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CHECK report for ComplexHeatmap on celaya2

This page was generated on 2019-10-16 12:55:22 -0400 (Wed, 16 Oct 2019).

Package 331/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ComplexHeatmap 2.0.0
Zuguang Gu
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ComplexHeatmap
Branch: RELEASE_3_9
Last Commit: 97863d8
Last Changed Date: 2019-05-02 11:53:53 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ComplexHeatmap
Version: 2.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ComplexHeatmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ComplexHeatmap_2.0.0.tar.gz
StartedAt: 2019-10-16 01:44:05 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:47:20 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 195.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ComplexHeatmap.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ComplexHeatmap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ComplexHeatmap_2.0.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.0.0’
* 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
anno_horizon       9.115  0.142   9.786
AnnotationFunction 7.147  0.121   7.280
* 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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ComplexHeatmap
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ComplexHeatmap’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ComplexHeatmap)

Tests output

ComplexHeatmap.Rcheck/tests/test-all.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 96 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 33.393   0.976  34.249 

Example timings

ComplexHeatmap.Rcheck/ComplexHeatmap-Ex.timings

nameusersystemelapsed
AdditiveUnit-class0.0010.0000.000
AdditiveUnit0.0000.0010.000
AnnotationFunction-class000
AnnotationFunction7.1470.1217.280
ColorMapping-class0.0000.0000.001
ColorMapping0.0160.0010.018
ComplexHeatmap-package0.0000.0010.000
Extract.AnnotationFunction0.0380.0020.041
Extract.Heatmap0.9320.0050.939
Extract.HeatmapAnnotation0.1070.0050.110
Extract.HeatmapList0.2330.0020.235
Extract.SingleAnnotation0.0310.0020.031
Extract.comb_mat0.0060.0010.007
Heatmap-class0.0010.0000.000
Heatmap0.0000.0000.001
HeatmapAnnotation-class0.0010.0000.001
HeatmapAnnotation0.0000.0000.001
HeatmapList-class0.0000.0000.001
HeatmapList000
Legend0.1530.0040.158
Legends-class0.0090.0000.009
Legends000
SingleAnnotation-class000
SingleAnnotation0.0940.0040.100
UpSet1.1840.0121.423
add.AdditiveUnit0.0010.0000.000
add_heatmap-Heatmap-method000
add_heatmap-HeatmapAnnotation-method0.0010.0000.000
add_heatmap-HeatmapList-method000
add_heatmap-dispatch0.0000.0010.000
adjust_dend_by_x0.0560.0040.060
adjust_heatmap_list-HeatmapList-method0.0000.0000.001
anno_barplot0.0550.0020.056
anno_block0.5530.0020.556
anno_boxplot0.0750.0020.079
anno_density0.8850.0280.918
anno_empty0.0340.0020.037
anno_histogram0.1950.0030.199
anno_horizon9.1150.1429.786
anno_image0.0000.0000.001
anno_joyplot0.7560.0250.823
anno_lines0.1480.0040.155
anno_link0.0000.0010.000
anno_mark0.9430.0061.184
anno_oncoprint_barplot0.0010.0000.000
anno_points0.0530.0020.098
anno_simple0.1240.0040.244
anno_summary0.6330.0040.745
anno_text0.2000.0050.208
anno_zoom0.5610.0030.564
annotation_axis_grob0.1450.0110.161
annotation_legend_size-HeatmapList-method000
c.HeatmapAnnotation0.0610.0020.063
cluster_within_group0.0440.0010.045
color_mapping_legend-ColorMapping-method000
columnAnnotation0.0010.0010.000
column_dend-Heatmap-method0.5120.0040.518
column_dend-HeatmapList-method1.6110.0081.624
column_dend-dispatch0.0000.0000.001
column_order-Heatmap-method0.5560.0030.563
column_order-HeatmapList-method1.7850.0071.798
column_order-dispatch0.0010.0000.000
comb_degree0.0040.0000.004
comb_name0.0020.0010.002
comb_size0.0030.0000.004
component_height-Heatmap-method0.0000.0000.001
component_height-HeatmapList-method000
component_height-dispatch0.0000.0000.001
component_width-Heatmap-method0.0010.0000.001
component_width-HeatmapList-method0.0000.0000.001
component_width-dispatch0.0010.0000.000
copy_all-AnnotationFunction-method0.0000.0010.000
copy_all-SingleAnnotation-method0.0000.0000.001
copy_all-dispatch0.0000.0000.001
decorate_annotation0.5280.0030.532
decorate_column_dend0.0010.0000.001
decorate_column_names000
decorate_column_title000
decorate_dend0.3210.0020.325
decorate_dimnames0.3720.0020.375
decorate_heatmap_body0.2160.0010.218
decorate_row_dend0.0010.0000.000
decorate_row_names000
decorate_row_title0.0010.0000.000
decorate_title0.3150.0010.318
default_axis_param0.0020.0010.002
default_get_type0.0000.0010.001
dend_heights0.0000.0000.001
