Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2022-01-26 13:07:23 -0500 (Wed, 26 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" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 simplifyEnrichment on tokay2


To the developers/maintainers of the simplifyEnrichment package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/simplifyEnrichment.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 1803/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simplifyEnrichment 1.4.0  (landing page)
Zuguang Gu
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/simplifyEnrichment
git_branch: RELEASE_3_14
git_last_commit: 549d5f1
git_last_commit_date: 2021-10-26 13:00:10 -0500 (Tue, 26 Oct 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: simplifyEnrichment
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:simplifyEnrichment.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings simplifyEnrichment_1.4.0.tar.gz
StartedAt: 2022-01-26 02:56:04 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 03:00:06 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 241.6 seconds
RetCode: 0
Status:   OK  
CheckDir: simplifyEnrichment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:simplifyEnrichment.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings simplifyEnrichment_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/simplifyEnrichment.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 'simplifyEnrichment/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'simplifyEnrichment' version '1.4.0'
* 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 'simplifyEnrichment' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
ht_clusters 9.04   0.24    9.28
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
ht_clusters 9.65   0.15   10.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.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

simplifyEnrichment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/simplifyEnrichment_1.4.0.tar.gz && rm -rf simplifyEnrichment.buildbin-libdir && mkdir simplifyEnrichment.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=simplifyEnrichment.buildbin-libdir simplifyEnrichment_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL simplifyEnrichment_1.4.0.zip && rm simplifyEnrichment_1.4.0.tar.gz simplifyEnrichment_1.4.0.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
 17 16.7M   17 3037k    0     0  3185k      0  0:00:05 --:--:--  0:00:05 3183k
 46 16.7M   46 7934k    0     0  4073k      0  0:00:04  0:00:01  0:00:03 4073k
 81 16.7M   81 13.6M    0     0  4728k      0  0:00:03  0:00:02  0:00:01 4728k
100 16.7M  100 16.7M    0     0  4993k      0  0:00:03  0:00:03 --:--:-- 4994k

install for i386

* installing *source* package 'simplifyEnrichment' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'simplifyEnrichment'
    finding HTML links ... done
    DO_similarity                           html  
    GO_similarity                           html  
    all_clustering_methods                  html  
    anno_word_cloud                         html  
    anno_word_cloud_from_GO                 html  
    binary_cut                              html  
    cluster_by_MCL                          html  
    cluster_by_apcluster                    html  
    cluster_by_dynamicTreeCut               html  
    cluster_by_hdbscan                      html  
    cluster_by_igraph                       html  
    cluster_by_kmeans                       html  
    cluster_by_mclust                       html  
    cluster_terms                           html  
    cmp_make_clusters                       html  
    cmp_make_plot                           html  
    compare_clustering_methods              html  
    count_word                              html  
    count_word_from_GO                      html  
    dend_node_apply                         html  
    difference_score                        html  
    edit_node                               html  
    export_to_shiny_app                     html  
    guess_ont                               html  
    heightDetails.word_cloud                html  
    ht_clusters                             html  
    partition_by_hclust                     html  
    partition_by_kmeans                     html  
    partition_by_kmeanspp                   html  
    partition_by_pam                        html  
    plot_binary_cut                         html  
    random_DO                               html  
    random_GO                               html  
    register_clustering_methods             html  
    remove_clustering_methods               html  
    reset_clustering_methods                html  
    scale_fontsize                          html  
    select_cutoff                           html  
    simplifyEnrichment                      html  
    simplifyGO                              html  
    simplifyGOFromMultipleLists             html  
    subset_enrichResult                     html  
    term_similarity                         html  
    term_similarity_from_KEGG               html  
    term_similarity_from_MSigDB             html  
    term_similarity_from_Reactome           html  
    term_similarity_from_enrichResult       html  
    term_similarity_from_gmt                html  
    widthDetails.word_cloud                 html  
    word_cloud_grob                         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 'simplifyEnrichment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'simplifyEnrichment' as simplifyEnrichment_1.4.0.zip
* DONE (simplifyEnrichment)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'simplifyEnrichment' successfully unpacked and MD5 sums checked

