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BioC 3.4: CHECK report for ComplexHeatmap on morelia

This page was generated on 2017-04-15 16:26:25 -0400 (Sat, 15 Apr 2017).

Package 252/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ComplexHeatmap 1.12.0
Zuguang Gu
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ComplexHeatmap
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ComplexHeatmap
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.12.0.tar.gz
StartedAt: 2017-04-15 00:18:22 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:20:42 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 139.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ComplexHeatmap.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.12.0’
* 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 ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
Heatmap          13.921  0.068  14.050
add.AdditiveUnit  5.021  0.011   5.147
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/ComplexHeatmap.Rcheck/00check.log’
for details.


ComplexHeatmap.Rcheck/00install.out:

* 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)

ComplexHeatmap.Rcheck/ComplexHeatmap-Ex.timings:

nameusersystemelapsed
AdditiveUnit-class000
AdditiveUnit0.0010.0000.000
ColorMapping-class0.0010.0000.000
ColorMapping0.0160.0010.018
ComplexHeatmap-package0.0000.0000.001
Heatmap-class0.0010.0000.001
Heatmap13.921 0.06814.050
HeatmapAnnotation-class0.0000.0000.001
HeatmapAnnotation0.1170.0010.117
HeatmapList-class4.4680.0194.490
HeatmapList0.0010.0000.001
Legend0.0010.0000.000
SingleAnnotation-class000
SingleAnnotation0.1010.0010.102
add.AdditiveUnit5.0210.0115.147
add_heatmap-Heatmap-method1.3050.0041.393
add_heatmap-HeatmapAnnotation-method0.4460.0010.469
add_heatmap-HeatmapList-method2.3130.0122.327
add_heatmap-dispatch0.0010.0000.001
anno_barplot0.0090.0010.011
anno_boxplot0.0280.0010.033
anno_density0.2290.0030.233
anno_histogram0.0570.0010.071
anno_link2.1190.0202.748
anno_oncoprint_barplot0.0000.0000.001
anno_points0.0260.0020.235
anno_text0.3240.0011.021
annotation_legend_size-HeatmapList-method0.0010.0000.001
color_mapping_legend-ColorMapping-method0.2150.0030.234
columnAnnotation0.0220.0000.023
column_anno_barplot0.0000.0000.001
column_anno_boxplot000
column_anno_density000
column_anno_histogram0.0000.0000.001
column_anno_link000
column_anno_points0.0010.0000.000
column_anno_text0.0010.0000.001
column_dend-Heatmap-method0.1250.0010.127
column_dend-HeatmapList-method0.2650.0010.266
column_dend-dispatch0.0010.0000.000
column_order-Heatmap-method0.0930.0000.094
column_order-HeatmapList-method0.2400.0000.241
column_order-dispatch0.0010.0000.000
component_height-Heatmap-method0.0010.0000.000
component_height-HeatmapList-method0.0010.0000.000
component_height-dispatch0.0000.0010.001
component_width-Heatmap-method0.0000.0000.001
component_width-HeatmapList-method0.0000.0000.001
component_width-dispatch0.0010.0000.001
decorate_annotation0.8590.0020.871
decorate_column_dend0.0000.0000.001
decorate_column_names0.0010.0000.000
decorate_column_title000
decorate_dend0.3980.0010.400
decorate_dimnames0.4720.0010.473
decorate_heatmap_body0.3520.0010.353
decorate_row_dend000
decorate_row_names000
decorate_row_title000
decorate_title0.4430.0010.445
densityHeatmap3.8630.0144.482
dist20.0050.0000.004
draw-Heatmap-method0.4410.0010.504
draw-HeatmapAnnotation-method0.1440.0040.154
draw-HeatmapList-method1.7860.0052.016
draw-SingleAnnotation-method0.1470.0030.152
draw-dispatch0.0010.0010.000
draw_annotation-Heatmap-method000
draw_annotation_legend-HeatmapList-method000
draw_dend-Heatmap-method0.0000.0000.001
draw_dimnames-Heatmap-method0.0010.0000.001
draw_heatmap_body-Heatmap-method0.0010.0000.001
draw_heatmap_legend-HeatmapList-method0.0010.0000.001
draw_heatmap_list-HeatmapList-method0.0000.0000.001
draw_title-Heatmap-method0.0000.0000.001
draw_title-HeatmapList-method0.0010.0000.000
draw_title-dispatch000
enhanced_basicplot1.1160.0021.119
get_color_mapping_list-HeatmapAnnotation-method0.0010.0000.001
get_color_mapping_param_list-HeatmapAnnotation-method000
grid.dendrogram0.0260.0010.027
heatmap_legend_size-HeatmapList-method0.0010.0000.000
ht_global_opt0.0010.0000.001
is_abs_unit0.0020.0000.002
make_column_cluster-Heatmap-method0.0010.0000.000
make_layout-Heatmap-method0.0010.0000.001
make_layout-HeatmapList-method0.0000.0010.001
make_layout-dispatch0.0000.0000.001
make_row_cluster-Heatmap-method000
map_to_colors-ColorMapping-method0.0230.0010.024
max_text_height0.0020.0000.002
max_text_width0.0020.0000.002
oncoPrint0.0010.0000.000
plotDataFrame3.1440.0103.221
prepare-Heatmap-method000
rowAnnotation0.0120.0000.012
row_anno_barplot0.0010.0000.001
row_anno_boxplot0.0010.0010.001
row_anno_density0.0010.0000.001
row_anno_histogram0.0000.0000.001
row_anno_link000
row_anno_points000
row_anno_text0.0010.0000.001
row_dend-Heatmap-method0.0950.0000.095
row_dend-HeatmapList-method0.2470.0010.247
row_dend-dispatch0.0010.0000.000
row_order-Heatmap-method0.0970.0000.098
row_order-HeatmapList-method0.3200.0010.321
row_order-dispatch0.0000.0000.001
selectArea000
set_component_height-Heatmap-method000
show-ColorMapping-method0.0000.0000.001
show-Heatmap-method0.8840.0040.899
show-HeatmapAnnotation-method000
show-HeatmapList-method0.0010.0000.000
show-SingleAnnotation-method0.0010.0000.000
show-dispatch0.0010.0000.001
unify_mat_list0.0010.0000.001