BioC 3.5: CHECK report for ComplexHeatmap on oaxaca

Package: ComplexHeatmap

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.13.0.tar.gz

StartedAt: 2017-03-04 01:05:34 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 01:07:47 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 133.3 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_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ComplexHeatmap.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.13.0’
* 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 17.188  0.073  17.309
* 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-3.5-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	0.001
ColorMapping-class	0.000	0.000	0.001
ColorMapping	0.091	0.002	0.101
ComplexHeatmap-package	0.001	0.000	0.000
Heatmap-class	0.001	0.000	0.001
Heatmap	17.188	0.073	17.309
HeatmapAnnotation-class	0.001	0.001	0.001
HeatmapAnnotation	0.213	0.007	0.220
HeatmapList-class	4.072	0.012	4.088
HeatmapList	0.001	0.000	0.000
Legend	0.001	0.000	0.000
SingleAnnotation-class	0.001	0.000	0.000
SingleAnnotation	0.100	0.001	0.101
add.AdditiveUnit	4.893	0.008	4.902
add_heatmap-Heatmap-method	1.302	0.008	1.331
add_heatmap-HeatmapAnnotation-method	0.425	0.001	0.427
add_heatmap-HeatmapList-method	1.859	0.005	1.878
add_heatmap-dispatch	0	0	0
anno_barplot	0.227	0.002	0.228
anno_boxplot	0.244	0.002	0.246
anno_density	0.388	0.004	0.393
anno_histogram	0.224	0.002	0.227
anno_link	1.939	0.021	1.961
anno_oncoprint_barplot	0.001	0.000	0.000
anno_points	0.025	0.002	0.028
anno_text	0.409	0.005	0.415
annotation_legend_size-HeatmapList-method	0	0	0
color_mapping_legend-ColorMapping-method	0.189	0.002	0.191
columnAnnotation	0.019	0.000	0.018
column_anno_barplot	0.000	0.000	0.001
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_link	0	0	0
column_anno_points	0.001	0.000	0.000
column_anno_text	0.001	0.000	0.000
column_dend-Heatmap-method	0.098	0.000	0.100
column_dend-HeatmapList-method	0.293	0.001	0.295
column_dend-dispatch	0.001	0.000	0.001
column_order-Heatmap-method	0.101	0.000	0.101
column_order-HeatmapList-method	0.281	0.001	0.282
column_order-dispatch	0.001	0.000	0.000
component_height-Heatmap-method	0	0	0
component_height-HeatmapList-method	0.000	0.000	0.001
component_height-dispatch	0.000	0.001	0.001
component_width-Heatmap-method	0.000	0.000	0.001
component_width-HeatmapList-method	0	0	0
component_width-dispatch	0.000	0.000	0.001
decorate_annotation	0.710	0.001	0.712
decorate_column_dend	0.000	0.000	0.001
decorate_column_names	0.000	0.001	0.001
decorate_column_title	0	0	0
decorate_dend	0.407	0.002	0.409
decorate_dimnames	0.424	0.001	0.426
decorate_heatmap_body	0.302	0.001	0.304
decorate_row_dend	0.001	0.000	0.001
decorate_row_names	0.001	0.000	0.000
decorate_row_title	0	0	0
decorate_title	0.270	0.001	0.271
densityHeatmap	4.272	0.011	4.291
dist2	0.027	0.000	0.028
draw-Heatmap-method	0.392	0.001	0.393
draw-HeatmapAnnotation-method	0.163	0.003	0.167
draw-HeatmapList-method	1.326	0.003	1.330
draw-SingleAnnotation-method	0.124	0.004	0.128
draw-dispatch	0.001	0.000	0.000
draw_annotation-Heatmap-method	0.001	0.000	0.001
draw_annotation_legend-HeatmapList-method	0	0	0
draw_dend-Heatmap-method	0	0	0
draw_dimnames-Heatmap-method	0.000	0.000	0.001
draw_heatmap_body-Heatmap-method	0	0	0
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	0	0
draw_title-HeatmapList-method	0	0	0
draw_title-dispatch	0.000	0.000	0.001
enhanced_basicplot	1.163	0.002	1.166
get_color_mapping_list-HeatmapAnnotation-method	0	0	0
get_color_mapping_param_list-HeatmapAnnotation-method	0.000	0.000	0.001
grid.dendrogram	0.029	0.001	0.030
heatmap_legend_size-HeatmapList-method	0.001	0.001	0.001
ht_global_opt	0.000	0.000	0.001
is_abs_unit	0.002	0.000	0.003
make_column_cluster-Heatmap-method	0.001	0.001	0.001
make_layout-Heatmap-method	0.000	0.000	0.001
make_layout-HeatmapList-method	0.000	0.000	0.001
make_layout-dispatch	0.000	0.000	0.001
make_row_cluster-Heatmap-method	0	0	0
map_to_colors-ColorMapping-method	0.032	0.001	0.033
max_text_height	0.004	0.000	0.003
max_text_width	0.003	0.000	0.003
oncoPrint	0.001	0.000	0.001
plotDataFrame	3.010	0.003	3.014
prepare-Heatmap-method	0.000	0.000	0.001
rowAnnotation	0.015	0.000	0.015
row_anno_barplot	0	0	0
row_anno_boxplot	0	0	0
row_anno_density	0.001	0.000	0.001
row_anno_histogram	0.000	0.000	0.001
row_anno_link	0.000	0.000	0.001
row_anno_points	0.001	0.000	0.001
row_anno_text	0.001	0.000	0.001
row_dend-Heatmap-method	0.097	0.000	0.097
row_dend-HeatmapList-method	0.247	0.000	0.247
row_dend-dispatch	0.001	0.000	0.000
row_order-Heatmap-method	0.111	0.001	0.112
row_order-HeatmapList-method	0.195	0.000	0.195
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	0.000	0.000	0.001
show-Heatmap-method	0.747	0.001	0.749
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	0.000
unify_mat_list	0.001	0.000	0.000