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This page was generated on 2021-09-20 15:06:02 -0400 (Mon, 20 Sep 2021).

CHECK results for ViSEAGO on machv2

To the developers/maintainers of the ViSEAGO package:
- Please 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 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 2008/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ViSEAGO 1.6.0  (landing page)
Aurelien Brionne
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/ViSEAGO
git_branch: RELEASE_3_13
git_last_commit: 320ba38
git_last_commit_date: 2021-05-19 12:44:50 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ViSEAGO
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ViSEAGO_1.6.0.tar.gz
StartedAt: 2021-09-20 01:08:25 -0400 (Mon, 20 Sep 2021)
EndedAt: 2021-09-20 01:12:34 -0400 (Mon, 20 Sep 2021)
EllapsedTime: 248.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ViSEAGO.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ViSEAGO_1.6.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ViSEAGO.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ViSEAGO/DESCRIPTION’ ... OK
* this is package ‘ViSEAGO’ version ‘1.6.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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:
  Note: possible error in 'listEnsembl(host = host, ': unused argument (host = host) 
  Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’
See ‘/Users/biocbuild/bbs-3.13-bioc/meat/ViSEAGO.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 ... 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
'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'
Ensembl2GO: possible error in listEnsembl(host = host, version =
  version): unused argument (host = host)
GOcount,ANY: no visible global function definition for ‘orca’
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’
MDSplot,ANY: no visible global function definition for ‘orca’
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’
show_heatmap,GO_clusters-character: no visible global function
  definition for ‘orca’
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 orca 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: 3 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/ViSEAGO.Rcheck/00check.log’
for details.



Installation output

ViSEAGO.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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’
Note: possible error in 'listEnsembl(host = host, ': unused argument (host = host) 
** 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
Bioconductor2GO0.0510.0040.056
Custom2GO0.2360.0100.247
Ensembl2GO0.0000.0010.001
EntrezGene2GO0.0000.0000.001
EntrezGene_orthologs000
GOclusters_heatmap-methods0.0880.0030.091
GOcount-methods0.2870.0420.331
GOterms_heatmap-methods0.0810.0020.084
MDSplot-methods0.0600.0020.063
Uniprot2GO0.0010.0000.001
Upset-methods2.3240.0592.393
annotate-methods0.0000.0010.002
available_organisms-methods0.1580.0450.206
build_GO_SS-methods0.0620.0020.063
clusters_cor-methods0.0530.0040.057
compare_clusters-methods0.0430.0030.047
compute_SS_distances-methods0.0470.0020.049
create_topGOdata-methods0.0160.0020.020
merge_enrich_terms-methods0.0880.0210.127
overLapper000
pkgdiagram0.1730.1380.315
runfgsea-methods0.0230.0020.025
show_heatmap-methods0.0570.0040.060
show_table-methods0.3410.0660.411
taxonomy0.0180.0030.371