Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:23 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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 739/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneTonic 1.6.1  (landing page)
Federico Marini
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/GeneTonic
git_branch: RELEASE_3_14
git_last_commit: c8bf092
git_last_commit_date: 2021-12-01 18:02:34 -0500 (Wed, 01 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.6.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneTonic.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeneTonic_1.6.1.tar.gz
StartedAt: 2022-01-20 20:23:19 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 20:41:10 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 1071.2 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneTonic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneTonic.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeneTonic_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeneTonic.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.6.1'
* 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
GeneTonic                7.24   0.46    7.89
ggs_backbone             7.39   0.27    7.83
gs_heatmap               7.52   0.14    7.67
gs_mds                   7.08   0.11    7.19
ggs_graph                6.84   0.17    7.01
summarize_ggs_hubgenes   6.21   0.22    6.42
export_for_iSEE          6.09   0.16    6.25
gs_scores                6.06   0.17    6.24
signature_volcano        5.74   0.07    5.81
gene_plot                5.45   0.11    5.57
gs_scoresheat            5.39   0.14    5.53
gs_dendro                5.22   0.20    5.42
enhance_table            4.98   0.22    5.22
gs_alluvial              4.85   0.33    5.21
enrichment_map           5.00   0.11    5.11
gs_summary_overview_pair 4.90   0.11    5.02
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
gs_scoresheat          9.58   0.20    9.78
summarize_ggs_hubgenes 8.14   0.29    8.53
gs_heatmap             8.29   0.08    8.36
ggs_backbone           8.06   0.11    8.50
gs_scores              7.89   0.17    8.06
gs_mds                 7.63   0.16    7.78
GeneTonic              7.49   0.13    7.61
ggs_graph              7.00   0.18    7.19
gs_summary_heat        6.26   0.30    6.56
gs_volcano             6.30   0.24    6.53
signature_volcano      6.11   0.22    6.33
gs_dendro              5.86   0.12    5.99
export_for_iSEE        5.78   0.16    5.97
checkup_GeneTonic      5.49   0.13    5.61
GeneTonic_list         5.31   0.23    5.54
checkup_gtl            5.29   0.19    5.49
gs_summary_overview    4.97   0.22    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://155.52.207.166/BBS/3.14/bioc/src/contrib/GeneTonic_1.6.1.tar.gz && rm -rf GeneTonic.buildbin-libdir && mkdir GeneTonic.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneTonic.buildbin-libdir GeneTonic_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GeneTonic_1.6.1.zip && rm GeneTonic_1.6.1.tar.gz GeneTonic_1.6.1.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 1835k    0 14875    0     0   111k      0  0:00:16 --:--:--  0:00:16  111k
100 1835k  100 1835k    0     0  2688k      0 --:--:-- --:--:-- --:--:-- 2687k

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_gsenrichResult                    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_1.6.1.zip
* DONE (GeneTonic)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GeneTonic' successfully unpacked and MD5 sums checked

Tests output

GeneTonic.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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...
--- Running gseGO...
preparing geneSet collections...
GSEA analysis...




leading edge analysis...
done...
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
- Done!
--- Test setup script completed!

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[ FAIL 0 | WARN 2 | SKIP 0 | PASS 243 ]
> 
> proc.time()
   user  system elapsed 
 149.01    8.28  210.67 

GeneTonic.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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...
--- Running gseGO...
preparing geneSet collections...
GSEA analysis...




leading edge analysis...
done...
Found 500 gene sets in `topGOtableResult` object.
Converting for usage in GeneTonic...
- Done!
--- Test setup script completed!

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[ FAIL 0 | WARN 2 | SKIP 0 | PASS 243 ]
> 
> proc.time()
   user  system elapsed 
 152.64    4.79  214.03 

Example timings

GeneTonic.Rcheck/examples_i386/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic7.240.467.89
GeneTonic_list4.620.244.86
check_colors000
checkup_GeneTonic4.730.265.00
checkup_gtl4.370.144.52
cluster_markov0.100.000.09
create_jaccard_matrix0.970.351.32
create_kappa_matrix2.400.152.56
deseqresult2df0.190.000.19
distill_enrichment4.740.194.92
enhance_table4.980.225.22
enrichment_map5.000.115.11
export_for_iSEE6.090.166.25
export_to_sif0.020.000.01
gene_plot5.450.115.57
geneinfo_2_html0.020.000.01
get_aggrscores4.620.124.75
get_expression_values4.080.204.28
ggs_backbone7.390.277.83
ggs_graph6.840.177.01
go_2_html0.030.000.03
gs_alluvial4.850.335.21
gs_dendro5.220.205.42
gs_fuzzyclustering0.700.000.71
gs_heatmap7.520.147.67
gs_horizon4.750.104.85
gs_mds7.080.117.19
gs_radar4.300.094.39
gs_scores6.060.176.24
gs_scoresheat5.390.145.53
gs_simplify0.990.000.99
gs_summary_heat4.390.074.45
gs_summary_overview4.660.124.78
gs_summary_overview_pair4.900.115.02
gs_volcano4.410.094.50
happy_hour4.400.114.51
map2color0.020.000.02
overlap_coefficient000
overlap_jaccard_index000
shake_davidResult0.020.000.03
shake_enrichResult2.710.032.75
shake_enrichrResult0.080.000.13
shake_fgseaResult0.170.000.17
shake_gprofilerResult0.240.020.50
shake_gsenrichResult2.480.142.62
shake_topGOtableResult0.000.020.02
signature_volcano5.740.075.81
styleColorBar_divergent0.280.020.29
summarize_ggs_hubgenes6.210.226.42

GeneTonic.Rcheck/examples_x64/GeneTonic-Ex.timings

nameusersystemelapsed
GeneTonic7.490.137.61
GeneTonic_list5.310.235.54
check_colors0.010.000.01
checkup_GeneTonic5.490.135.61
checkup_gtl5.290.195.49
cluster_markov0.100.000.09
create_jaccard_matrix0.920.060.99
create_kappa_matrix3.220.033.25
deseqresult2df0.140.000.14
distill_enrichment4.320.124.44
enhance_table4.470.114.58
enrichment_map4.690.114.80
export_for_iSEE5.780.165.97
export_to_sif0.030.000.03
gene_plot4.300.194.48
geneinfo_2_html000
get_aggrscores4.750.114.86
get_expression_values3.280.173.46
ggs_backbone8.060.118.50
ggs_graph7.000.187.19
go_2_html0.020.000.01
gs_alluvial4.140.154.36
gs_dendro5.860.125.99
gs_fuzzyclustering0.750.000.75
gs_heatmap8.290.088.36
gs_horizon4.010.094.11
gs_mds7.630.167.78
gs_radar3.790.254.05
gs_scores7.890.178.06
gs_scoresheat9.580.209.78
gs_simplify1.390.001.45
gs_summary_heat6.260.306.56
gs_summary_overview4.970.225.19
gs_summary_overview_pair4.690.204.89
gs_volcano6.300.246.53
happy_hour4.300.144.44
map2color0.010.000.02
overlap_coefficient000
overlap_jaccard_index000
shake_davidResult0.020.000.01
shake_enrichResult2.170.172.35
shake_enrichrResult0.10.00.1
shake_fgseaResult0.230.000.23
shake_gprofilerResult0.160.010.17
shake_gsenrichResult2.260.082.35
shake_topGOtableResult0.000.020.01
signature_volcano6.110.226.33
styleColorBar_divergent0.220.040.26
summarize_ggs_hubgenes8.140.298.53