Zuguang Gu
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 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 -0400 (Wed, 01 Dec 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:42 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 1811/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| simplifyEnrichment 1.5.2 (landing page) Zuguang Gu
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| 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: 2022-03-17 20:18:22 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:27:13 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 530.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: simplifyEnrichment.Rcheck |
| Warnings: 1 |
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###
### 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
###
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* 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 346.55 9.33 355.89
* 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.
simplifyEnrichment.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL simplifyEnrichment
###
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* 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' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'RUVcorr' is missing or broken
done
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
8.54 0.64 9.17
simplifyEnrichment.Rcheck/simplifyEnrichment-Ex.timings
| name | user | system | elapsed | |
| DO_similarity | 0 | 0 | 0 | |
| GO_similarity | 0 | 0 | 0 | |
| all_clustering_methods | 0 | 0 | 0 | |
| anno_word_cloud | 1.80 | 0.08 | 1.87 | |
| anno_word_cloud_from_GO | 0 | 0 | 0 | |
| area_above_ecdf | 0 | 0 | 0 | |
| binary_cut | 1.33 | 0.00 | 1.33 | |
| cluster_by_MCL | 0 | 0 | 0 | |
| cluster_by_apcluster | 0 | 0 | 0 | |
| cluster_by_dynamicTreeCut | 0 | 0 | 0 | |
| cluster_by_hdbscan | 0 | 0 | 0 | |
| cluster_by_igraph | 0 | 0 | 0 | |
| cluster_by_kmeans | 0 | 0 | 0 | |
| cluster_by_mclust | 0 | 0 | 0 | |
| cluster_by_pam | 0 | 0 | 0 | |
| cluster_terms | 0 | 0 | 0 | |
| cmp_make_clusters | 0 | 0 | 0 | |
| cmp_make_plot | 0 | 0 | 0 | |
| compare_clustering_methods | 0 | 0 | 0 | |
| count_words | 0.33 | 0.01 | 0.34 | |
| dend_node_apply | 0 | 0 | 0 | |
| difference_score | 1.28 | 0.00 | 1.28 | |
| edit_node | 0 | 0 | 0 | |
| export_to_shiny_app | 0 | 0 | 0 | |
| guess_ont | 0 | 0 | 0 | |
| heightDetails.word_cloud | 0 | 0 | 0 | |
| ht_clusters | 346.55 | 9.33 | 355.89 | |
| keyword_enrichment_from_GO | 0 | 0 | 0 | |
| partition_by_hclust | 0 | 0 | 0 | |
| partition_by_kmeans | 0 | 0 | 0 | |
| partition_by_kmeanspp | 0 | 0 | 0 | |
| partition_by_pam | 0 | 0 | 0 | |
| plot_binary_cut | 0 | 0 | 0 | |
| random_DO | 0 | 0 | 0 | |
| random_GO | 0 | 0 | 0 | |
| register_clustering_methods | 0 | 0 | 0 | |
| remove_clustering_methods | 0 | 0 | 0 | |
| reset_clustering_methods | 0 | 0 | 0 | |
| scale_fontsize | 0 | 0 | 0 | |
| se_opt | 0 | 0 | 0 | |
| select_cutoff | 0 | 0 | 0 | |
| simplifyEnrichment | 0 | 0 | 0 | |
| simplifyGO | 0 | 0 | 0 | |
| simplifyGOFromMultipleLists | 0 | 0 | 0 | |
| subset_enrichResult | 0 | 0 | 0 | |
| term_similarity | 0 | 0 | 0 | |
| term_similarity_from_KEGG | 0 | 0 | 0 | |
| term_similarity_from_MSigDB | 0 | 0 | 0 | |
| term_similarity_from_Reactome | 0 | 0 | 0 | |
| term_similarity_from_enrichResult | 0 | 0 | 0 | |
| term_similarity_from_gmt | 0 | 0 | 0 | |
| widthDetails.word_cloud | 0 | 0 | 0 | |
| word_cloud_grob | 0.08 | 0.02 | 0.09 | |