Multiple platform build/check report for BioC 3.13 - CHECK results for GeneTonic on tokay2

Package: GeneTonic

Version: 1.4.1

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneTonic.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneTonic_1.4.1.tar.gz

StartedAt: 2021-10-14 23:34:14 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 23:49:49 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 935.0 seconds

RetCode: 0

Status: OK

CheckDir: GeneTonic.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneTonic.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneTonic_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GeneTonic.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.4.1'
* 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_heatmap               8.32   0.27    8.58
gs_mds                   8.18   0.18    8.36
GeneTonic                7.86   0.39    8.42
ggs_backbone             7.53   0.27    9.69
ggs_graph                7.47   0.17    7.64
signature_volcano        7.29   0.20    7.49
summarize_ggs_hubgenes   6.86   0.19    7.05
gs_scores                6.37   0.20    6.58
export_for_iSEE          6.01   0.21    6.26
gs_scoresheat            5.86   0.25    6.10
gene_plot                5.72   0.16    5.88
gs_dendro                5.25   0.15    5.43
distill_enrichment       5.00   0.18    5.17
enhance_table            5.00   0.17    5.17
gs_summary_overview_pair 4.99   0.14    5.12
gs_volcano               4.95   0.15    5.11
gs_alluvial              4.82   0.19    5.00
checkup_gtl              4.91   0.10    5.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
ggs_backbone           7.93   0.29    8.55
gs_heatmap             7.67   0.20    7.87
summarize_ggs_hubgenes 7.41   0.29    7.68
gs_mds                 7.47   0.21    7.67
ggs_graph              7.26   0.24    7.50
signature_volcano      7.23   0.19    7.42
gs_scoresheat          7.17   0.11    7.28
gs_scores              6.54   0.14    6.67
GeneTonic              6.39   0.24    6.62
export_for_iSEE        5.83   0.14    5.97
gs_alluvial            5.46   0.19    5.64
gs_horizon             5.25   0.17    5.42
gs_dendro              5.13   0.17    5.29
checkup_gtl            4.99   0.18    5.15
checkup_GeneTonic      4.97   0.12    5.10
gs_volcano             4.93   0.10    5.01
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GeneTonic_1.4.1.tar.gz && rm -rf GeneTonic.buildbin-libdir && mkdir GeneTonic.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneTonic.buildbin-libdir GeneTonic_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GeneTonic_1.4.1.zip && rm GeneTonic_1.4.1.tar.gz GeneTonic_1.4.1.zip
###
##############################################################################
##############################################################################


  % 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 1831k  100 1831k    0     0  3033k      0 --:--:-- --:--:-- --:--:-- 3037k

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  
    GeneTonic_list                          html  
    check_colors                            html  
    checkup_GeneTonic                       html  
    checkup_gtl                             html  
    cluster_markov                          html  
    create_jaccard_matrix                   html  
    create_kappa_matrix                     html  
    describe_gtl                            html  
    deseqresult2df                          html  
    distill_enrichment                      html  
    dot-check_pandoc                        html  
    enhance_table                           html  
    enrichment_map                          html  
    enrichr_output_macrophage               html  
    export_for_iSEE                         html  
    finding level-2 HTML links ... done

    export_to_sif                           html  
    fgseaRes                                html  
    gene_plot                               html  
    geneinfo_2_html                         html  
    get_aggrscores                          html  
    get_expression_values                   html  
    ggs_backbone                            html  
    ggs_graph                               html  
    go_2_html                               html  
    gostres_macrophage                      html  
    gs_alluvial                             html  
    gs_dendro                               html  
    gs_fuzzyclustering                      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  
    overlap_coefficient                     html  
    overlap_jaccard_index                   html  
    res_macrophage_IFNg_vs_naive            html  
    shake_davidResult                       html  
    shake_enrichResult                      html  
    shake_enrichrResult                     html  
    shake_fgseaResult                       html  
    shake_gprofilerResult                   html  
    shake_topGOtableResult                  html  
    signature_volcano                       html  
    styleColorBar_divergent                 html  
    summarize_ggs_hubgenes                  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_1.4.1.zip
* DONE (GeneTonic)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GeneTonic' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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!
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 235 ]
> 
> proc.time()
   user  system elapsed 
 140.40    9.00  149.67


