Zuguang Gu
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ComplexHeatmap |
| Branch: RELEASE_3_7 |
| Last Commit: be0dd9d |
| Last Changed Date: 2018-06-19 09:49:32 -0400 (Tue, 19 Jun 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:27:25 -0400 (Wed, 17 Oct 2018).
| Package 296/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ComplexHeatmap 1.18.1 Zuguang Gu
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: ComplexHeatmap |
| Version: 1.18.1 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ComplexHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ComplexHeatmap_1.18.1.tar.gz |
| StartedAt: 2018-10-15 23:27:19 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 23:28:34 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 75.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ComplexHeatmap.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ComplexHeatmap.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ComplexHeatmap_1.18.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ComplexHeatmap.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.18.1’
* 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 ... WARNING
Codoc mismatches from documentation object 'ht_global_opt':
ht_global_opt
Code: function(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE,
ADD = FALSE)
Docs: function(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE)
Argument names in code not in docs:
ADD
* 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 12.272 0.036 12.327
* 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 WARNING
See
‘/home/biocbuild/bbs-3.7-bioc/meat/ComplexHeatmap.Rcheck/00check.log’
for details.
ComplexHeatmap.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ComplexHeatmap ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-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)
ComplexHeatmap.Rcheck/tests/test-all.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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
0.884 0.056 0.937
ComplexHeatmap.Rcheck/ComplexHeatmap-Ex.timings
| name | user | system | elapsed | |
| AdditiveUnit-class | 0.000 | 0.000 | 0.001 | |
| AdditiveUnit | 0.000 | 0.000 | 0.001 | |
| ColorMapping-class | 0 | 0 | 0 | |
| ColorMapping | 0.016 | 0.000 | 0.016 | |
| ComplexHeatmap-package | 0 | 0 | 0 | |
| Heatmap-class | 0.000 | 0.000 | 0.001 | |
| Heatmap | 12.272 | 0.036 | 12.327 | |
| HeatmapAnnotation-class | 0 | 0 | 0 | |
| HeatmapAnnotation | 0.032 | 0.000 | 0.030 | |
| HeatmapList-class | 2.368 | 0.000 | 2.368 | |
| HeatmapList | 0.000 | 0.000 | 0.001 | |
| Legend | 0.232 | 0.000 | 0.233 | |
| SingleAnnotation-class | 0.000 | 0.000 | 0.001 | |
| SingleAnnotation | 0.024 | 0.000 | 0.026 | |
| add.AdditiveUnit | 2.984 | 0.004 | 2.991 | |
| add_heatmap-Heatmap-method | 0.752 | 0.000 | 0.754 | |
| add_heatmap-HeatmapAnnotation-method | 0.460 | 0.000 | 0.458 | |
| add_heatmap-HeatmapList-method | 1.040 | 0.000 | 1.042 | |
| add_heatmap-dispatch | 0.000 | 0.000 | 0.001 | |
| adjust_dend_by_leaf_width | 1.148 | 0.020 | 1.170 | |
| anno_barplot | 0.012 | 0.000 | 0.014 | |
| anno_boxplot | 0.024 | 0.000 | 0.023 | |
| anno_density | 0.140 | 0.000 | 0.142 | |
| anno_histogram | 0.064 | 0.000 | 0.066 | |
| anno_link | 1.168 | 0.004 | 1.174 | |
| anno_oncoprint_barplot | 0 | 0 | 0 | |
| anno_points | 0.024 | 0.000 | 0.021 | |
| anno_text | 0.256 | 0.000 | 0.255 | |
| annotation_legend_size-HeatmapList-method | 0.000 | 0.000 | 0.001 | |
| color_mapping_legend-ColorMapping-method | 0.172 | 0.000 | 0.174 | |
| columnAnnotation | 0.004 | 0.000 | 0.006 | |
| column_anno_barplot | 0.000 | 0.000 | 0.001 | |
| column_anno_boxplot | 0 | 0 | 0 | |
| column_anno_density | 0 | 0 | 0 | |
| column_anno_histogram | 0 | 0 | 0 | |
| column_anno_link | 0.000 | 0.000 | 0.001 | |
| column_anno_points | 0.000 | 0.000 | 0.001 | |
| column_anno_text | 0 | 0 | 0 | |
| column_dend-Heatmap-method | 0.036 | 0.000 | 0.037 | |
| column_dend-HeatmapList-method | 0.148 | 0.000 | 0.146 | |
| column_dend-dispatch | 0 | 0 | 0 | |