dend_xy0.0370.0010.037
dendrogramGrob0.0010.0010.001
densityHeatmap2.2890.0192.912
dim.Heatmap0.0000.0000.001
dist20.0210.0020.030
draw-AnnotationFunction-method0.0010.0010.001
draw-Heatmap-method000
draw-HeatmapAnnotation-method0.0000.0000.001
draw-HeatmapList-method000
draw-Legends-method0.0290.0010.032
draw-SingleAnnotation-method0.0000.0010.001
draw-dispatch0.0000.0000.001
draw_annotation-Heatmap-method000
draw_annotation_legend-HeatmapList-method0.0010.0010.000
draw_dend-Heatmap-method000
draw_dimnames-Heatmap-method0.0000.0000.001
draw_heatmap_body-Heatmap-method0.0000.0010.001
draw_heatmap_legend-HeatmapList-method0.0010.0000.001
draw_heatmap_list-HeatmapList-method0.0000.0010.001
draw_title-Heatmap-method0.0000.0000.001
draw_title-HeatmapList-method0.0010.0000.001
draw_title-dispatch0.0000.0000.001
extract_comb0.0130.0000.014
getXY_in_parent_vp0.0270.0010.030
get_color_mapping_list-HeatmapAnnotation-method000
get_legend_param_list-HeatmapAnnotation-method0.0010.0010.001
grid.annotation_axis000
grid.boxplot0.0240.0010.026
grid.dendrogram1.0550.0751.132
grid.draw.Legends0.0230.0000.023
heatmap_legend_size-HeatmapList-method0.0010.0000.001
height.AnnotationFunction0.0200.0020.023
height.Heatmap000
height.HeatmapAnnotation000
height.HeatmapList0.0000.0010.001
height.Legends0.0310.0060.036
height.SingleAnnotation000
heightAssign.AnnotationFunction0.0010.0010.001
heightAssign.HeatmapAnnotation0.0000.0010.000
heightAssign.SingleAnnotation0.0000.0000.001
heightDetails.annotation_axis0.0010.0000.001
heightDetails.legend000
heightDetails.legend_body0.0000.0000.001
heightDetails.packed_legends000
ht_global_opt0.0010.0000.001
ht_opt0.0100.0030.013
is_abs_unit0.0020.0010.002
length.HeatmapAnnotation000
length.HeatmapList0.0000.0000.001
list_components0.0000.0010.001
list_to_matrix0.0030.0020.005
make_column_cluster-Heatmap-method0.0010.0000.001
make_comb_mat0.0200.0020.022
make_layout-Heatmap-method000
make_layout-HeatmapList-method0.0010.0000.000
make_layout-dispatch0.0000.0000.001
make_row_cluster-Heatmap-method0.0010.0010.001
map_to_colors-ColorMapping-method0.0290.0020.030
max_text_height0.0060.0000.006
max_text_width0.0060.0000.006
merge_dendrogram0.1610.0040.166
names.HeatmapAnnotation0.0330.0010.034
names.HeatmapList0.0000.0010.001
namesAssign.HeatmapAnnotation0.030.000.03
ncol.Heatmap0.0010.0000.001
nobs.AnnotationFunction0.0080.0000.008
nobs.HeatmapAnnotation0.0010.0010.000
nobs.SingleAnnotation000
normalize_comb_mat0.0010.0000.000
nrow.Heatmap000
oncoPrint0.0010.0000.001
order.comb_mat0.0000.0000.001
packLegend0.1030.0020.107
pct_v_pct000
pindex0.0090.0010.011
prepare-Heatmap-method0.0000.0000.001
print.comb_mat000
re_size-HeatmapAnnotation-method0.0000.0010.001
restore_matrix0.7100.0050.717
rowAnnotation0.0000.0010.000
row_anno_barplot0.0010.0000.001
row_anno_boxplot000
row_anno_density000
row_anno_histogram0.0000.0010.000
row_anno_link0.0000.0000.001
row_anno_points0.0000.0010.000
row_anno_text000
row_dend-Heatmap-method0.4180.0030.423
row_dend-HeatmapList-method1.1140.0071.124
row_dend-dispatch0.0000.0000.001
row_order-Heatmap-method0.4800.0040.486
row_order-HeatmapList-method1.3680.0061.377
row_order-dispatch0.0010.0000.001
set_component_height-Heatmap-method0.0000.0000.001
set_component_width-Heatmap-method0.0000.0000.001
set_name0.0020.0000.003
set_size0.0030.0000.003
show-AnnotationFunction-method0.0010.0000.001
show-ColorMapping-method0.0000.0010.000
show-Heatmap-method0.0000.0010.001
show-HeatmapAnnotation-method0.0010.0000.001
show-HeatmapList-method0.0000.0000.001
show-SingleAnnotation-method0.0000.0010.001
show-dispatch000
size.AnnotationFunction0.0180.0000.018
size.HeatmapAnnotation000
size.SingleAnnotation0.0000.0010.001
sizeAssign.AnnotationFunction0.0070.0000.007
sizeAssign.HeatmapAnnotation000
sizeAssign.SingleAnnotation0.0000.0000.001
smartAlign20.1600.0060.171
str.comb_mat0.0010.0000.001
subset_gp0.0000.0010.000
subset_matrix_by_row0.0010.0000.001
subset_vector0.0000.0000.001
summary.Heatmap000
summary.HeatmapList000
t.comb_mat0.0010.0000.002
test_alter_fun0.1230.0010.124
unify_mat_list0.0000.0000.001
upset_right_annotation0.0010.0010.000
upset_top_annotation000
width.AnnotationFunction0.0190.0000.019
width.Heatmap0.0010.0000.001
width.HeatmapAnnotation0.0010.0010.000
width.HeatmapList0.0000.0000.001
width.Legends0.0250.0000.025
width.SingleAnnotation0.0010.0000.000
widthAssign.AnnotationFunction0.0000.0010.001
widthAssign.HeatmapAnnotation000
widthAssign.SingleAnnotation000
widthDetails.annotation_axis0.0000.0010.001
widthDetails.legend0.0010.0010.000
widthDetails.legend_body0.0000.0000.001
widthDetails.packed_legends000