BioC 3.3: CHECK report for ComplexHeatmap on moscato2

Package: ComplexHeatmap

Version: 1.10.2

Command: rm -rf ComplexHeatmap.buildbin-libdir ComplexHeatmap.Rcheck && mkdir ComplexHeatmap.buildbin-libdir ComplexHeatmap.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ComplexHeatmap.buildbin-libdir ComplexHeatmap_1.10.2.tar.gz >ComplexHeatmap.Rcheck\00install.out 2>&1 && cp ComplexHeatmap.Rcheck\00install.out ComplexHeatmap-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ComplexHeatmap.buildbin-libdir --install="check:ComplexHeatmap-install.out" --force-multiarch --no-vignettes --timings ComplexHeatmap_1.10.2.tar.gz

StartedAt: 2016-10-13 02:29:36 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:34:31 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 295.2 seconds

RetCode: 0

Status:  OK

CheckDir: ComplexHeatmap.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf ComplexHeatmap.buildbin-libdir ComplexHeatmap.Rcheck && mkdir ComplexHeatmap.buildbin-libdir ComplexHeatmap.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ComplexHeatmap.buildbin-libdir ComplexHeatmap_1.10.2.tar.gz >ComplexHeatmap.Rcheck\00install.out 2>&1 && cp ComplexHeatmap.Rcheck\00install.out ComplexHeatmap-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=ComplexHeatmap.buildbin-libdir --install="check:ComplexHeatmap-install.out" --force-multiarch --no-vignettes --timings ComplexHeatmap_1.10.2.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/ComplexHeatmap.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'ComplexHeatmap' can be installed ... OK
* checking installed package size ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
Heatmap           17.50   0.02   17.66
add.AdditiveUnit   6.54   0.02    6.55
HeatmapList-class  5.81   0.00    5.80
densityHeatmap     5.23   0.01    5.38
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
Heatmap           23.20   0.06   23.36
add.AdditiveUnit   9.30   0.00    9.29
HeatmapList-class  6.74   0.00    7.61
densityHeatmap     5.92   0.02    5.95
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  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
  'E:/biocbld/bbs-3.3-bioc/meat/ComplexHeatmap.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'ComplexHeatmap' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ComplexHeatmap' as ComplexHeatmap_1.10.2.zip
* DONE (ComplexHeatmap)

