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This page was generated on 2022-01-21 13:07:18 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for ViSEAGO on tokay2


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 2052/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ViSEAGO 1.8.0  (landing page)
Aurelien Brionne
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/ViSEAGO
git_branch: RELEASE_3_14
git_last_commit: c5fd4b9
git_last_commit_date: 2021-10-26 12:52:59 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.8.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ViSEAGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ViSEAGO_1.8.0.tar.gz
StartedAt: 2022-01-21 04:38:57 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 04:43:21 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 264.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ViSEAGO.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ViSEAGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ViSEAGO_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ViSEAGO.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ViSEAGO/DESCRIPTION' ... OK
* this is package 'ViSEAGO' version '1.8.0'
* 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 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 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ViSEAGO.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 12.6Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
available_organisms-methods 0.25   0.16    5.94
** running examples for arch 'x64' ... 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/ViSEAGO.Rcheck/00check.log'
for details.



Installation output

ViSEAGO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ViSEAGO_1.8.0.tar.gz && rm -rf ViSEAGO.buildbin-libdir && mkdir ViSEAGO.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ViSEAGO.buildbin-libdir ViSEAGO_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ViSEAGO_1.8.0.zip && rm ViSEAGO_1.8.0.tar.gz ViSEAGO_1.8.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 27 6608k   27 1833k    0     0  3340k      0  0:00:01 --:--:--  0:00:01 3339k
100 6608k  100 6608k    0     0  4857k      0  0:00:01  0:00:01 --:--:-- 4862k

install for i386

* 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
  converting help for package 'ViSEAGO'
    finding HTML links ... done
    Bioconductor2GO                         html  
    Custom2GO                               html  
    Ensembl2GO                              html  
    EntrezGene2GO                           html  
    EntrezGene_orthologs                    html  
    GO_SS-class                             html  
    GO_clusters-class                       html  
    GOclusters_heatmap-methods              html  
    GOcount-methods                         html  
    GOterms_heatmap-methods                 html  
    MDSplot-methods                         html  
    Uniprot2GO                              html  
    Upset-methods                           html  
    ViSEAGO                                 html  
    annotate-methods                        html  
    available_organisms-methods             html  
    build_GO_SS-methods                     html  
    clusters_cor-methods                    html  
    compare_clusters-methods                html  
    compute_SS_distances-methods            html  
    create_topGOdata-methods                html  
    enrich_GO_terms-class                   html  
    fgsea-class                             html  
    gene2GO-class                           html  
    genomic_ressource-class                 html  
    merge_enrich_terms-methods              html  
    myGOs                                   html  
    overLapper                              html  
    finding level-2 HTML links ... done

    pkgdiagram                              html  
    runfgsea-methods                        html  
    show_heatmap-methods                    html  
    show_table-methods                      html  
    taxonomy                                html  
** 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

install for x64

* installing *source* package 'ViSEAGO' ...
** testing if installed package can be loaded
Warning: replacing previous import 'data.table::set' by 'dendextend::set' when loading 'ViSEAGO'
* MD5 sums
packaged installation of 'ViSEAGO' as ViSEAGO_1.8.0.zip
* DONE (ViSEAGO)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ViSEAGO' successfully unpacked and MD5 sums checked

Tests output


Example timings

ViSEAGO.Rcheck/examples_i386/ViSEAGO-Ex.timings

nameusersystemelapsed
Bioconductor2GO0.040.000.10
Custom2GO0.190.010.21
Ensembl2GO000
EntrezGene2GO000
EntrezGene_orthologs000
GOclusters_heatmap-methods0.040.020.07
GOcount-methods0.830.060.93
GOterms_heatmap-methods0.080.000.08
MDSplot-methods0.060.000.06
Uniprot2GO000
Upset-methods0.990.501.50
annotate-methods000
available_organisms-methods0.250.165.94
build_GO_SS-methods0.070.010.10
clusters_cor-methods0.070.020.07
compare_clusters-methods0.060.000.07
compute_SS_distances-methods0.080.000.07
create_topGOdata-methods0.010.000.16
merge_enrich_terms-methods0.130.024.16
overLapper000
pkgdiagram0.190.090.51
runfgsea-methods0.010.020.03
show_heatmap-methods0.060.010.08
show_table-methods0.380.060.78
taxonomy0.050.020.36

ViSEAGO.Rcheck/examples_x64/ViSEAGO-Ex.timings

nameusersystemelapsed
Bioconductor2GO0.050.020.06
Custom2GO0.130.000.12
Ensembl2GO000
EntrezGene2GO000
EntrezGene_orthologs000
GOclusters_heatmap-methods0.030.010.05
GOcount-methods0.190.050.23
GOterms_heatmap-methods0.040.000.05
MDSplot-methods0.030.000.03
Uniprot2GO000
Upset-methods1.500.031.53
annotate-methods000
available_organisms-methods0.110.020.13
build_GO_SS-methods0.030.000.03
clusters_cor-methods0.040.000.03
compare_clusters-methods0.040.000.05
compute_SS_distances-methods0.030.000.03
create_topGOdata-methods0.020.000.01
merge_enrich_terms-methods0.060.000.07
overLapper000
pkgdiagram0.160.040.20
runfgsea-methods0.030.000.02
show_heatmap-methods0.050.000.04
show_table-methods0.210.030.24
taxonomy0.000.070.40