Multiple platform build/check report for BioC 3.11 - CHECK report for GeneTonic on tokay2

Package: GeneTonic

Version: 1.0.1

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneTonic.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GeneTonic_1.0.1.tar.gz

StartedAt: 2020-10-17 04:22:22 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 04:37:24 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 902.2 seconds

RetCode: 0

Status: OK

CheckDir: GeneTonic.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneTonic.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GeneTonic_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/GeneTonic.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneTonic/DESCRIPTION' ... OK
* this is package 'GeneTonic' version '1.0.1'
* package encoding: UTF-8
* 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 whether package 'GeneTonic' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
gs_mds                   8.95   0.48    9.45
gs_heatmap               8.50   0.28    8.78
ggs_graph                7.54   0.49    8.02
GeneTonic                7.47   0.39    9.25
gs_scoresheat            7.50   0.30    7.80
gs_scores                7.19   0.41    7.61
gs_dendro                6.80   0.14    6.94
get_aggrscores           6.26   0.28    6.55
gs_alluvial              5.82   0.34    6.61
enrichment_map           5.47   0.18    5.64
gs_horizon               5.36   0.24    5.59
enhance_table            5.33   0.21    5.64
gene_plot                5.18   0.23    5.42
gs_summary_overview_pair 4.96   0.17    5.13
gs_summary_overview      4.76   0.26    5.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
gs_mds            8.71   0.17   11.33
GeneTonic         6.87   0.25    7.12
gs_scores         6.55   0.37    6.92
gs_scoresheat     6.44   0.33    6.77
ggs_graph         6.33   0.31    6.64
gs_heatmap        6.35   0.22    6.57
gs_dendro         5.66   0.21    5.86
enhance_table     5.29   0.33    5.62
happy_hour        4.96   0.28    5.25
gs_radar          4.86   0.36    7.43
checkup_GeneTonic 4.96   0.20    5.18
gs_horizon        4.81   0.17    6.04
gs_alluvial       3.43   0.28   22.18
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/GeneTonic_1.0.1.tar.gz && rm -rf GeneTonic.buildbin-libdir && mkdir GeneTonic.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneTonic.buildbin-libdir GeneTonic_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL GeneTonic_1.0.1.zip && rm GeneTonic_1.0.1.tar.gz GeneTonic_1.0.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  863k  100  863k    0     0  11.9M      0 --:--:-- --:--:-- --:--:-- 13.3M

install for i386

* installing *source* package 'GeneTonic' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GeneTonic'
    finding HTML links ... done
    GeneTonic-pkg                           html  
    GeneTonic                               html  
    check_colors                            html  
    checkup_GeneTonic                       html  
    create_jaccard_matrix                   html  
    create_kappa_matrix                     html  
    deseqresult2df                          html  
    dot-check_pandoc                        html  
    enhance_table                           html  
    enrichment_map                          html  
    gene_plot                               html  
    geneinfo_2_html                         html  
    get_aggrscores                          html  
    get_expression_values                   html  
    ggs_graph                               html  
    go_2_html                               html  
    gs_alluvial                             html  
    gs_dendro                               html  
    gs_heatmap                              html  
    gs_horizon                              html  
    gs_mds                                  html  
    gs_radar                                html  
    gs_scores                               html  
    gs_scoresheat                           html  
    gs_simplify                             html  
    gs_summary_heat                         html  
    gs_summary_overview                     html  
    gs_summary_overview_pair                html  
    gs_volcano                              html  
    happy_hour                              html  
    map2color                               html  
    finding level-2 HTML links ... done

    overlap_coefficient                     html  
    overlap_jaccard_index                   html  
    res_macrophage_IFNg_vs_naive            html  
    shake_enrichResult                      html  
    shake_topGOtableResult                  html  
    styleColorBar_divergent                 html  
    topgoDE_macrophage_IFNg_vs_naive        html  
** 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

install for x64

* installing *source* package 'GeneTonic' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneTonic' as GeneTonic_1.0.1.zip
* DONE (GeneTonic)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'GeneTonic' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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)
> library(GeneTonic)

