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CHECK report for ComplexHeatmap on celaya2

This page was generated on 2019-04-09 13:13:46 -0400 (Tue, 09 Apr 2019).

Package 326/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ComplexHeatmap 1.99.7
Zuguang Gu
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/ComplexHeatmap
Branch: master
Last Commit: 02ad1d0
Last Changed Date: 2019-03-29 04:28:36 -0400 (Fri, 29 Mar 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: ComplexHeatmap
Version: 1.99.7
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_1.99.7.tar.gz
StartedAt: 2019-04-09 00:56:20 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:59:42 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 201.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ComplexHeatmap.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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_1.99.7.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ComplexHeatmap.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.99.7’
* 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       8.854  0.140  10.765
AnnotationFunction 7.332  0.104   7.923
* 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 36.273   1.112  39.542 

Example timings

ComplexHeatmap.Rcheck/ComplexHeatmap-Ex.timings

nameusersystemelapsed
AdditiveUnit-class0.0000.0000.001
AdditiveUnit0.0000.0010.000
AnnotationFunction-class0.0000.0000.001
AnnotationFunction7.3320.1047.923
ColorMapping-class0.0010.0000.000
ColorMapping0.0190.0010.021
ComplexHeatmap-package000
Extract.AnnotationFunction0.0430.0020.046
Extract.Heatmap1.0980.0081.472
Extract.HeatmapAnnotation0.0830.0030.086
Extract.HeatmapList0.2830.0040.288
Extract.SingleAnnotation0.0370.0020.039
Extract.comb_mat0.0140.0010.014
Heatmap-class0.0010.0010.000
Heatmap0.0000.0000.001
HeatmapAnnotation-class000
HeatmapAnnotation0.0010.0010.001
HeatmapList-class0.0010.0010.000
HeatmapList0.0000.0000.001
Legend0.1400.0040.145
Legends-class0.0130.0010.013
Legends0.0010.0000.001
SingleAnnotation-class0.0000.0000.001
SingleAnnotation0.1690.0050.175
UpSet1.2830.0151.299
add.AdditiveUnit0.0000.0000.001
add_heatmap-Heatmap-method0.0000.0000.001
add_heatmap-HeatmapAnnotation-method0.0010.0000.001
add_heatmap-HeatmapList-method0.0000.0010.000
add_heatmap-dispatch000
adjust_dend_by_x0.0500.0040.055
adjust_heatmap_list-HeatmapList-method000
anno_barplot0.0420.0020.043
anno_block0.5190.0020.521
anno_boxplot0.0700.0020.073
anno_density0.8130.0270.841
anno_empty0.0340.0020.037
anno_histogram0.1850.0030.189
anno_horizon 8.854 0.14010.765
anno_image0.0000.0000.001
anno_joyplot0.8310.0290.875
anno_lines0.1480.0040.156
anno_link0.0000.0010.000
anno_mark1.0300.0101.128
anno_oncoprint_barplot000
anno_points0.0500.0020.053
anno_simple0.1180.0040.128
anno_summary0.6130.0020.616
anno_text0.1930.0040.200
anno_zoom0.7200.0040.726
annotation_axis_grob0.1270.0110.142
annotation_legend_size-HeatmapList-method000
c.HeatmapAnnotation0.0790.0010.081
cluster_within_group0.0370.0010.038
color_mapping_legend-ColorMapping-method000
columnAnnotation000
column_dend-Heatmap-method0.4830.0040.487
column_dend-HeatmapList-method1.8430.0091.853
column_dend-dispatch0.0000.0000.001
column_order-Heatmap-method0.5680.0020.571
column_order-HeatmapList-method1.9490.0092.308
column_order-dispatch000
comb_degree0.0030.0010.003
comb_name0.0040.0010.003
comb_size0.0030.0010.004
component_height-Heatmap-method0.0010.0010.000
component_height-HeatmapList-method000
component_height-dispatch000
component_width-Heatmap-method0.0010.0010.001
component_width-HeatmapList-method0.0000.0000.001
component_width-dispatch000
copy_all-AnnotationFunction-method0.0010.0000.000
copy_all-SingleAnnotation-method0.0000.0010.001
copy_all-dispatch000
decorate_annotation0.5470.0020.549
decorate_column_dend0.0000.0000.001
decorate_column_names0.0000.0010.001
decorate_column_title0.0010.0000.001
decorate_dend0.2880.0010.291
decorate_dimnames0.3670.0010.370
decorate_heatmap_body0.2250.0010.227
decorate_row_dend0.0010.0000.000
decorate_row_names0.0010.0000.001
decorate_row_title0.0010.0000.000
decorate_title0.3490.0020.351
default_axis_param0.0010.0010.003
default_get_type0.0000.0000.001
dend_heights0.0000.0000.001
dend_xy0.0300.0010.030
dendrogramGrob0.0010.0000.000
densityHeatmap2.3620.0182.388
dim.Heatmap0.0000.0010.001
dist20.0210.0020.049
draw-AnnotationFunction-method0.0010.0000.001
draw-Heatmap-method0.0010.0010.000
