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CHECK report for ViSEAGO on tokay2

This page was generated on 2020-10-17 11:57:59 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ViSEAGO PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1876/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ViSEAGO 1.2.0
Aurelien Brionne
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ViSEAGO
Branch: RELEASE_3_11
Last Commit: 22f848a
Last Changed Date: 2020-04-27 15:28:30 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR  OK 

Summary

Package: ViSEAGO
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ViSEAGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ViSEAGO_1.2.0.tar.gz
StartedAt: 2020-10-17 09:13:18 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 09:18:25 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 307.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ViSEAGO.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ViSEAGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ViSEAGO_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ViSEAGO.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.2.0'
* 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 ... OK
* checking installed package size ... OK
* 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.
* 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 : <anonymous>: 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'
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 : <anonymous> : esummary : <anonymous>: no
  visible binding for global variable 'start'
merge_enrich_terms,list : <anonymous> : esummary : <anonymous>: no
  visible binding for global variable 'end'
Undefined global functions or variables:
  . ENTREZID EVIDENCE GO GO.ID IC N ONTOLOGY end start text
Consider adding
  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 ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/ViSEAGO.Rcheck/00check.log'
for details.



Installation output

ViSEAGO.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ViSEAGO_1.2.0.tar.gz && rm -rf ViSEAGO.buildbin-libdir && mkdir ViSEAGO.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ViSEAGO.buildbin-libdir ViSEAGO_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ViSEAGO_1.2.0.zip && rm ViSEAGO_1.2.0.tar.gz ViSEAGO_1.2.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2225k  100 2225k    0     0  25.1M      0 --:--:-- --:--:-- --:--:-- 27.5M

install for i386

* installing *source* package 'ViSEAGO' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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  
    gene2GO-class                           html  
    genomic_ressource-class                 html  
    merge_enrich_terms-methods              html  
    myGOs                                   html  
    overLapper                              html  
    finding level-2 HTML links ... done

    pkgdiagram                              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
** testing if installed package can be loaded from final location
** 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
* MD5 sums
packaged installation of 'ViSEAGO' as ViSEAGO_1.2.0.zip
* DONE (ViSEAGO)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ViSEAGO' successfully unpacked and MD5 sums checked

Tests output


Example timings

ViSEAGO.Rcheck/examples_i386/ViSEAGO-Ex.timings

nameusersystemelapsed
Bioconductor2GO0.080.020.24
Custom2GO0.190.000.19
Ensembl2GO000
EntrezGene2GO000
EntrezGene_orthologs000
GOclusters_heatmap-methods0.090.020.11
GOcount-methods0.750.030.96
GOterms_heatmap-methods0.140.000.14
MDSplot-methods0.110.010.13
Uniprot2GO0.000.020.92
Upset-methods0.560.200.81
annotate-methods000
available_organisms-methods0.130.070.48
build_GO_SS-methods0.150.010.18
clusters_cor-methods0.110.000.11
compare_clusters-methods0.090.020.11
compute_SS_distances-methods0.090.000.09
create_topGOdata-methods0.020.000.02
merge_enrich_terms-methods0.010.000.01
overLapper000
pkgdiagram0.200.111.06
show_heatmap-methods0.130.000.13
show_table-methods0.390.111.30
taxonomy0.000.010.23

ViSEAGO.Rcheck/examples_x64/ViSEAGO-Ex.timings

nameusersystemelapsed
Bioconductor2GO0.070.000.06
Custom2GO0.120.010.14
Ensembl2GO000
EntrezGene2GO000
EntrezGene_orthologs000
GOclusters_heatmap-methods0.040.020.06
GOcount-methods0.600.050.74
GOterms_heatmap-methods0.110.000.11
MDSplot-methods0.100.000.09
Uniprot2GO0.000.010.77
Upset-methods0.740.061.23
annotate-methods000
available_organisms-methods0.120.040.19
build_GO_SS-methods0.130.000.12
clusters_cor-methods0.110.000.11
compare_clusters-methods0.110.000.11
compute_SS_distances-methods0.090.010.11
create_topGOdata-methods0.010.000.02
merge_enrich_terms-methods0.020.000.01
overLapper000
pkgdiagram0.220.130.89
show_heatmap-methods0.080.030.11
show_table-methods0.360.041.14
taxonomy0.010.020.21