BioC 3.3: CHECK report for ComplexHeatmap on oaxaca

Package: ComplexHeatmap

Version: 1.10.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.10.2.tar.gz

StartedAt: 2016-10-13 00:30:37 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 00:32:59 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 142.5 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_1.10.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-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 ‘1.10.2’
* 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  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
* 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 ... NOTE
+.AdditiveUnit: no visible global function definition for ‘new’
AdditiveUnit: no visible global function definition for ‘new’
ColorMapping: no visible global function definition for ‘new’
Heatmap: no visible global function definition for ‘new’
HeatmapAnnotation: no visible global function definition for ‘new’
HeatmapList: no visible global function definition for ‘new’
SingleAnnotation: no visible global function definition for ‘new’
add_heatmap,Heatmap: no visible global function definition for ‘new’
add_heatmap,HeatmapAnnotation: no visible global function definition
  for ‘new’
draw,Heatmap: no visible global function definition for ‘new’
draw_heatmap_body,Heatmap: no visible global function definition for
  ‘getFromNamespace’
show,HeatmapAnnotation: no visible global function definition for
  ‘show’
Undefined global functions or variables:
  getFromNamespace new show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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           16.013  0.086  16.852
add.AdditiveUnit   5.454  0.019   5.488
HeatmapList-class  5.178  0.017   5.228
* 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: 2 NOTEs
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	0.001
AdditiveUnit	0.000	0.000	0.001
ColorMapping-class	0	0	0
ColorMapping	0.023	0.001	0.025
ComplexHeatmap-package	0.001	0.000	0.001
Heatmap-class	0.001	0.000	0.001
Heatmap	16.013	0.086	16.852
HeatmapAnnotation-class	0.001	0.001	0.000
HeatmapAnnotation	0.116	0.000	0.116
HeatmapList-class	5.178	0.017	5.228
HeatmapList	0.001	0.000	0.000
Legend	0.001	0.000	0.000
SingleAnnotation-class	0.001	0.000	0.001
SingleAnnotation	0.086	0.001	0.087
add.AdditiveUnit	5.454	0.019	5.488
add_heatmap-Heatmap-method	1.241	0.005	1.249
add_heatmap-HeatmapAnnotation-method	0.448	0.002	0.450
add_heatmap-HeatmapList-method	2.138	0.005	2.147
add_heatmap-dispatch	0.001	0.000	0.001
anno_barplot	0.013	0.000	0.014
anno_boxplot	0.030	0.001	0.032
anno_density	0.239	0.005	0.245
anno_histogram	0.070	0.002	0.072
anno_link	1.921	0.019	1.943
anno_points	0.027	0.001	0.030
anno_text	0.408	0.002	0.423
annotation_legend_size-HeatmapList-method	0	0	0
color_mapping_legend-ColorMapping-method	0.240	0.006	0.247
columnAnnotation	0.016	0.000	0.016
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	0.000	0.001	0.001
column_anno_link	0.001	0.000	0.000
column_anno_points	0.001	0.000	0.001
column_anno_text	0.001	0.001	0.000
column_dend-Heatmap-method	0.096	0.000	0.096
column_dend-HeatmapList-method	0.307	0.001	0.309
column_dend-dispatch	0.001	0.000	0.001
column_order-Heatmap-method	0.104	0.000	0.105
column_order-HeatmapList-method	0.281	0.001	0.283
column_order-dispatch	0.001	0.000	0.000
component_height-Heatmap-method	0.000	0.000	0.001
component_height-HeatmapList-method	0.000	0.000	0.001
component_height-dispatch	0.001	0.000	0.000
component_width-Heatmap-method	0.001	0.000	0.000
component_width-HeatmapList-method	0.000	0.000	0.001
component_width-dispatch	0.000	0.000	0.001
decorate_annotation	0.822	0.002	0.827
decorate_column_dend	0.000	0.000	0.001
decorate_column_names	0.001	0.000	0.000
decorate_column_title	0.001	0.000	0.001
decorate_dend	0.434	0.001	0.436
decorate_dimnames	0.489	0.001	0.491
decorate_heatmap_body	0.398	0.001	0.399
decorate_row_dend	0	0	0
decorate_row_names	0.001	0.000	0.000
decorate_row_title	0.001	0.000	0.000
decorate_title	0.361	0.001	0.369
densityHeatmap	4.169	0.018	4.196
dist2	0.008	0.000	0.007
draw-Heatmap-method	0.505	0.002	0.507
draw-HeatmapAnnotation-method	0.174	0.003	0.179
draw-HeatmapList-method	1.887	0.007	1.900
draw-SingleAnnotation-method	0.140	0.004	0.609
draw-dispatch	0.001	0.000	0.001
draw_annotation-Heatmap-method	0.000	0.000	0.001
draw_annotation_legend-HeatmapList-method	0	0	0
draw_dend-Heatmap-method	0	0	0
draw_dimnames-Heatmap-method	0	0	0
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	0.001	0.000	0.001
draw_title-Heatmap-method	0.001	0.000	0.001
draw_title-HeatmapList-method	0	0	0
draw_title-dispatch	0	0	0
enhanced_basicplot	1.220	0.004	1.225
get_color_mapping_list-HeatmapAnnotation-method	0.001	0.000	0.001
get_color_mapping_param_list-HeatmapAnnotation-method	0.001	0.000	0.001
grid.dendrogram	0.029	0.002	0.029
heatmap_legend_size-HeatmapList-method	0.001	0.000	0.001
ht_global_opt	0.001	0.000	0.001
is_abs_unit	0.003	0.000	0.003
make_column_cluster-Heatmap-method	0.001	0.000	0.000
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	0.001	0.001
make_row_cluster-Heatmap-method	0.001	0.000	0.001
map_to_colors-ColorMapping-method	0.028	0.001	0.029
max_text_height	0.003	0.000	0.004
max_text_width	0.003	0.000	0.003
oncoPrint	0.000	0.001	0.000
plotDataFrame	3.456	0.006	3.574
prepare-Heatmap-method	0.000	0.000	0.001
rowAnnotation	0.017	0.000	0.016
row_anno_barplot	0	0	0
row_anno_boxplot	0.000	0.000	0.001
row_anno_density	0.001	0.000	0.000
row_anno_histogram	0.001	0.001	0.000
row_anno_link	0.001	0.000	0.001
row_anno_points	0.001	0.000	0.000
row_anno_text	0.001	0.001	0.000
row_dend-Heatmap-method	0.095	0.000	0.095
row_dend-HeatmapList-method	0.285	0.004	0.288
row_dend-dispatch	0.001	0.000	0.001
row_order-Heatmap-method	0.1	0.0	0.1
row_order-HeatmapList-method	0.281	0.001	0.282
row_order-dispatch	0.001	0.000	0.001
selectArea	0.000	0.000	0.001
set_component_height-Heatmap-method	0.001	0.000	0.001
show-ColorMapping-method	0.001	0.000	0.001
show-Heatmap-method	0.901	0.004	0.906
show-HeatmapAnnotation-method	0.001	0.000	0.001
show-HeatmapList-method	0.000	0.000	0.001
show-SingleAnnotation-method	0.000	0.000	0.001
show-dispatch	0.000	0.000	0.001
unify_mat_list	0	0	0