BioC 3.4: CHECK report for ComplexHeatmap on morelia

Package: ComplexHeatmap

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.12.0.tar.gz

StartedAt: 2017-04-15 00:18:22 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:20:42 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 139.3 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.12.0’
* 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 ... 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          13.921  0.068  14.050
add.AdditiveUnit  5.021  0.011   5.147
* 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	0	0
AdditiveUnit	0.001	0.000	0.000
ColorMapping-class	0.001	0.000	0.000
ColorMapping	0.016	0.001	0.018
ComplexHeatmap-package	0.000	0.000	0.001
Heatmap-class	0.001	0.000	0.001
Heatmap	13.921	0.068	14.050
HeatmapAnnotation-class	0.000	0.000	0.001
HeatmapAnnotation	0.117	0.001	0.117
HeatmapList-class	4.468	0.019	4.490
HeatmapList	0.001	0.000	0.001
Legend	0.001	0.000	0.000
SingleAnnotation-class	0	0	0
SingleAnnotation	0.101	0.001	0.102
add.AdditiveUnit	5.021	0.011	5.147
add_heatmap-Heatmap-method	1.305	0.004	1.393
add_heatmap-HeatmapAnnotation-method	0.446	0.001	0.469
add_heatmap-HeatmapList-method	2.313	0.012	2.327
add_heatmap-dispatch	0.001	0.000	0.001
anno_barplot	0.009	0.001	0.011
anno_boxplot	0.028	0.001	0.033
anno_density	0.229	0.003	0.233
anno_histogram	0.057	0.001	0.071
anno_link	2.119	0.020	2.748
anno_oncoprint_barplot	0.000	0.000	0.001
anno_points	0.026	0.002	0.235
anno_text	0.324	0.001	1.021
annotation_legend_size-HeatmapList-method	0.001	0.000	0.001
color_mapping_legend-ColorMapping-method	0.215	0.003	0.234
columnAnnotation	0.022	0.000	0.023
column_anno_barplot	0.000	0.000	0.001
column_anno_boxplot	0	0	0
column_anno_density	0	0	0
column_anno_histogram	0.000	0.000	0.001
column_anno_link	0	0	0
column_anno_points	0.001	0.000	0.000
column_anno_text	0.001	0.000	0.001
column_dend-Heatmap-method	0.125	0.001	0.127
column_dend-HeatmapList-method	0.265	0.001	0.266
column_dend-dispatch	0.001	0.000	0.000
column_order-Heatmap-method	0.093	0.000	0.094
column_order-HeatmapList-method	0.240	0.000	0.241
column_order-dispatch	0.001	0.000	0.000
component_height-Heatmap-method	0.001	0.000	0.000
component_height-HeatmapList-method	0.001	0.000	0.000
component_height-dispatch	0.000	0.001	0.001
component_width-Heatmap-method	0.000	0.000	0.001
component_width-HeatmapList-method	0.000	0.000	0.001
component_width-dispatch	0.001	0.000	0.001
decorate_annotation	0.859	0.002	0.871
decorate_column_dend	0.000	0.000	0.001
decorate_column_names	0.001	0.000	0.000
decorate_column_title	0	0	0
decorate_dend	0.398	0.001	0.400
decorate_dimnames	0.472	0.001	0.473
decorate_heatmap_body	0.352	0.001	0.353
decorate_row_dend	0	0	0
decorate_row_names	0	0	0
decorate_row_title	0	0	0
decorate_title	0.443	0.001	0.445
densityHeatmap	3.863	0.014	4.482
dist2	0.005	0.000	0.004
draw-Heatmap-method	0.441	0.001	0.504
draw-HeatmapAnnotation-method	0.144	0.004	0.154
draw-HeatmapList-method	1.786	0.005	2.016
draw-SingleAnnotation-method	0.147	0.003	0.152
draw-dispatch	0.001	0.001	0.000
draw_annotation-Heatmap-method	0	0	0
draw_annotation_legend-HeatmapList-method	0	0	0
draw_dend-Heatmap-method	0.000	0.000	0.001
draw_dimnames-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	0.001
draw_heatmap_list-HeatmapList-method	0.000	0.000	0.001
draw_title-Heatmap-method	0.000	0.000	0.001
draw_title-HeatmapList-method	0.001	0.000	0.000
draw_title-dispatch	0	0	0
enhanced_basicplot	1.116	0.002	1.119
get_color_mapping_list-HeatmapAnnotation-method	0.001	0.000	0.001
get_color_mapping_param_list-HeatmapAnnotation-method	0	0	0
grid.dendrogram	0.026	0.001	0.027
heatmap_legend_size-HeatmapList-method	0.001	0.000	0.000
ht_global_opt	0.001	0.000	0.001
is_abs_unit	0.002	0.000	0.002
make_column_cluster-Heatmap-method	0.001	0.000	0.000
make_layout-Heatmap-method	0.001	0.000	0.001
make_layout-HeatmapList-method	0.000	0.001	0.001
make_layout-dispatch	0.000	0.000	0.001
make_row_cluster-Heatmap-method	0	0	0
map_to_colors-ColorMapping-method	0.023	0.001	0.024
max_text_height	0.002	0.000	0.002
max_text_width	0.002	0.000	0.002
oncoPrint	0.001	0.000	0.000
plotDataFrame	3.144	0.010	3.221
prepare-Heatmap-method	0	0	0
rowAnnotation	0.012	0.000	0.012
row_anno_barplot	0.001	0.000	0.001
row_anno_boxplot	0.001	0.001	0.001
row_anno_density	0.001	0.000	0.001
row_anno_histogram	0.000	0.000	0.001
row_anno_link	0	0	0
row_anno_points	0	0	0
row_anno_text	0.001	0.000	0.001
row_dend-Heatmap-method	0.095	0.000	0.095
row_dend-HeatmapList-method	0.247	0.001	0.247
row_dend-dispatch	0.001	0.000	0.000
row_order-Heatmap-method	0.097	0.000	0.098
row_order-HeatmapList-method	0.320	0.001	0.321
row_order-dispatch	0.000	0.000	0.001
selectArea	0	0	0
set_component_height-Heatmap-method	0	0	0
show-ColorMapping-method	0.000	0.000	0.001
show-Heatmap-method	0.884	0.004	0.899
show-HeatmapAnnotation-method	0	0	0
show-HeatmapList-method	0.001	0.000	0.000
show-SingleAnnotation-method	0.001	0.000	0.000
show-dispatch	0.001	0.000	0.001
unify_mat_list	0.001	0.000	0.001