name	user	system	elapsed
AdditiveUnit-class	0	0	0
AdditiveUnit	0	0	0
ColorMapping-class	0	0	0
ColorMapping	0.02	0.00	0.06
ComplexHeatmap-package	0	0	0
Heatmap-class	0	0	0
Heatmap	17.50	0.02	17.66
HeatmapAnnotation-class	0	0	0
HeatmapAnnotation	0.2	0.0	0.2
HeatmapList-class	5.81	0.00	5.80
HeatmapList	0	0	0
Legend	0	0	0
SingleAnnotation-class	0.01	0.00	0.02
SingleAnnotation	0.11	0.01	0.12
add.AdditiveUnit	6.54	0.02	6.55
add_heatmap-Heatmap-method	1.65	0.00	1.66
add_heatmap-HeatmapAnnotation-method	0.67	0.00	0.67
add_heatmap-HeatmapList-method	2.97	0.00	2.96
add_heatmap-dispatch	0	0	0
anno_barplot	0.03	0.00	0.03
anno_boxplot	0.04	0.00	0.05
anno_density	0.32	0.00	0.31
anno_histogram	0.09	0.00	0.10
anno_link	3.4	0.0	3.4
anno_points	0.05	0.00	0.04
anno_text	0.57	0.00	0.58
annotation_legend_size-HeatmapList-method	0	0	0
color_mapping_legend-ColorMapping-method	0.29	0.00	0.28
columnAnnotation	0.03	0.00	0.03
column_anno_barplot	0	0	0
column_anno_boxplot	0	0	0
column_anno_density	0	0	0
column_anno_histogram	0	0	0
column_anno_link	0	0	0
column_anno_points	0	0	0
column_anno_text	0	0	0
column_dend-Heatmap-method	0.14	0.00	0.14
column_dend-HeatmapList-method	0.38	0.00	0.37
column_dend-dispatch	0	0	0
column_order-Heatmap-method	0.12	0.00	0.13
column_order-HeatmapList-method	0.36	0.00	0.36
column_order-dispatch	0	0	0
component_height-Heatmap-method	0.01	0.00	0.02
component_height-HeatmapList-method	0	0	0
component_height-dispatch	0	0	0
component_width-Heatmap-method	0	0	0
component_width-HeatmapList-method	0	0	0
component_width-dispatch	0	0	0
decorate_annotation	0.97	0.00	0.97
decorate_column_dend	0	0	0
decorate_column_names	0	0	0
decorate_column_title	0	0	0
decorate_dend	0.55	0.00	0.55
decorate_dimnames	0.64	0.00	0.64
decorate_heatmap_body	0.41	0.00	0.40
decorate_row_dend	0	0	0
decorate_row_names	0	0	0
decorate_row_title	0	0	0
decorate_title	0.51	0.00	0.52
densityHeatmap	5.23	0.01	5.38
dist2	0	0	0
draw-Heatmap-method	0.76	0.00	0.83
draw-HeatmapAnnotation-method	0.28	0.00	0.28
draw-HeatmapList-method	2.47	0.00	2.46
draw-SingleAnnotation-method	0.18	0.00	0.18
draw-dispatch	0	0	0
draw_annotation-Heatmap-method	0	0	0
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	0	0
draw_heatmap_legend-HeatmapList-method	0	0	0
draw_heatmap_list-HeatmapList-method	0	0	0
draw_title-Heatmap-method	0	0	0
draw_title-HeatmapList-method	0	0	0
draw_title-dispatch	0.01	0.00	0.02
enhanced_basicplot	1.38	0.00	1.37
get_color_mapping_list-HeatmapAnnotation-method	0	0	0
get_color_mapping_param_list-HeatmapAnnotation-method	0	0	0
grid.dendrogram	0.04	0.00	0.04
heatmap_legend_size-HeatmapList-method	0	0	0
ht_global_opt	0	0	0
is_abs_unit	0	0	0
make_column_cluster-Heatmap-method	0	0	0
make_layout-Heatmap-method	0.02	0.00	0.02
make_layout-HeatmapList-method	0	0	0
make_layout-dispatch	0	0	0
make_row_cluster-Heatmap-method	0	0	0
map_to_colors-ColorMapping-method	0.03	0.00	0.03
max_text_height	0	0	0
max_text_width	0.02	0.00	0.02
oncoPrint	0	0	0
plotDataFrame	3.82	0.02	3.83
prepare-Heatmap-method	0	0	0
rowAnnotation	0.01	0.00	0.02
row_anno_barplot	0	0	0
row_anno_boxplot	0	0	0
row_anno_density	0.02	0.00	0.02
row_anno_histogram	0	0	0
row_anno_link	0	0	0
row_anno_points	0	0	0
row_anno_text	0	0	0
row_dend-Heatmap-method	0.14	0.00	0.14
row_dend-HeatmapList-method	0.5	0.0	0.5
row_dend-dispatch	0	0	0
row_order-Heatmap-method	0.09	0.00	0.09
row_order-HeatmapList-method	0.36	0.00	0.38
row_order-dispatch	0	0	0
selectArea	0	0	0
set_component_height-Heatmap-method	0.01	0.00	0.01
show-ColorMapping-method	0	0	0
show-Heatmap-method	1.08	0.00	1.08
show-HeatmapAnnotation-method	0	0	0
show-HeatmapList-method	0	0	0
show-SingleAnnotation-method	0.02	0.00	0.02
show-dispatch	0	0	0
unify_mat_list	0	0	0

