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CHECK report for ComplexHeatmap on malbec1

This page was generated on 2019-04-16 11:51:12 -0400 (Tue, 16 Apr 2019).

Package 314/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ComplexHeatmap 1.20.0
Zuguang Gu
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/ComplexHeatmap
Branch: RELEASE_3_8
Last Commit: 1501ecc
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ComplexHeatmap
Version: 1.20.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ComplexHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ComplexHeatmap_1.20.0.tar.gz
StartedAt: 2019-04-15 23:07:49 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:09:38 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 108.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ComplexHeatmap.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ComplexHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ComplexHeatmap_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.20.0’
* 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 ... 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
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
Heatmap 20.536  0.036  20.733
* 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: OK


Installation output

ComplexHeatmap.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ComplexHeatmap
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘ComplexHeatmap’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ComplexHeatmap)

Tests output

ComplexHeatmap.Rcheck/tests/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> suppressWarnings(suppressPackageStartupMessages(library(ComplexHeatmap)))
> 
> test_check("ComplexHeatmap")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 17 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  1.044   0.052   1.095 

Example timings

ComplexHeatmap.Rcheck/ComplexHeatmap-Ex.timings

nameusersystemelapsed
AdditiveUnit-class000
AdditiveUnit000
ColorMapping-class000
ColorMapping0.0760.0000.077
ComplexHeatmap-package000
Heatmap-class000
Heatmap20.536 0.03620.733
HeatmapAnnotation-class000
HeatmapAnnotation0.0480.0000.049
HeatmapList-class3.8840.0123.906
HeatmapList000
Legend0.4040.0000.407
SingleAnnotation-class000
SingleAnnotation0.0360.0000.040
add.AdditiveUnit4.3040.0044.315
add_heatmap-Heatmap-method1.3240.0001.325
add_heatmap-HeatmapAnnotation-method0.6360.0000.636
add_heatmap-HeatmapList-method1.6680.0001.673
add_heatmap-dispatch000
adjust_dend_by_leaf_width1.5480.0161.563
anno_barplot0.0160.0000.015
anno_boxplot0.0400.0000.041
anno_density0.4200.0040.423
anno_histogram0.0560.0040.060
anno_link2.2400.0122.252
anno_oncoprint_barplot000
anno_points0.0320.0000.032
anno_text0.4560.0000.455
annotation_legend_size-HeatmapList-method000
color_mapping_legend-ColorMapping-method0.2960.0040.300
columnAnnotation0.0080.0000.011
column_anno_barplot0.0000.0000.001
column_anno_boxplot000
column_anno_density000
column_anno_histogram000
column_anno_link000
column_anno_points000
column_anno_text0.0000.0000.001
column_dend-Heatmap-method0.0440.0000.046
column_dend-HeatmapList-method0.2320.0000.232
column_dend-dispatch0.0000.0000.001
column_order-Heatmap-method0.0560.0000.059
column_order-HeatmapList-method0.2240.0000.223
column_order-dispatch000
component_height-Heatmap-method000
component_height-HeatmapList-method000
component_height-dispatch000
component_width-Heatmap-method0.0000.0000.001
component_width-HeatmapList-method0.0040.0000.000
component_width-dispatch000
decorate_annotation0.6280.0000.627
decorate_column_dend000
decorate_column_names000
decorate_column_title000
decorate_dend0.2640.0040.265
decorate_dimnames0.4480.0040.453
decorate_heatmap_body0.3720.0000.375
decorate_row_dend000
decorate_row_names000
decorate_row_title0.0000.0000.001
decorate_title0.4360.0000.437
densityHeatmap4.1600.0164.187
dist20.0240.0000.026
draw-Heatmap-method0.6040.0000.603
draw-HeatmapAnnotation-method0.1280.0040.130
draw-HeatmapList-method1.4960.0041.501
draw-SingleAnnotation-method0.0960.0000.097
draw-dispatch000
draw_annotation-Heatmap-method0.0000.0000.001
draw_annotation_legend-HeatmapList-method000
draw_dend-Heatmap-method000
draw_dimnames-Heatmap-method000
draw_heatmap_body-Heatmap-method000
draw_heatmap_legend-HeatmapList-method000
draw_heatmap_list-HeatmapList-method0.0000.0000.001
draw_title-Heatmap-method000
draw_title-HeatmapList-method000
draw_title-dispatch000
enhanced_basicplot1.1960.0001.198
get_color_mapping_list-HeatmapAnnotation-method000
get_color_mapping_param_list-HeatmapAnnotation-method000
grid.dendrogram0.0160.0000.015
grid.dendrogram20.0160.0000.016
heatmap_legend_size-HeatmapList-method000
ht_global_opt000
is_abs_unit0.0000.0000.001
make_column_cluster-Heatmap-method000
make_layout-Heatmap-method000
make_layout-HeatmapList-method000
make_layout-dispatch0.0000.0000.001
make_row_cluster-Heatmap-method000
map_to_colors-ColorMapping-method0.0160.0000.016
max_text_height0.0000.0000.002
max_text_width0.0040.0000.002
oncoPrint000
packLegend1.4920.0001.495
plotDataFrame3.8440.0123.861
prepare-Heatmap-method000
rowAnnotation0.0120.0000.010
row_anno_barplot000
row_anno_boxplot000
row_anno_density000
row_anno_histogram0.0040.0000.001
row_anno_link0.0000.0000.001
row_anno_points000
row_anno_text000
row_dend-Heatmap-method0.0760.0040.079
row_dend-HeatmapList-method0.2520.0000.253
row_dend-dispatch000
row_order-Heatmap-method0.0680.0000.066
row_order-HeatmapList-method0.2280.0000.228
row_order-dispatch000
selectArea000
set_component_height-Heatmap-method000
show-ColorMapping-method000
show-Heatmap-method0.8080.0040.812
show-HeatmapAnnotation-method0.0000.0000.001
show-HeatmapList-method000
show-SingleAnnotation-method0.0000.0000.001
show-dispatch000
unify_mat_list000