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BioC 3.2: CHECK report for ComplexHeatmap on oaxaca

This page was generated on 2016-04-23 10:29:05 -0700 (Sat, 23 Apr 2016).

Package 217/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ComplexHeatmap 1.6.0
Zuguang Gu
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ComplexHeatmap
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ComplexHeatmap
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.6.0.tar.gz
StartedAt: 2016-04-22 23:05:36 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:06:56 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 80.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ComplexHeatmap.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ComplexHeatmap_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.6.0’
* 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 ... [4s/4s] OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
* 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 ... WARNING
Codoc mismatches from documentation object 'ht_global_opt':
ht_global_opt
  Code: function(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE)
  Docs: function(..., RESET = FALSE, READ.ONLY = NULL)
  Argument names in code not in docs:
    LOCAL

* 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 ... [34s/34s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
Heatmap 11.057   0.07  11.193
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [1s/1s]
 [1s/1s] 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-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-class0.0010.0000.001
AdditiveUnit000
ColorMapping-class000
ColorMapping0.0300.0010.031
ComplexHeatmap-package0.0010.0000.001
Heatmap-class0.0010.0000.000
Heatmap11.057 0.07011.193
HeatmapAnnotation-class0.0010.0000.001
HeatmapAnnotation0.0610.0010.061
HeatmapList-class3.8040.0163.825
HeatmapList0.0000.0000.001
SingleAnnotation-class000
SingleAnnotation0.0540.0000.055
add.AdditiveUnit3.6110.0113.625
add_heatmap-Heatmap-method0.9870.0030.991
add_heatmap-HeatmapAnnotation-method0.3320.0010.333
add_heatmap-HeatmapList-method1.5530.0041.558
add_heatmap-dispatch0.0000.0000.001
anno_barplot0.0110.0010.012
anno_boxplot0.0320.0010.033
anno_density0.2220.0040.228
anno_histogram0.0530.0010.055
anno_points0.0050.0000.006
anno_text0.3790.0020.381
annotation_legend_size-HeatmapList-method000
color_mapping_legend-ColorMapping-method0.2180.0020.221
columnAnnotation0.010.000.01
column_anno_barplot0.0010.0000.001
column_anno_boxplot0.0010.0010.001
column_anno_density0.0000.0000.001
column_anno_histogram000
column_anno_points000
column_anno_text0.0010.0000.001
column_dend-Heatmap-method0.0010.0000.000
column_dend-HeatmapList-method0.0010.0000.000
column_dend-dispatch0.0010.0000.001
column_order-Heatmap-method0.0010.0000.001
column_order-HeatmapList-method0.0010.0000.001
column_order-dispatch000
component_height-Heatmap-method000
component_height-HeatmapList-method0.0000.0010.000
component_height-dispatch0.0010.0000.001
component_width-Heatmap-method0.0010.0000.001
component_width-HeatmapList-method0.0010.0000.001
component_width-dispatch0.0010.0000.001
decorate_annotation0.6160.0020.618
decorate_column_dend0.0010.0000.001
decorate_column_names0.0010.0000.001
decorate_column_title0.0000.0000.001
decorate_dend0.3090.0060.316
decorate_dimnames0.3360.0010.337
decorate_heatmap_body0.2990.0010.300
decorate_row_dend0.0010.0000.000
decorate_row_names0.0000.0000.001
decorate_row_title0.0000.0010.000
decorate_title0.3340.0000.335
densityHeatmap2.9600.0122.980
dist20.0020.0000.002
draw-Heatmap-method0.2360.0010.238
draw-HeatmapAnnotation-method0.1230.0030.126
draw-HeatmapList-method1.1320.0021.135
draw-SingleAnnotation-method0.1280.0030.137
draw-dispatch000
draw_annotation-Heatmap-method0.0010.0000.001
draw_annotation_legend-HeatmapList-method0.0010.0000.000
draw_dend-Heatmap-method0.0010.0000.000
draw_dimnames-Heatmap-method0.0010.0000.001
draw_heatmap_body-Heatmap-method0.0000.0010.000
draw_heatmap_legend-HeatmapList-method0.0000.0000.001
draw_heatmap_list-HeatmapList-method000
draw_title-Heatmap-method0.0010.0000.001
draw_title-HeatmapList-method0.0010.0010.000
draw_title-dispatch0.0010.0000.001
enhanced_basicplot0.8530.0020.855
get_color_mapping_list-HeatmapAnnotation-method000
get_color_mapping_param_list-HeatmapAnnotation-method0.0010.0000.001
grid.dendrogram0.0240.0000.025
heatmap_legend_size-HeatmapList-method0.0010.0000.001
ht_global_opt0.0010.0000.001
is_abs_unit0.0010.0000.002
make_column_cluster-Heatmap-method000
make_layout-Heatmap-method0.0000.0000.001
make_layout-HeatmapList-method0.0010.0000.000
make_layout-dispatch0.0010.0000.001
make_row_cluster-Heatmap-method0.0010.0000.000
map_to_colors-ColorMapping-method0.0360.0000.037
max_text_height0.0140.0000.014
max_text_width0.0140.0000.014
oncoPrint0.0010.0000.001
plotDataFrame2.4070.0052.413
prepare-Heatmap-method0.0010.0000.001
rowAnnotation0.0130.0000.013
row_anno_barplot0.0010.0000.001
row_anno_boxplot0.0000.0000.001
row_anno_density0.0000.0000.001
row_anno_histogram0.0000.0000.001
row_anno_points0.0010.0000.000
row_anno_text0.0010.0000.001
row_dend-Heatmap-method0.0000.0000.001
row_dend-HeatmapList-method0.0010.0000.001
row_dend-dispatch0.0010.0010.001
row_order-Heatmap-method0.0010.0000.000
row_order-HeatmapList-method000
row_order-dispatch0.0010.0000.001
select0.0010.0000.001
set_component_height-Heatmap-method000
show-ColorMapping-method000
show-Heatmap-method0.5850.0040.589
show-HeatmapAnnotation-method000
show-HeatmapList-method0.0010.0000.000
show-SingleAnnotation-method0.0000.0000.001
show-dispatch000
unify_mat_list000