Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

This page was generated on 2024-03-04 11:38:00 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 2231/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ViSEAGO 1.16.0  (landing page)
Aurelien Brionne
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/ViSEAGO
git_branch: RELEASE_3_18
git_last_commit: 21e6693
git_last_commit_date: 2023-10-24 11:15:09 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for ViSEAGO on lconway


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: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2024-03-04 00:09:26 -0500 (Mon, 04 Mar 2024)
EndedAt: 2024-03-04 00:12:58 -0500 (Mon, 04 Mar 2024)
EllapsedTime: 211.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ViSEAGO.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/ViSEAGO.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ViSEAGO/DESCRIPTION’ ... OK
* this is package ‘ViSEAGO’ version ‘1.16.0’
* 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 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’
See ‘/Users/biocbuild/bbs-3.18-bioc/meat/ViSEAGO.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 12.3Mb
  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 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
'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.
Namespace in Imports field not imported from: ‘processx’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotate,character-genomic_ressource: warning in getBM(attributes =
  c("ensembl_gene_id", "go_id", "go_linkage_type", "namespace_1003"),
  filters = unlist(go_filter[grep("with GO ID", ignore.case = TRUE,
  go_filter$description), "name", with = FALSE]), value = TRUE, mart =
  myspecies): partial argument match of 'value' to 'values'
compute_SS_distances,ANY-character: warning in select(GO.db, keys =
  onto$values, column = "TERM"): partial argument match of 'column' to
  'columns'
merge_enrich_terms,list : genes_symbols_add: warning in
  getBM(attributes = c("ensembl_gene_id", "external_gene_name"), value
  = TRUE, mart = myspecies): partial argument match of 'value' to
  'values'
GOterms_heatmap,GO_SS: no visible binding for global variable ‘GO.ID’
MDSplot,ANY: no visible binding for global variable ‘text’
MDSplot,ANY: no visible binding for global variable ‘GO.cluster’
Upset,ANY: no visible global function definition for ‘png’
Upset,ANY: no visible global function definition for ‘dev.off’
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 ‘GO’
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 : genes_symbols_add : esummary : <anonymous>:
  no visible binding for global variable ‘start’
merge_enrich_terms,list : genes_symbols_add : esummary : <anonymous>:
  no visible binding for global variable ‘end’
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 GO.ID GO.cluster IC Id N NES ONTOLOGY
  Significant_genes dev.off end genes_frequency leadingEdge log2err
  nMoreExtreme padj pathway png pval size start text
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "text")
  importFrom("stats", "end", "start")
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 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 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: 4 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/ViSEAGO.Rcheck/00check.log’
for details.



Installation output

ViSEAGO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ViSEAGO
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘ViSEAGO’ ...
** 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’
** 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’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ 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
Bioconductor2GO0.0380.0040.043
Custom2GO0.1620.0090.173
Ensembl2GO0.0000.0000.001
EntrezGene2GO000
EntrezGene_orthologs0.0000.0000.001
GOclusters_heatmap-methods0.0450.0030.047
GOcount-methods0.3270.0520.384
GOterms_heatmap-methods0.0370.0020.039
MDSplot-methods0.0390.0020.041
Uniprot2GO000
Upset-methods2.0260.1402.147
annotate-methods0.0010.0010.002
available_organisms-methods0.0930.0340.139
build_GO_SS-methods0.0280.0010.029
clusters_cor-methods0.0440.0020.047
compare_clusters-methods0.0390.0020.042
compute_SS_distances-methods0.0400.0020.042
create_topGOdata-methods0.0140.0030.018
merge_enrich_terms-methods0.0780.0250.139
overLapper0.0000.0010.000
pkgdiagram0.1000.0900.193
runfgsea-methods0.0200.0020.023
show_heatmap-methods0.0430.0030.046
show_table-methods0.2000.0380.245
taxonomy0.0180.0050.292