draw-HeatmapAnnotation-method0.0000.0000.001
draw-HeatmapList-method000
draw-Legends-method0.0270.0000.030
draw-SingleAnnotation-method0.0000.0000.001
draw-dispatch0.0010.0000.000
draw_annotation-Heatmap-method000
draw_annotation_legend-HeatmapList-method0.0010.0000.001
draw_dend-Heatmap-method000
draw_dimnames-Heatmap-method0.0010.0000.001
draw_heatmap_body-Heatmap-method0.0000.0000.001
draw_heatmap_legend-HeatmapList-method000
draw_heatmap_list-HeatmapList-method000
draw_title-Heatmap-method000
draw_title-HeatmapList-method0.0000.0000.001
draw_title-dispatch0.0010.0010.001
extract_comb0.0030.0010.004
getXY_in_parent_vp0.0280.0020.030
get_color_mapping_list-HeatmapAnnotation-method0.0010.0000.000
get_legend_param_list-HeatmapAnnotation-method000
grid.annotation_axis0.0010.0000.000
grid.boxplot0.0260.0010.027
grid.dendrogram2.7250.1472.889
grid.draw.Legends0.0270.0010.027
heatmap_legend_size-HeatmapList-method0.0000.0000.001
height.AnnotationFunction0.0180.0000.019
height.Heatmap0.0000.0000.001
height.HeatmapAnnotation0.0010.0000.001
height.HeatmapList000
height.Legends0.0270.0010.028
height.SingleAnnotation0.0000.0010.001
heightAssign.AnnotationFunction0.0010.0010.000
heightAssign.HeatmapAnnotation0.0000.0000.001
heightAssign.SingleAnnotation0.0000.0000.001
heightDetails.annotation_axis000
heightDetails.legend0.0000.0010.001
heightDetails.legend_body0.0010.0000.000
heightDetails.packed_legends000
ht_global_opt0.0010.0000.000
ht_opt0.0110.0010.012
is_abs_unit0.0020.0010.002
length.HeatmapAnnotation0.0000.0000.001
length.HeatmapList000
list_components0.0010.0000.001
list_to_matrix0.0030.0020.006
make_column_cluster-Heatmap-method0.0010.0010.000
make_comb_mat0.0090.0030.011
make_layout-Heatmap-method000
make_layout-HeatmapList-method0.0010.0000.000
make_layout-dispatch0.0000.0010.001
make_row_cluster-Heatmap-method0.0010.0000.000
map_to_colors-ColorMapping-method0.0290.0010.031
max_text_height0.0060.0000.006
max_text_width0.0050.0000.005
merge_dendrogram0.4120.0060.418
names.HeatmapAnnotation0.0390.0000.039
names.HeatmapList0.0000.0010.000
namesAssign.HeatmapAnnotation0.0340.0010.035
ncol.Heatmap000
nobs.AnnotationFunction0.0090.0000.009
nobs.HeatmapAnnotation0.0000.0000.001
nobs.SingleAnnotation0.0000.0000.001
normalize_comb_mat0.0000.0000.001
nrow.Heatmap000
oncoPrint0.0000.0010.000
order.comb_mat0.0000.0000.001
packLegend0.1360.0030.140
pct_v_pct000
pindex0.0080.0010.009
prepare-Heatmap-method0.0000.0000.001
print.comb_mat0.0000.0010.001
re_size-HeatmapAnnotation-method000
restore_matrix0.8660.0470.914
rowAnnotation0.0000.0000.001
row_anno_barplot000
row_anno_boxplot0.0000.0000.001
row_anno_density0.0000.0000.001
row_anno_histogram0.0010.0010.001
row_anno_link0.0000.0010.001
row_anno_points0.0000.0010.001
row_anno_text000
row_dend-Heatmap-method0.6030.0040.656
row_dend-HeatmapList-method1.3880.0091.400
row_dend-dispatch0.0010.0000.001
row_order-Heatmap-method0.5690.0030.573
row_order-HeatmapList-method1.3400.0091.350
row_order-dispatch000
set_component_height-Heatmap-method0.0010.0000.000
set_component_width-Heatmap-method0.0000.0010.001
set_name0.0020.0010.003
set_size0.0010.0000.002
show-AnnotationFunction-method0.0000.0000.001
show-ColorMapping-method000
show-Heatmap-method0.0000.0000.001
show-HeatmapAnnotation-method0.0000.0000.001
show-HeatmapList-method000
show-SingleAnnotation-method0.0010.0010.000
show-dispatch0.0000.0000.001
size.AnnotationFunction0.0170.0010.018
size.HeatmapAnnotation0.0000.0010.000
size.SingleAnnotation0.0010.0000.001
sizeAssign.AnnotationFunction0.0100.0000.011
sizeAssign.HeatmapAnnotation000
sizeAssign.SingleAnnotation0.0000.0010.001
smartAlign20.1390.0060.148
str.comb_mat0.0010.0000.001
subset_gp0.0010.0000.002
subset_matrix_by_row0.0000.0000.001
subset_vector0.0010.0000.001
summary.Heatmap0.0000.0000.001
summary.HeatmapList0.0010.0000.000
t.comb_mat0.0020.0000.003
test_alter_fun0.1350.0020.137
unify_mat_list0.0000.0010.001
upset_right_annotation000
upset_top_annotation0.0010.0000.001
width.AnnotationFunction0.0120.0000.013
width.Heatmap0.0010.0000.001
width.HeatmapAnnotation0.0000.0010.001
width.HeatmapList000
width.Legends0.0270.0000.027
width.SingleAnnotation0.0000.0010.001
widthAssign.AnnotationFunction000
widthAssign.HeatmapAnnotation000
widthAssign.SingleAnnotation000
widthDetails.annotation_axis000
widthDetails.legend0.0010.0010.000
widthDetails.legend_body000
widthDetails.packed_legends0.0010.0000.001