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This page was generated on 2021-09-22 15:05:16 -0400 (Wed, 22 Sep 2021).

CHECK results for GeneTonic on tokay2

To the developers/maintainers of the GeneTonic package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneTonic.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 730/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 1.4.1  (landing page)
Federico Marini
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: RELEASE_3_13
git_last_commit: 32c4e77
git_last_commit_date: 2021-06-04 17:41:55 -0400 (Fri, 04 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

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: 2021-09-21 23:11:12 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 23:26:58 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 945.9 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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             9.36   0.14    9.50
ggs_backbone           8.61   0.25   12.14
gs_mds                 8.14   0.16    8.30
gs_scoresheat          7.88   0.25    8.13
gs_scores              7.70   0.32    8.04
signature_volcano      7.45   0.25    7.70
ggs_graph              7.42   0.19    7.61
GeneTonic              7.22   0.38    8.20
summarize_ggs_hubgenes 6.70   0.12    6.83
gs_dendro              5.71   0.14    5.85
export_for_iSEE        5.56   0.08    5.64
gs_horizon             5.45   0.08    5.53
gs_radar               5.11   0.36    5.47
gs_alluvial            5.18   0.20    5.39
GeneTonic_list         5.01   0.20    5.22
gene_plot              5.02   0.15    5.17
happy_hour             4.95   0.11    5.06
enhance_table          4.92   0.14    5.07
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
ggs_backbone             7.34   0.38    8.54
gs_heatmap               7.42   0.27    7.69
ggs_graph                7.25   0.19    7.50
GeneTonic                7.12   0.17    7.30
summarize_ggs_hubgenes   7.07   0.20    7.28
gs_mds                   7.12   0.14    7.27
signature_volcano        6.97   0.20    7.17
gs_scores                6.87   0.28    7.16
gs_scoresheat            6.72   0.17    6.90
gs_horizon               5.54   0.17    5.70
gs_dendro                5.40   0.13    5.53
gs_volcano               5.14   0.22    5.45
gs_summary_overview_pair 5.05   0.14    5.19
* 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


Installation output

GeneTonic.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
  0 1831k    0 10675    0     0  67230      0  0:00:27 --:--:--  0:00:27 67138
 55 1831k   55 1020k    0     0   879k      0  0:00:02  0:00:01  0:00:01  878k
100 1831k  100 1831k    0     0   953k      0  0:00:01  0:00:01 --:--:--  953k

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

Tests output

GeneTonic.Rcheck/tests_i386/testthat.Rout


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 
 142.35    9.09  152.50 

GeneTonic.Rcheck/tests_x64/testthat.Rout


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 
 134.53    3.45  142.14 

Example timings

GeneTonic.Rcheck/examples_i386/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic7.220.388.20
GeneTonic_list5.010.205.22
check_colors000
checkup_GeneTonic4.370.164.53
checkup_gtl4.960.045.00
cluster_markov0.090.000.09
create_jaccard_matrix0.750.501.25
create_kappa_matrix2.250.172.42
deseqresult2df0.170.000.18
distill_enrichment4.490.114.59
enhance_table4.920.145.07
enrichment_map4.110.134.24
export_for_iSEE5.560.085.64
export_to_sif0.010.000.02
gene_plot5.020.155.17
geneinfo_2_html000
get_aggrscores4.850.144.98
get_expression_values4.090.164.25
ggs_backbone 8.61 0.2512.14
ggs_graph7.420.197.61
go_2_html0.020.000.01
gs_alluvial5.180.205.39
gs_dendro5.710.145.85
gs_fuzzyclustering1.120.001.12
gs_heatmap9.360.149.50
gs_horizon5.450.085.53
gs_mds8.140.168.30
gs_radar5.110.365.47
gs_scores7.700.328.04
gs_scoresheat7.880.258.13
gs_simplify1.040.021.06
gs_summary_heat4.270.124.39
gs_summary_overview4.530.254.78
gs_summary_overview_pair4.850.134.97
gs_volcano4.760.144.91
happy_hour4.950.115.06
map2color0.020.000.01
overlap_coefficient000
overlap_jaccard_index000
shake_davidResult0.020.000.04
shake_enrichResult3.180.063.25
shake_enrichrResult0.120.000.16
shake_fgseaResult0.240.030.26
shake_gprofilerResult0.150.020.25
shake_topGOtableResult0.020.000.02
signature_volcano7.450.257.70
styleColorBar_divergent0.220.050.27
summarize_ggs_hubgenes6.700.126.83

GeneTonic.Rcheck/examples_x64/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic7.120.177.30
GeneTonic_list4.140.224.36
check_colors000
checkup_GeneTonic4.550.144.69
checkup_gtl4.370.294.67
cluster_markov0.080.000.08
create_jaccard_matrix0.890.040.92
create_kappa_matrix2.640.002.64
deseqresult2df0.130.000.12
distill_enrichment4.110.094.20
enhance_table4.600.194.78
enrichment_map3.820.123.95
export_for_iSEE4.780.134.91
export_to_sif0.020.000.02
gene_plot3.920.204.12
geneinfo_2_html0.020.000.02
get_aggrscores4.400.134.53
get_expression_values3.440.213.65
ggs_backbone7.340.388.54
ggs_graph7.250.197.50
go_2_html0.010.000.02
gs_alluvial3.960.174.13
gs_dendro5.400.135.53
gs_fuzzyclustering0.720.010.73
gs_heatmap7.420.277.69
gs_horizon5.540.175.70
gs_mds7.120.147.27
gs_radar4.310.274.59
gs_scores6.870.287.16
gs_scoresheat6.720.176.90
gs_simplify1.150.001.15
gs_summary_heat4.470.114.58
gs_summary_overview4.390.174.56
gs_summary_overview_pair5.050.145.19
gs_volcano5.140.225.45
happy_hour4.110.174.28
map2color0.010.000.02
overlap_coefficient000
overlap_jaccard_index000
shake_davidResult0.020.000.01
shake_enrichResult3.190.083.27
shake_enrichrResult0.060.000.06
shake_fgseaResult0.120.000.13
shake_gprofilerResult0.100.000.09
shake_topGOtableResult000
signature_volcano6.970.207.17
styleColorBar_divergent0.280.052.48
summarize_ggs_hubgenes7.070.207.28