Tests output

simplifyEnrichment.Rcheck/tests_i386/test-all.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)
> suppressWarnings(suppressPackageStartupMessages(library(simplifyEnrichment)))
> 
> test_check("simplifyEnrichment")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
   9.51    0.54   10.20 

simplifyEnrichment.Rcheck/tests_x64/test-all.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)
> suppressWarnings(suppressPackageStartupMessages(library(simplifyEnrichment)))
> 
> test_check("simplifyEnrichment")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  11.26    0.57   11.89 

Example timings

simplifyEnrichment.Rcheck/examples_i386/simplifyEnrichment-Ex.timings

nameusersystemelapsed
DO_similarity000
GO_similarity000
all_clustering_methods000
anno_word_cloud1.220.161.41
anno_word_cloud_from_GO000
binary_cut1.560.011.58
cluster_by_MCL000
cluster_by_apcluster000
cluster_by_dynamicTreeCut000
cluster_by_hdbscan000
cluster_by_igraph000
cluster_by_kmeans000
cluster_by_mclust000
cluster_terms000
cmp_make_clusters000
cmp_make_plot000
compare_clustering_methods000
count_word0.150.020.15
count_word_from_GO0.140.000.14
dend_node_apply0.010.000.02
difference_score2.000.042.05
edit_node000
export_to_shiny_app1.630.081.70
guess_ont000
heightDetails.word_cloud000
ht_clusters9.040.249.28
partition_by_hclust000
partition_by_kmeans000
partition_by_kmeanspp000
partition_by_pam000
plot_binary_cut000
random_DO000
random_GO000
register_clustering_methods000
remove_clustering_methods000
reset_clustering_methods000
scale_fontsize000
select_cutoff000
simplifyEnrichment000
simplifyGO000
simplifyGOFromMultipleLists000
subset_enrichResult000
term_similarity000
term_similarity_from_KEGG000
term_similarity_from_MSigDB000
term_similarity_from_Reactome000
term_similarity_from_enrichResult000
term_similarity_from_gmt000
widthDetails.word_cloud000
word_cloud_grob0.110.000.11

simplifyEnrichment.Rcheck/examples_x64/simplifyEnrichment-Ex.timings

nameusersystemelapsed
DO_similarity000
GO_similarity000
all_clustering_methods000
anno_word_cloud1.840.031.87
anno_word_cloud_from_GO000
binary_cut1.470.021.49
cluster_by_MCL000
cluster_by_apcluster000
cluster_by_dynamicTreeCut000
cluster_by_hdbscan000
cluster_by_igraph000
cluster_by_kmeans000
cluster_by_mclust000
cluster_terms000
cmp_make_clusters000
cmp_make_plot000
compare_clustering_methods000
count_word0.110.010.13
count_word_from_GO0.110.000.11
dend_node_apply000
difference_score1.510.051.56
edit_node000
export_to_shiny_app1.540.001.53
guess_ont000
heightDetails.word_cloud000
ht_clusters 9.65 0.1510.08
partition_by_hclust000
partition_by_kmeans000
partition_by_kmeanspp000
partition_by_pam000
plot_binary_cut000
random_DO000
random_GO000
register_clustering_methods000
remove_clustering_methods000
reset_clustering_methods000
scale_fontsize000
select_cutoff000
simplifyEnrichment000
simplifyGO000
simplifyGOFromMultipleLists000
subset_enrichResult000
term_similarity000
term_similarity_from_KEGG000
term_similarity_from_MSigDB000
term_similarity_from_Reactome000
term_similarity_from_enrichResult000
term_similarity_from_gmt000
widthDetails.word_cloud000
word_cloud_grob0.130.000.12