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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!
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 235 ]
> 
> proc.time()
   user  system elapsed 
 144.78    3.23  148.09

name	user	system	elapsed
GeneTonic	7.86	0.39	8.42
GeneTonic_list	4.81	0.19	5.00
check_colors	0	0	0
checkup_GeneTonic	4.49	0.19	4.69
checkup_gtl	4.91	0.10	5.04
cluster_markov	0.09	0.00	0.10
create_jaccard_matrix	0.97	0.32	1.28
create_kappa_matrix	2.46	0.17	2.62
deseqresult2df	0.17	0.01	0.19
distill_enrichment	5.00	0.18	5.17
enhance_table	5.00	0.17	5.17
enrichment_map	4.55	0.19	4.74
export_for_iSEE	6.01	0.21	6.26
export_to_sif	0.02	0.00	0.02
gene_plot	5.72	0.16	5.88
geneinfo_2_html	0.01	0.00	0.01
get_aggrscores	4.81	0.14	4.95
get_expression_values	3.72	0.17	3.89
ggs_backbone	7.53	0.27	9.69
ggs_graph	7.47	0.17	7.64
go_2_html	0.01	0.00	0.01
gs_alluvial	4.82	0.19	5.00
gs_dendro	5.25	0.15	5.43
gs_fuzzyclustering	0.68	0.02	0.70
gs_heatmap	8.32	0.27	8.58
gs_horizon	4.78	0.18	4.97
gs_mds	8.18	0.18	8.36
gs_radar	4.68	0.25	4.92
gs_scores	6.37	0.20	6.58
gs_scoresheat	5.86	0.25	6.10
gs_simplify	1.03	0.00	1.04
gs_summary_heat	4.38	0.12	4.50
gs_summary_overview	4.67	0.07	4.74
gs_summary_overview_pair	4.99	0.14	5.12
gs_volcano	4.95	0.15	5.11
happy_hour	4.64	0.22	4.86
map2color	0.02	0.00	0.02
overlap_coefficient	0	0	0
overlap_jaccard_index	0	0	0
shake_davidResult	0.01	0.00	0.01
shake_enrichResult	3.22	0.13	3.34
shake_enrichrResult	0.11	0.00	0.13
shake_fgseaResult	0.22	0.01	0.23
shake_gprofilerResult	0.17	0.00	0.25
shake_topGOtableResult	0.01	0.00	0.01
signature_volcano	7.29	0.20	7.49
styleColorBar_divergent	0.25	0.03	0.28
summarize_ggs_hubgenes	6.86	0.19	7.05

name	user	system	elapsed
GeneTonic	6.39	0.24	6.62
GeneTonic_list	4.53	0.25	4.78
check_colors	0.01	0.00	0.01
checkup_GeneTonic	4.97	0.12	5.10
checkup_gtl	4.99	0.18	5.15
cluster_markov	0.08	0.00	0.08
create_jaccard_matrix	0.85	0.04	0.89
create_kappa_matrix	3.14	0.02	3.15
deseqresult2df	0.11	0.03	0.14
distill_enrichment	3.87	0.03	3.91
enhance_table	3.96	0.06	4.03
enrichment_map	4.33	0.13	4.45
export_for_iSEE	5.83	0.14	5.97
export_to_sif	0.03	0.00	0.03
gene_plot	4.15	0.23	4.39
geneinfo_2_html	0.02	0.00	0.01
get_aggrscores	4.69	0.08	4.77
get_expression_values	2.66	0.13	2.79
ggs_backbone	7.93	0.29	8.55
ggs_graph	7.26	0.24	7.50
go_2_html	0.03	0.00	0.03
gs_alluvial	5.46	0.19	5.64
gs_dendro	5.13	0.17	5.29
gs_fuzzyclustering	0.98	0.00	0.99
gs_heatmap	7.67	0.20	7.87
gs_horizon	5.25	0.17	5.42
gs_mds	7.47	0.21	7.67
gs_radar	3.40	0.17	3.58
gs_scores	6.54	0.14	6.67
gs_scoresheat	7.17	0.11	7.28
gs_simplify	1.09	0.03	1.13
gs_summary_heat	3.61	0.08	3.68
gs_summary_overview	3.78	0.17	3.96
gs_summary_overview_pair	3.70	0.15	3.86
gs_volcano	4.93	0.10	5.01
happy_hour	3.79	0.14	3.94
map2color	0.01	0.00	0.01
overlap_coefficient	0	0	0
overlap_jaccard_index	0	0	0
shake_davidResult	0.02	0.00	0.02
shake_enrichResult	1.97	0.12	2.09
shake_enrichrResult	0.06	0.00	0.06
shake_fgseaResult	0.13	0.00	0.13
shake_gprofilerResult	0.07	0.02	0.09
shake_topGOtableResult	0.02	0.00	0.02
signature_volcano	7.23	0.19	7.42
styleColorBar_divergent	0.24	0.04	0.77
summarize_ggs_hubgenes	7.41	0.29	7.68

CHECK results for GeneTonic on tokay2

Summary

Command output

Installation output

Tests output

Example timings