| column_order-Heatmap-method | 0.032 | 0.004 | 0.037 | |
| column_order-HeatmapList-method | 0.136 | 0.000 | 0.137 | |
| column_order-dispatch | 0 | 0 | 0 | |
| component_height-Heatmap-method | 0 | 0 | 0 | |
| component_height-HeatmapList-method | 0 | 0 | 0 | |
| component_height-dispatch | 0.000 | 0.000 | 0.001 | |
| component_width-Heatmap-method | 0.000 | 0.000 | 0.001 | |
| component_width-HeatmapList-method | 0.000 | 0.000 | 0.001 | |
| component_width-dispatch | 0.000 | 0.000 | 0.001 | |
| decorate_annotation | 0.468 | 0.004 | 0.475 | |
| decorate_column_dend | 0 | 0 | 0 | |
| decorate_column_names | 0.000 | 0.000 | 0.001 | |
| decorate_column_title | 0.000 | 0.000 | 0.001 | |
| decorate_dend | 0.272 | 0.000 | 0.272 | |
| decorate_dimnames | 0.324 | 0.000 | 0.324 | |
| decorate_heatmap_body | 0.252 | 0.000 | 0.254 | |
| decorate_row_dend | 0 | 0 | 0 | |
| decorate_row_names | 0 | 0 | 0 | |
| decorate_row_title | 0.000 | 0.000 | 0.001 | |
| decorate_title | 0.288 | 0.004 | 0.291 | |
| densityHeatmap | 2.576 | 0.000 | 2.578 | |
| dist2 | 0.020 | 0.000 | 0.019 | |
| draw-Heatmap-method | 0.336 | 0.004 | 0.340 | |
| draw-HeatmapAnnotation-method | 0.080 | 0.000 | 0.079 | |
| draw-HeatmapList-method | 1.036 | 0.000 | 1.039 | |
| draw-SingleAnnotation-method | 0.052 | 0.000 | 0.053 | |
| draw-dispatch | 0.000 | 0.000 | 0.001 | |
| draw_annotation-Heatmap-method | 0.000 | 0.000 | 0.001 | |
| draw_annotation_legend-HeatmapList-method | 0 | 0 | 0 | |
| draw_dend-Heatmap-method | 0 | 0 | 0 | |
| draw_dimnames-Heatmap-method | 0 | 0 | 0 | |
| draw_heatmap_body-Heatmap-method | 0.000 | 0.000 | 0.001 | |
| draw_heatmap_legend-HeatmapList-method | 0 | 0 | 0 | |
| draw_heatmap_list-HeatmapList-method | 0 | 0 | 0 | |
| draw_title-Heatmap-method | 0.000 | 0.000 | 0.001 | |
| draw_title-HeatmapList-method | 0.000 | 0.000 | 0.001 | |
| draw_title-dispatch | 0.004 | 0.000 | 0.000 | |
| enhanced_basicplot | 0.848 | 0.000 | 0.851 | |
| get_color_mapping_list-HeatmapAnnotation-method | 0.000 | 0.000 | 0.001 | |
| get_color_mapping_param_list-HeatmapAnnotation-method | 0 | 0 | 0 | |
| grid.dendrogram | 0.016 | 0.000 | 0.015 | |
| grid.dendrogram2 | 0.016 | 0.000 | 0.016 | |
| heatmap_legend_size-HeatmapList-method | 0 | 0 | 0 | |
| ht_global_opt | 0 | 0 | 0 | |
| is_abs_unit | 0.000 | 0.000 | 0.001 | |
| make_column_cluster-Heatmap-method | 0.000 | 0.000 | 0.001 | |
| make_layout-Heatmap-method | 0 | 0 | 0 | |
| make_layout-HeatmapList-method | 0.000 | 0.000 | 0.001 | |
| make_layout-dispatch | 0.000 | 0.000 | 0.001 | |
| make_row_cluster-Heatmap-method | 0 | 0 | 0 | |
| map_to_colors-ColorMapping-method | 0.020 | 0.000 | 0.018 | |
| max_text_height | 0.004 | 0.000 | 0.002 | |
| max_text_width | 0.000 | 0.000 | 0.001 | |
| oncoPrint | 0.000 | 0.000 | 0.001 | |
| packLegend | 0.768 | 0.000 | 0.769 | |
| plotDataFrame | 2.424 | 0.012 | 2.438 | |
| prepare-Heatmap-method | 0.000 | 0.000 | 0.001 | |
| rowAnnotation | 0.004 | 0.000 | 0.005 | |
| row_anno_barplot | 0 | 0 | 0 | |
| row_anno_boxplot | 0 | 0 | 0 | |
| row_anno_density | 0.000 | 0.000 | 0.001 | |
| row_anno_histogram | 0.000 | 0.000 | 0.001 | |
| row_anno_link | 0.000 | 0.000 | 0.001 | |
| row_anno_points | 0.000 | 0.000 | 0.001 | |
| row_anno_text | 0 | 0 | 0 | |
| row_dend-Heatmap-method | 0.036 | 0.000 | 0.035 | |
| row_dend-HeatmapList-method | 0.148 | 0.000 | 0.147 | |
| row_dend-dispatch | 0 | 0 | 0 | |
| row_order-Heatmap-method | 0.036 | 0.000 | 0.034 | |
| row_order-HeatmapList-method | 0.140 | 0.000 | 0.142 | |
| row_order-dispatch | 0 | 0 | 0 | |
| selectArea | 0 | 0 | 0 | |
| set_component_height-Heatmap-method | 0.000 | 0.000 | 0.001 | |
| show-ColorMapping-method | 0.004 | 0.000 | 0.001 | |
| show-Heatmap-method | 0.640 | 0.000 | 0.641 | |
| show-HeatmapAnnotation-method | 0.000 | 0.000 | 0.001 | |
| show-HeatmapList-method | 0.000 | 0.000 | 0.001 | |
| show-SingleAnnotation-method | 0.000 | 0.000 | 0.001 | |
| show-dispatch | 0 | 0 | 0 | |
| unify_mat_list | 0.004 | 0.000 | 0.000 | |