> 
> test_check("GeneTonic")
--- Loading packages...
- Done!
--- Generating objects for the testing setup...
using counts and average transcript lengths from tximeta
'select()' returned 1:many mapping between keys and columns
estimating size factors
using 'avgTxLength' from assays(dds), correcting for library size
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
- Done!
--- Running enrichGO...
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
- Done!
--- Test setup script completed!
== testthat results  ===========================================================
[ OK: 120 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 145.15   10.68  155.98


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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)
> library(GeneTonic)

> 
> test_check("GeneTonic")
--- Loading packages...
- Done!
--- Generating objects for the testing setup...
using counts and average transcript lengths from tximeta
'select()' returned 1:many mapping between keys and columns
estimating size factors
using 'avgTxLength' from assays(dds), correcting for library size
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
- Done!
--- Running enrichGO...
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
- Done!
--- Test setup script completed!
== testthat results  ===========================================================
[ OK: 120 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 149.06    2.84  151.93

name	user	system	elapsed
GeneTonic	7.47	0.39	9.25
check_colors	0	0	0
checkup_GeneTonic	4.25	0.22	4.47
create_jaccard_matrix	1.08	0.16	1.24
create_kappa_matrix	3.32	0.14	3.46
deseqresult2df	0.22	0.00	0.22
enhance_table	5.33	0.21	5.64
enrichment_map	5.47	0.18	5.64
gene_plot	5.18	0.23	5.42
geneinfo_2_html	0.02	0.00	0.01
get_aggrscores	6.26	0.28	6.55
get_expression_values	4.23	0.17	4.40
ggs_graph	7.54	0.49	8.02
go_2_html	0.03	0.00	0.03
gs_alluvial	5.82	0.34	6.61
gs_dendro	6.80	0.14	6.94
gs_heatmap	8.50	0.28	8.78
gs_horizon	5.36	0.24	5.59
gs_mds	8.95	0.48	9.45
gs_radar	4.57	0.30	5.00
gs_scores	7.19	0.41	7.61
gs_scoresheat	7.5	0.3	7.8
gs_simplify	1.64	0.10	1.74
gs_summary_heat	4.55	0.19	4.73
gs_summary_overview	4.76	0.26	5.03
gs_summary_overview_pair	4.96	0.17	5.13
gs_volcano	4.75	0.19	4.94
happy_hour	4.38	0.20	4.58
map2color	0.02	0.00	0.02
overlap_coefficient	0	0	0
overlap_jaccard_index	0	0	0
shake_enrichResult	2.11	0.07	2.19
shake_topGOtableResult	0	0	0
styleColorBar_divergent	0.29	0.03	0.32

name	user	system	elapsed
GeneTonic	6.87	0.25	7.12
check_colors	0.02	0.00	0.02
checkup_GeneTonic	4.96	0.20	5.18
create_jaccard_matrix	1.05	0.03	1.08
create_kappa_matrix	3.90	0.04	3.94
deseqresult2df	0.21	0.01	0.22
enhance_table	5.29	0.33	5.62
enrichment_map	4.11	0.23	4.35
gene_plot	4.30	0.16	4.45
geneinfo_2_html	0.02	0.00	0.01
get_aggrscores	4.43	0.11	4.55
get_expression_values	3.52	0.17	3.69
ggs_graph	6.33	0.31	6.64
go_2_html	0.03	0.00	0.04
gs_alluvial	3.43	0.28	22.18
gs_dendro	5.66	0.21	5.86
gs_heatmap	6.35	0.22	6.57
gs_horizon	4.81	0.17	6.04
gs_mds	8.71	0.17	11.33
gs_radar	4.86	0.36	7.43
gs_scores	6.55	0.37	6.92
gs_scoresheat	6.44	0.33	6.77
gs_simplify	2.22	0.00	2.22
gs_summary_heat	4.65	0.28	4.94
gs_summary_overview	4.27	0.22	4.48
gs_summary_overview_pair	3.98	0.14	4.13
gs_volcano	4.58	0.19	4.76
happy_hour	4.96	0.28	5.25
map2color	0.11	0.01	0.13
overlap_coefficient	0	0	0
overlap_jaccard_index	0	0	0
shake_enrichResult	2.88	0.13	3.00
shake_topGOtableResult	0.01	0.00	0.01
styleColorBar_divergent	0.50	0.08	0.58

CHECK report for GeneTonic on tokay2

Summary

Command output

Installation output

Tests output

Example timings