Multiple platform build/check report for BioC 3.12 - CHECK report for GeneTonic on tokay1

Package: GeneTonic

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneTonic.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GeneTonic_1.2.0.tar.gz

StartedAt: 2021-05-06 03:04:29 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 03:19:37 -0400 (Thu, 06 May 2021)

EllapsedTime: 908.3 seconds

RetCode: 0

Status: OK

CheckDir: GeneTonic.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneTonic.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GeneTonic_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GeneTonic.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.2.0'
* 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
GeneTonic         8.43   0.40    9.50
ggs_graph         7.05   0.19    7.23
gs_mds            6.55   0.16    6.71
gs_heatmap        6.21   0.34    6.56
gs_scores         5.86   0.34    6.28
gs_scoresheat     5.74   0.32    6.08
checkup_GeneTonic 5.25   0.25    5.58
gene_plot         5.24   0.17    5.41
gs_dendro         5.07   0.24    5.57
export_for_iSEE   5.10   0.16    5.33
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
gs_mds            9.09   0.21    9.29
GeneTonic         6.65   0.32    6.98
gs_scores         6.64   0.28    6.94
gs_heatmap        6.48   0.22    6.70
ggs_graph         6.09   0.22    6.31
gs_scoresheat     5.66   0.27    5.92
gs_dendro         5.70   0.15    5.86
gs_horizon        5.61   0.20    5.83
checkup_GeneTonic 5.03   0.25    5.28
happy_hour        4.91   0.19    5.09
gs_radar          4.55   0.26    7.91
* 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 http://172.29.0.3/BBS/3.12/bioc/src/contrib/GeneTonic_1.2.0.tar.gz && rm -rf GeneTonic.buildbin-libdir && mkdir GeneTonic.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneTonic.buildbin-libdir GeneTonic_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GeneTonic_1.2.0.zip && rm GeneTonic_1.2.0.tar.gz GeneTonic_1.2.0.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 1810k  100 1810k    0     0  34.3M      0 --:--:-- --:--:-- --:--:-- 35.3M

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  
    cluster_markov                          html  
    create_jaccard_matrix                   html  
    create_kappa_matrix                     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_graph                               html  
    go_2_html                               html  
    gostres_macrophage                      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  
    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  
    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_1.2.0.zip
* DONE (GeneTonic)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GeneTonic' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 1 | SKIP 0 | PASS 173 ]
> 
> proc.time()
   user  system elapsed 
 159.18   10.15  169.43


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 1 | SKIP 0 | PASS 173 ]
> 
> proc.time()
   user  system elapsed 
 152.00    3.84  155.95

name	user	system	elapsed
GeneTonic	8.43	0.40	9.50
check_colors	0.00	0.02	0.02
checkup_GeneTonic	5.25	0.25	5.58
cluster_markov	0.11	0.00	0.11
create_jaccard_matrix	1.09	0.11	1.20
create_kappa_matrix	3.19	0.16	3.34
deseqresult2df	0.17	0.00	0.17
distill_enrichment	4.04	0.14	4.22
enhance_table	4.34	0.17	4.52
enrichment_map	4.59	0.17	4.78
export_for_iSEE	5.10	0.16	5.33
export_to_sif	0.02	0.00	0.02
gene_plot	5.24	0.17	5.41
geneinfo_2_html	0.01	0.00	0.02
get_aggrscores	4.43	0.24	4.68
get_expression_values	3.53	0.15	3.69
ggs_graph	7.05	0.19	7.23
go_2_html	0.03	0.00	0.03
gs_alluvial	3.83	0.20	4.13
gs_dendro	5.07	0.24	5.57
gs_heatmap	6.21	0.34	6.56
gs_horizon	4.45	0.25	4.70
gs_mds	6.55	0.16	6.71
gs_radar	4.17	0.34	4.53
gs_scores	5.86	0.34	6.28
gs_scoresheat	5.74	0.32	6.08
gs_simplify	1.14	0.00	1.14
gs_summary_heat	3.55	0.23	3.78
gs_summary_overview	4.20	0.22	4.47
gs_summary_overview_pair	3.59	0.16	3.76
gs_volcano	4.05	0.15	4.21
happy_hour	3.45	0.22	3.67
map2color	0.01	0.00	0.02
overlap_coefficient	0	0	0
overlap_jaccard_index	0	0	0
shake_davidResult	0.02	0.00	0.02
shake_enrichResult	2.83	0.13	2.95
shake_enrichrResult	0.05	0.00	0.08
shake_fgseaResult	0.16	0.00	0.16
shake_gprofilerResult	0.11	0.00	0.15
shake_topGOtableResult	0	0	0
styleColorBar_divergent	0.28	0.06	0.36

name	user	system	elapsed
GeneTonic	6.65	0.32	6.98
check_colors	0.01	0.00	0.01
checkup_GeneTonic	5.03	0.25	5.28
cluster_markov	0.11	0.00	0.11
create_jaccard_matrix	1.07	0.07	1.13
create_kappa_matrix	3.03	0.04	3.08
deseqresult2df	0.14	0.02	0.15
distill_enrichment	4.33	0.23	4.56
enhance_table	3.92	0.11	4.03
enrichment_map	4.69	0.18	4.86
export_for_iSEE	4.53	0.14	4.67
export_to_sif	0.03	0.00	0.03
gene_plot	4.32	0.20	4.52
geneinfo_2_html	0.01	0.00	0.02
get_aggrscores	4.11	0.11	4.21
get_expression_values	3.16	0.14	3.30
ggs_graph	6.09	0.22	6.31
go_2_html	0.03	0.00	0.04
gs_alluvial	4.19	0.19	4.71
gs_dendro	5.70	0.15	5.86
gs_heatmap	6.48	0.22	6.70
gs_horizon	5.61	0.20	5.83
gs_mds	9.09	0.21	9.29
gs_radar	4.55	0.26	7.91
gs_scores	6.64	0.28	6.94
gs_scoresheat	5.66	0.27	5.92
gs_simplify	1.20	0.00	1.21
gs_summary_heat	4.27	0.20	4.47
gs_summary_overview	4.34	0.21	4.55
gs_summary_overview_pair	3.98	0.20	4.19
gs_volcano	4.14	0.13	4.27
happy_hour	4.91	0.19	5.09
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	2.71	0.09	2.80
shake_enrichrResult	0.09	0.00	0.09
shake_fgseaResult	0.19	0.00	0.19
shake_gprofilerResult	0.09	0.00	0.09
shake_topGOtableResult	0.02	0.00	0.02
styleColorBar_divergent	0.31	0.05	0.44

CHECK report for GeneTonic on tokay1

Summary

Command output

Installation output

Tests output

Example timings