Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 2298/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ViSEAGO 1.22.0  (landing page)
Aurelien Brionne
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/ViSEAGO
git_branch: RELEASE_3_21
git_last_commit: 7d2965b
git_last_commit_date: 2025-04-15 11:47:53 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  

CHECK results for ViSEAGO on nebbiolo1

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.

raw results


Summary

Package: ViSEAGO
Version: 1.22.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ViSEAGO_1.22.0.tar.gz
StartedAt: 2025-10-16 04:46:17 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 04:50:28 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 251.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ViSEAGO.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ViSEAGO_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ViSEAGO.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ViSEAGO/DESCRIPTION’ ... OK
* this is package ‘ViSEAGO’ version ‘1.22.0’
* 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/ViSEAGO.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is 10.3Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ViSEAGO.Rcheck/00check.log’
for details.

Installation output

ViSEAGO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ViSEAGO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘ViSEAGO’ ...
** this is package ‘ViSEAGO’ version ‘1.22.0’
** 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)

Tests output


Example timings

ViSEAGO.Rcheck/ViSEAGO-Ex.timings

nameusersystemelapsed
Bioconductor2GO0.0260.0040.032
Custom2GO0.0000.0010.000
Ensembl2GO000
EntrezGene2GO000
EntrezGene_orthologs000
GOclusters_heatmap-methods0.0390.0050.043
GOcount-methods0.1790.0200.199
GOterms_heatmap-methods0.0350.0010.036
MDSplot-methods0.0330.0030.036
Uniprot2GO0.0000.0000.001
Upset-methods2.5260.1862.698
annotate-methods0.0000.0010.000
available_organisms-methods0.0820.0080.091
build_GO_SS-methods0.0340.0010.036
clusters_cor-methods0.0370.0010.038
compare_clusters-methods0.0350.0020.038
compute_SS_distances-methods0.0350.0030.037
create_topGOdata-methods0.0090.0030.014
merge_enrich_terms-methods0.1050.0170.104
overLapper000
pkgdiagram0.0980.0280.122
runfgsea-methods0.0200.0010.013
show_heatmap-methods0.0420.0010.037
show_table-methods0.1590.0100.167
taxonomy0.0600.0020.236