0	0	0
row_anno_density	0	0	0
row_anno_histogram	0	0	0
row_anno_link	0.000	0.000	0.001
row_anno_points	0.000	0.000	0.001
row_anno_text	0	0	0
row_dend-Heatmap-method	0.068	0.000	0.068
row_dend-HeatmapList-method	0.204	0.001	0.204
row_dend-dispatch	0.001	0.000	0.000
row_order-Heatmap-method	0.072	0.001	0.073
row_order-HeatmapList-method	0.194	0.000	0.194
row_order-dispatch	0.001	0.000	0.001
selectArea	0.001	0.000	0.001
set_component_height-Heatmap-method	0.001	0.000	0.001
show-ColorMapping-method	0	0	0
show-Heatmap-method	0.572	0.003	0.575
show-HeatmapAnnotation-method	0.000	0.000	0.001
show-HeatmapList-method	0	0	0
show-SingleAnnotation-method	0	0	0
show-dispatch	0	0	0
unify_mat_list	0	0	0