##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAnswers.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeneAnswers_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneAnswers/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneAnswers' version '2.36.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'igraph', 'KEGGREST', 'RCurl', 'annotate', 'Biobase', 'XML',
  'RSQLite', 'MASS', 'Heatplus', 'RColorBrewer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'GeneAnswers' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'GeneAnswers' is deprecated and will be removed from
  Warning: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers'
  Warning: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers'
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 34.7Mb
  sub-directories of 1Mb or more:
    External  32.4Mb
    data       1.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'annotate'
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'Biobase' 'Heatplus' 'KEGGREST' 'MASS' 'RColorBrewer' 'XML' 'igraph'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'GO.db' 'biomaRt' 'reactome.db'
  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
File 'GeneAnswers/R/zzz.R':
  .onLoad calls:
    require(Biobase)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

getHomoGeneIDs: no visible global function definition for 'useMart'
getHomoGeneIDs: no visible global function definition for 'getLDS'
getTotalGeneNumber: no visible global function definition for
  'count.mappedkeys'
getTotalGeneNumber: no visible binding for global variable
  'reactomePATHNAME2ID'
Undefined global functions or variables:
  count.mappedkeys getLDS reactomePATHNAME2ID useMart
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'queryKegg'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
getConceptTable            289.33   0.86  444.31
groupReport                285.22   0.37  434.27
drawTable                  283.03   0.55  436.13
geneAnswersReadable         47.89   0.33   48.23
GeneAnswers-class           35.03   1.98   43.69
geneAnswersSort             31.55   0.09   31.64
geneAnswersConcepts         29.94   0.25   30.42
geneAnswersHeatmap          29.44   0.64   30.08
buildNet                    29.25   0.20   29.45
geneAnswersConceptRelation  28.79   0.61   29.40
geneAnswersConceptNet       28.82   0.29   29.11
GeneAnswers-package         28.13   0.83   28.95
getMultiLayerGraphIDs       28.37   0.39   28.77
geneAnswersHomoMapping      27.65   0.30   27.96
geneAnswersBuilder          26.50   0.65   27.15
getConnectedGraph           26.66   0.37   27.06
geneAnswersChartPlots       26.81   0.07   26.88
getGOList                   18.38   1.56  670.08
getPATHList                  5.22   0.00    9.20
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
drawTable                  323.72   0.52  492.13
groupReport                311.47   0.34  471.00
getConceptTable            309.96   0.62  500.28
geneAnswersReadable         49.35   0.25   49.59
GeneAnswers-class           28.53   0.89   29.42
geneAnswersBuilder          28.94   0.28   29.22
geneAnswersSort             28.67   0.03   28.70
buildNet                    27.00   0.01   27.03
geneAnswersHomoMapping      26.94   0.05   26.99
geneAnswersHeatmap          26.68   0.02   26.70
getConnectedGraph           26.43   0.25   26.69
geneAnswersConceptRelation  26.53   0.05   26.61
geneAnswersChartPlots       25.69   0.06   25.75
geneAnswersConceptNet       25.30   0.22   25.51
geneAnswersConcepts         25.48   0.01   25.53
getMultiLayerGraphIDs       24.70   0.11   24.84
GeneAnswers-package         24.69   0.11   24.80
getGOList                   14.39   0.22   14.63
getPATHList                  5.55   0.00    9.96
* 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: 2 WARNINGs, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck/00check.log'
for details.