Aurelien Brionne
| Snapshot Date: 2025-10-29 19:52 -0400 (Wed, 29 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/ViSEAGO |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9020dee |
| git_last_commit_date: 2025-10-29 10:53:03 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-30 12:36 -0400 (Thu, 30 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 | ||||
| Package 2319/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ViSEAGO 1.24.0 (landing page) Aurelien Brionne
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the ViSEAGO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ViSEAGO.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ViSEAGO |
| Version: 1.24.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ViSEAGO_1.24.0.tar.gz |
| StartedAt: 2025-10-30 07:40:00 -0400 (Thu, 30 Oct 2025) |
| EndedAt: 2025-10-30 07:43:48 -0400 (Thu, 30 Oct 2025) |
| EllapsedTime: 227.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ViSEAGO.Rcheck |
| Warnings: 4 |
##############################################################################
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ViSEAGO_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ViSEAGO.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ViSEAGO/DESCRIPTION’ ... OK
* this is package ‘ViSEAGO’ version ‘1.24.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ViSEAGO’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’
Warning: replacing previous import ‘dendextend::cutree’ by ‘stats::cutree’ when loading ‘ViSEAGO’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ViSEAGO’
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/ViSEAGO.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
installed size is 12.4Mb
sub-directories of 1Mb or more:
extdata 10.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
GPL-3 bioconductor.org
Standardizable: FALSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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
'library' or 'require' call not declared from: ‘topGO’
'library' or 'require' call to ‘topGO’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GOterms_heatmap,GO_SS: no visible binding for global variable ‘GO.ID’
MDSplot,ANY: no visible binding for global variable ‘GO.cluster’
annotate,character-genomic_ressource: no visible global function
definition for ‘.’
annotate,character-genomic_ressource: no visible binding for global
variable ‘ENTREZID’
annotate,character-genomic_ressource: no visible binding for global
variable ‘EVIDENCE’
annotate,character-genomic_ressource: no visible binding for global
variable ‘ONTOLOGY’
compute_SS_distances,ANY-character: no visible binding for global
variable ‘N’
compute_SS_distances,ANY-character: no visible binding for global
variable ‘IC’
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable ‘pval’
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable ‘pathway’
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable ‘Id’
merge_enrich_terms,list : <anonymous>: no visible global function
definition for ‘.’
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable ‘padj’
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable ‘nMoreExtreme’
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable ‘ES’
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable ‘NES’
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable ‘size’
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable ‘genes_frequency’
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable ‘log2err’
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable ‘leadingEdge’
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable ‘Significant_genes’
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable ‘GO.ID’
runfgsea,ANY-gene2GO-character: no visible binding for global variable
‘genes_frequency’
runfgsea,ANY-gene2GO-character: no visible binding for global variable
‘leadingEdge’
runfgsea,ANY-gene2GO-character: no visible binding for global variable
‘size’
runfgsea,ANY-gene2GO-character: no visible binding for global variable
‘pathway’
Undefined global functions or variables:
. ENTREZID ES EVIDENCE GO.ID GO.cluster IC Id N NES ONTOLOGY
Significant_genes genes_frequency leadingEdge log2err nMoreExtreme
padj pathway pval size
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
overLapper.Rd: upset
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
myGOs.RData 876Kb 517Kb xz
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/ViSEAGO.Rcheck/00check.log’
for details.
ViSEAGO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ViSEAGO ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘ViSEAGO’ ... ** this is package ‘ViSEAGO’ version ‘1.24.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘dendextend::cutree’ by ‘stats::cutree’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ViSEAGO’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘dendextend::cutree’ by ‘stats::cutree’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ViSEAGO’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘dendextend::cutree’ by ‘stats::cutree’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ViSEAGO’ ** testing if installed package keeps a record of temporary installation path * DONE (ViSEAGO)
ViSEAGO.Rcheck/ViSEAGO-Ex.timings
| name | user | system | elapsed | |
| Bioconductor2GO | 0.041 | 0.004 | 0.046 | |
| Custom2GO | 0.000 | 0.000 | 0.001 | |
| Ensembl2GO | 0.000 | 0.000 | 0.001 | |
| EntrezGene2GO | 0.000 | 0.000 | 0.001 | |
| EntrezGene_orthologs | 0.000 | 0.000 | 0.001 | |
| GOclusters_heatmap-methods | 0.048 | 0.005 | 0.054 | |
| GOcount-methods | 0.220 | 0.053 | 0.284 | |
| GOterms_heatmap-methods | 0.034 | 0.002 | 0.036 | |
| MDSplot-methods | 0.037 | 0.003 | 0.041 | |
| Uniprot2GO | 0 | 0 | 0 | |
| Upset-methods | 2.779 | 0.157 | 2.946 | |
| annotate-methods | 0.000 | 0.001 | 0.001 | |
| available_organisms-methods | 0.098 | 0.034 | 0.141 | |
| build_GO_SS-methods | 0.038 | 0.002 | 0.039 | |
| clusters_cor-methods | 0.037 | 0.003 | 0.040 | |
| compare_clusters-methods | 0.030 | 0.003 | 0.033 | |
| compute_SS_distances-methods | 0.036 | 0.002 | 0.038 | |
| create_topGOdata-methods | 0.016 | 0.003 | 0.019 | |
| merge_enrich_terms-methods | 0.083 | 0.026 | 0.143 | |
| overLapper | 0.001 | 0.000 | 0.001 | |
| pkgdiagram | 0.111 | 0.103 | 0.227 | |
| runfgsea-methods | 0.022 | 0.002 | 0.025 | |
| show_heatmap-methods | 0.036 | 0.003 | 0.040 | |
| show_table-methods | 0.191 | 0.038 | 0.236 | |
| taxonomy | 0.020 | 0.004 | 0.223 | |