name	user	system	elapsed
AdditiveUnit-class	0	0	0
AdditiveUnit	0	0	0
ColorMapping-class	0.02	0.00	0.01
ColorMapping	0.00	0.00	0.03
ComplexHeatmap-package	0	0	0
Heatmap-class	0	0	0
Heatmap	23.20	0.06	23.36
HeatmapAnnotation-class	0	0	0
HeatmapAnnotation	0.12	0.00	0.12
HeatmapList-class	6.74	0.00	7.61
HeatmapList	0	0	0
Legend	0	0	0
SingleAnnotation-class	0	0	0
SingleAnnotation	0.11	0.00	0.11
add.AdditiveUnit	9.30	0.00	9.29
add_heatmap-Heatmap-method	1.81	0.00	1.86
add_heatmap-HeatmapAnnotation-method	0.51	0.00	0.51
add_heatmap-HeatmapList-method	2.87	0.00	3.47
add_heatmap-dispatch	0	0	0
anno_barplot	0.02	0.00	0.01
anno_boxplot	0.05	0.00	0.05
anno_density	0.25	0.02	0.26
anno_histogram	0.03	0.01	0.05
anno_link	2.70	0.02	2.78
anno_points	0.03	0.01	0.17
anno_text	0.53	0.00	0.53
annotation_legend_size-HeatmapList-method	0	0	0
color_mapping_legend-ColorMapping-method	0.36	0.00	0.36
columnAnnotation	0.01	0.00	0.01
column_anno_barplot	0	0	0
column_anno_boxplot	0	0	0
column_anno_density	0	0	0
column_anno_histogram	0	0	0
column_anno_link	0	0	0
column_anno_points	0	0	0
column_anno_text	0	0	0
column_dend-Heatmap-method	0.17	0.00	0.17
column_dend-HeatmapList-method	0.39	0.00	0.39
column_dend-dispatch	0	0	0
column_order-Heatmap-method	0.21	0.00	0.22
column_order-HeatmapList-method	0.46	0.00	0.45
column_order-dispatch	0	0	0
component_height-Heatmap-method	0	0	0
component_height-HeatmapList-method	0	0	0
component_height-dispatch	0	0	0
component_width-Heatmap-method	0	0	0
component_width-HeatmapList-method	0	0	0
component_width-dispatch	0	0	0
decorate_annotation	1.16	0.00	1.15
decorate_column_dend	0	0	0
decorate_column_names	0.01	0.00	0.02
decorate_column_title	0	0	0
decorate_dend	0.47	0.00	0.47
decorate_dimnames	0.56	0.00	0.56
decorate_heatmap_body	0.42	0.00	0.42
decorate_row_dend	0	0	0
decorate_row_names	0	0	0
decorate_row_title	0	0	0
decorate_title	0.49	0.00	0.48
densityHeatmap	5.92	0.02	5.95
dist2	0	0	0
draw-Heatmap-method	0.75	0.00	0.74
draw-HeatmapAnnotation-method	0.30	0.01	0.32
draw-HeatmapList-method	2.99	0.00	2.99
draw-SingleAnnotation-method	0.19	0.00	0.19
draw-dispatch	0	0	0
draw_annotation-Heatmap-method	0	0	0
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	0	0
draw_heatmap_legend-HeatmapList-method	0	0	0
draw_heatmap_list-HeatmapList-method	0	0	0
draw_title-Heatmap-method	0	0	0
draw_title-HeatmapList-method	0	0	0
draw_title-dispatch	0	0	0
enhanced_basicplot	1.78	0.00	1.78
get_color_mapping_list-HeatmapAnnotation-method	0	0	0
get_color_mapping_param_list-HeatmapAnnotation-method	0	0	0
grid.dendrogram	0.05	0.00	0.04
heatmap_legend_size-HeatmapList-method	0	0	0
ht_global_opt	0.01	0.00	0.02
is_abs_unit	0	0	0
make_column_cluster-Heatmap-method	0	0	0
make_layout-Heatmap-method	0	0	0
make_layout-HeatmapList-method	0.01	0.00	0.02
make_layout-dispatch	0	0	0
make_row_cluster-Heatmap-method	0	0	0
map_to_colors-ColorMapping-method	0.05	0.00	0.04
max_text_height	0	0	0
max_text_width	0.01	0.00	0.02
oncoPrint	0	0	0
plotDataFrame	4.26	0.00	4.26
prepare-Heatmap-method	0	0	0
rowAnnotation	0.17	0.00	0.17
row_anno_barplot	0	0	0
row_anno_boxplot	0	0	0
row_anno_density	0	0	0
row_anno_histogram	0	0	0
row_anno_link	0	0	0
row_anno_points	0	0	0
row_anno_text	0	0	0
row_dend-Heatmap-method	0.11	0.00	0.11
row_dend-HeatmapList-method	0.35	0.00	0.34
row_dend-dispatch	0	0	0
row_order-Heatmap-method	0.17	0.00	0.17
row_order-HeatmapList-method	0.45	0.00	0.45
row_order-dispatch	0	0	0
selectArea	0.02	0.00	0.02
set_component_height-Heatmap-method	0	0	0
show-ColorMapping-method	0	0	0
show-Heatmap-method	1.32	0.00	1.33
show-HeatmapAnnotation-method	0	0	0
show-HeatmapList-method	0	0	0
show-SingleAnnotation-method	0	0	0
show-dispatch	0	0	0
unify_mat_list	0	0	0