BioC 3.3: CHECK report for ComplexHeatmap on morelia

Package: ComplexHeatmap

Version: 1.9.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.9.5.tar.gz

StartedAt: 2016-04-21 00:51:37 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 00:53:28 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 111.6 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_1.9.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.9.5’
* 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/6s] OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
* 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 ... [47s/50s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
Heatmap 13.433  0.071  14.477
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [1s/2s]
 [1s/2s] 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	0.000
AdditiveUnit	0	0	0
ColorMapping-class	0.000	0.000	0.001
ColorMapping	0.026	0.001	0.028
ComplexHeatmap-package	0.000	0.000	0.001
Heatmap-class	0	0	0
Heatmap	13.433	0.071	14.477
HeatmapAnnotation-class	0.000	0.000	0.001
HeatmapAnnotation	0.079	0.001	0.080
HeatmapList-class	4.386	0.016	4.581
HeatmapList	0.001	0.000	0.001
SingleAnnotation-class	0.001	0.001	0.000
SingleAnnotation	0.085	0.001	0.087
add.AdditiveUnit	4.624	0.011	4.808
add_heatmap-Heatmap-method	1.213	0.003	1.219
add_heatmap-HeatmapAnnotation-method	0.489	0.001	0.492
add_heatmap-HeatmapList-method	2.005	0.004	2.021
add_heatmap-dispatch	0.001	0.000	0.000
anno_barplot	0.015	0.001	0.016
anno_boxplot	0.039	0.001	0.040
anno_density	0.271	0.004	0.276
anno_histogram	0.076	0.002	0.080
anno_link	2.124	0.025	2.281
anno_points	0.026	0.001	0.030
anno_text	0.430	0.002	0.433
annotation_legend_size-HeatmapList-method	0.001	0.000	0.001
color_mapping_legend-ColorMapping-method	0.256	0.002	0.259
columnAnnotation	0.017	0.000	0.017
column_anno_barplot	0.001	0.000	0.001
column_anno_boxplot	0.000	0.000	0.001
column_anno_density	0	0	0
column_anno_histogram	0.001	0.000	0.001
column_anno_link	0.001	0.001	0.001
column_anno_points	0.000	0.000	0.001
column_anno_text	0.000	0.000	0.001
column_dend-Heatmap-method	0.107	0.001	0.107
column_dend-HeatmapList-method	0.281	0.000	0.282
column_dend-dispatch	0.000	0.000	0.001
column_order-Heatmap-method	0.100	0.000	0.101
column_order-HeatmapList-method	0.289	0.001	0.291
column_order-dispatch	0.001	0.000	0.000
component_height-Heatmap-method	0.001	0.000	0.001
component_height-HeatmapList-method	0.001	0.000	0.001
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	0.858	0.002	0.878
decorate_column_dend	0.000	0.000	0.001
decorate_column_names	0.000	0.000	0.001
decorate_column_title	0.001	0.000	0.001
decorate_dend	0.482	0.001	0.497
decorate_dimnames	0.559	0.001	0.598
decorate_heatmap_body	0.432	0.001	0.434
decorate_row_dend	0.000	0.000	0.001
decorate_row_names	0.000	0.000	0.001
decorate_row_title	0.001	0.001	0.000
decorate_title	0.447	0.001	0.449
densityHeatmap	4.083	0.018	4.646
dist2	0.01	0.00	0.01
draw-Heatmap-method	0.428	0.002	0.430
draw-HeatmapAnnotation-method	0.173	0.004	0.226
draw-HeatmapList-method	1.665	0.005	1.702
draw-SingleAnnotation-method	0.148	0.005	0.156
draw-dispatch	0.000	0.000	0.001
draw_annotation-Heatmap-method	0.001	0.000	0.001
draw_annotation_legend-HeatmapList-method	0.001	0.000	0.000
draw_dend-Heatmap-method	0.001	0.000	0.001
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	0	0
draw_title-HeatmapList-method	0.000	0.000	0.001
draw_title-dispatch	0.000	0.000	0.001
enhanced_basicplot	1.296	0.004	1.314
get_color_mapping_list-HeatmapAnnotation-method	0.001	0.000	0.001
get_color_mapping_param_list-HeatmapAnnotation-method	0.001	0.000	0.000
grid.dendrogram	0.029	0.001	0.031
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	0.001	0.002
make_column_cluster-Heatmap-method	0.001	0.000	0.001
make_layout-Heatmap-method	0	0	0
make_layout-HeatmapList-method	0.000	0.000	0.001
make_layout-dispatch	0.000	0.000	0.001
make_row_cluster-Heatmap-method	0.000	0.000	0.001
map_to_colors-ColorMapping-method	0.030	0.001	0.031
max_text_height	0.002	0.000	0.002
max_text_width	0.004	0.000	0.003
oncoPrint	0.001	0.000	0.000
plotDataFrame	3.777	0.007	4.118
prepare-Heatmap-method	0.000	0.001	0.001
rowAnnotation	0.016	0.001	0.018
row_anno_barplot	0.001	0.000	0.000
row_anno_boxplot	0.001	0.000	0.001
row_anno_density	0.001	0.001	0.001
row_anno_histogram	0.001	0.000	0.002
row_anno_link	0.001	0.000	0.001
row_anno_points	0.001	0.000	0.000
row_anno_text	0.001	0.000	0.001
row_dend-Heatmap-method	0.107	0.000	0.108
row_dend-HeatmapList-method	0.280	0.001	0.281
row_dend-dispatch	0.001	0.000	0.001
row_order-Heatmap-method	0.116	0.001	0.117
row_order-HeatmapList-method	0.310	0.001	0.313
row_order-dispatch	0.000	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	0.001	0.000	0.001
show-Heatmap-method	0.738	0.002	0.744
show-HeatmapAnnotation-method	0.001	0.000	0.000
show-HeatmapList-method	0.001	0.000	0.001
show-SingleAnnotation-method	0.001	0.000	0.000
show-dispatch	0.001	0.000	0.001
unify_mat_list	0.000	0.000	0.001