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This page was generated on 2022-01-27 11:08:02 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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 riesling1


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 1800/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simplifyEnrichment 1.5.2  (landing page)
Zuguang Gu
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/simplifyEnrichment
git_branch: master
git_last_commit: 75f5d20
git_last_commit_date: 2021-12-01 17:19:09 -0500 (Wed, 01 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'BiocGenerics' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: simplifyEnrichment
Version: 1.5.2
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:simplifyEnrichment.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings simplifyEnrichment_1.5.2.tar.gz
StartedAt: 2022-01-26 20:09:02 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 20:17:23 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 501.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: simplifyEnrichment.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:simplifyEnrichment.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings simplifyEnrichment_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/simplifyEnrichment.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.5.2'
* 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 ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   5.9Mb
* 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
* 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 ... WARNING
'::' or ':::' import not declared from: 'stopwords'
Unexported object imported by a ':::' call: 'clusterProfiler:::get_GO_data'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
all_GO_word_count : <anonymous>: no visible global function definition
  for 'count_word'
import_pathway_common: no visible global function definition for
  'download.file'
import_pathway_common: no visible global function definition for
  'read.table'
import_pathway_common : <anonymous>: no visible global function
  definition for 'graph.edgelist'
reach: no visible global function definition for 'E'
reach: no visible global function definition for 'shortest.paths'
simplifyPathway: no visible binding for global variable 'term_id'
simplifyPathway: no visible global function definition for
  'get_gene_desc_from_PANTHER'
simplifyPathway: no visible global function definition for
  'get_gene_desc_from_PathBank'
simplifyPathway: no visible binding for global variable 'go_id'
spread: no visible global function definition for 'E'
spread: no visible global function definition for 'shortest.paths'
Undefined global functions or variables:
  E count_word download.file get_gene_desc_from_PANTHER
  get_gene_desc_from_PathBank go_id graph.edgelist read.table
  shortest.paths term_id
Consider adding
  importFrom("utils", "download.file", "read.table")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
ht_clusters 327.83   13.7  341.56
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 1 WARNING, 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/simplifyEnrichment.Rcheck/00check.log'
for details.



Installation output

simplifyEnrichment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL simplifyEnrichment
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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  
    area_above_ecdf                         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_by_pam                          html  
    cluster_terms                           html  
    cmp_make_clusters                       html  
    cmp_make_plot                           html  
    compare_clustering_methods              html  
    count_words                             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  
    keyword_enrichment_from_GO              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  
    se_opt                                  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
* DONE (simplifyEnrichment)
Making 'packages.html' ... done

Tests output

simplifyEnrichment.Rcheck/tests/test-all.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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 
   7.57    0.57    8.15 

Example timings

simplifyEnrichment.Rcheck/simplifyEnrichment-Ex.timings

nameusersystemelapsed
DO_similarity000
GO_similarity000
all_clustering_methods000
anno_word_cloud2.360.112.47
anno_word_cloud_from_GO000
area_above_ecdf000
binary_cut1.550.031.58
cluster_by_MCL0.010.000.01
cluster_by_apcluster000
cluster_by_dynamicTreeCut000
cluster_by_hdbscan000
cluster_by_igraph000
cluster_by_kmeans000
cluster_by_mclust000
cluster_by_pam000
cluster_terms000
cmp_make_clusters000
cmp_make_plot000
compare_clustering_methods000
count_words0.570.000.56
dend_node_apply000
difference_score1.890.031.93
edit_node000
export_to_shiny_app000
guess_ont000
heightDetails.word_cloud000
ht_clusters327.83 13.70341.56
keyword_enrichment_from_GO000
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
se_opt000
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_grob0.10.00.1