BioC 3.2: CHECK report for ComplexHeatmap on oaxaca

Package: ComplexHeatmap

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.6.0.tar.gz

StartedAt: 2015-10-27 02:37:51 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:39:32 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 101.1 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.6.0’
* 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 ... [4s/4s] OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
* 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 ... [38s/47s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
Heatmap 11.629  0.063  11.723
* 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-3.2-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	0.000	0.000	0.001
ColorMapping	0.030	0.001	0.031
ComplexHeatmap-package	0	0	0
Heatmap-class	0.000	0.000	0.001
Heatmap	11.629	0.063	11.723
HeatmapAnnotation-class	0	0	0
HeatmapAnnotation	0.107	0.002	0.110
HeatmapList-class	3.640	0.014	3.658
HeatmapList	0	0	0
SingleAnnotation-class	0.000	0.000	0.001
SingleAnnotation	0.078	0.001	0.079
add.AdditiveUnit	4.016	0.008	4.029
add_heatmap-Heatmap-method	1.085	0.003	1.089
add_heatmap-HeatmapAnnotation-method	0.416	0.002	0.419
add_heatmap-HeatmapList-method	1.765	0.004	1.791
add_heatmap-dispatch	0.000	0.000	0.001
anno_barplot	0.014	0.001	1.679
anno_boxplot	0.031	0.002	0.986
anno_density	0.248	0.005	4.443
anno_histogram	0.055	0.002	0.780
anno_points	0.006	0.000	0.729
anno_text	0.322	0.001	0.418
annotation_legend_size-HeatmapList-method	0.001	0.000	0.000
color_mapping_legend-ColorMapping-method	0.233	0.002	0.275
columnAnnotation	0.011	0.000	0.011
column_anno_barplot	0	0	0
column_anno_boxplot	0	0	0
column_anno_density	0.001	0.000	0.000
column_anno_histogram	0	0	0
column_anno_points	0.000	0.000	0.001
column_anno_text	0.001	0.000	0.001
column_dend-Heatmap-method	0.000	0.000	0.001
column_dend-HeatmapList-method	0	0	0
column_dend-dispatch	0.001	0.001	0.000
column_order-Heatmap-method	0	0	0
column_order-HeatmapList-method	0.000	0.000	0.001
column_order-dispatch	0	0	0
component_height-Heatmap-method	0.001	0.000	0.001
component_height-HeatmapList-method	0.001	0.000	0.000
component_height-dispatch	0.001	0.000	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	0.000	0.000	0.001
decorate_annotation	0.787	0.001	0.790
decorate_column_dend	0	0	0
decorate_column_names	0.001	0.000	0.001
decorate_column_title	0.000	0.000	0.001
decorate_dend	0.389	0.001	0.390
decorate_dimnames	0.435	0.001	0.435
decorate_heatmap_body	0.338	0.001	0.339
decorate_row_dend	0.000	0.000	0.001
decorate_row_names	0.000	0.000	0.001
decorate_row_title	0	0	0
decorate_title	0.396	0.002	0.398
densityHeatmap	3.571	0.018	3.597
dist2	0.003	0.001	0.004
draw-Heatmap-method	0.294	0.001	0.331
draw-HeatmapAnnotation-method	0.160	0.003	0.200
draw-HeatmapList-method	1.263	0.002	1.265
draw-SingleAnnotation-method	0.141	0.004	0.147
draw-dispatch	0.000	0.000	0.001
draw_annotation-Heatmap-method	0	0	0
draw_annotation_legend-HeatmapList-method	0.001	0.000	0.001
draw_dend-Heatmap-method	0.001	0.001	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	0.000	0.001	0.000
draw_heatmap_list-HeatmapList-method	0	0	0
draw_title-Heatmap-method	0.001	0.000	0.000
draw_title-HeatmapList-method	0.000	0.000	0.001
draw_title-dispatch	0.000	0.001	0.000
enhanced_basicplot	1.153	0.002	1.158
get_color_mapping_list-HeatmapAnnotation-method	0.000	0.000	0.001
get_color_mapping_param_list-HeatmapAnnotation-method	0.001	0.000	0.000
grid.dendrogram	0.029	0.000	0.030
heatmap_legend_size-HeatmapList-method	0.001	0.000	0.001
ht_global_opt	0.001	0.000	0.001
is_abs_unit	0.002	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	0.000	0.000	0.001
make_layout-dispatch	0	0	0
make_row_cluster-Heatmap-method	0.001	0.000	0.001
map_to_colors-ColorMapping-method	0.036	0.001	0.037
max_text_height	0.013	0.000	0.012
max_text_width	0.011	0.000	0.011
oncoPrint	0.001	0.000	0.001
plotDataFrame	3.254	0.011	3.266
prepare-Heatmap-method	0.001	0.000	0.001
rowAnnotation	0.014	0.000	0.014
row_anno_barplot	0.000	0.000	0.001
row_anno_boxplot	0	0	0
row_anno_density	0.001	0.000	0.000
row_anno_histogram	0.000	0.000	0.001
row_anno_points	0.000	0.001	0.001
row_anno_text	0.001	0.000	0.000
row_dend-Heatmap-method	0.001	0.000	0.001
row_dend-HeatmapList-method	0.001	0.000	0.001
row_dend-dispatch	0.001	0.000	0.001
row_order-Heatmap-method	0.001	0.000	0.001
row_order-HeatmapList-method	0.001	0.000	0.000
row_order-dispatch	0.001	0.000	0.001
select	0.001	0.000	0.001
set_component_height-Heatmap-method	0.000	0.000	0.001
show-ColorMapping-method	0.000	0.000	0.001
show-Heatmap-method	0.668	0.002	0.671
show-HeatmapAnnotation-method	0.001	0.001	0.001
show-HeatmapList-method	0	0	0
show-SingleAnnotation-method	0.000	0.000	0.001
show-dispatch	0.000	0.000	0.001
unify_mat_list	0.000	0.000	0.001