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CHECK report for GeneAnswers on machv2

This page was generated on 2021-05-10 12:14:36 -0400 (Mon, 10 May 2021).

To the developers/maintainers of the GeneAnswers package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 700/2016HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneAnswers 2.33.0  (landing page)
Lei Huang and Gang Feng
Snapshot Date: 2021-05-09 14:50:05 -0400 (Sun, 09 May 2021)
URL: https://git.bioconductor.org/packages/GeneAnswers
Branch: master
Last Commit: 02ac664
Last Changed Date: 2021-03-01 21:20:41 -0400 (Mon, 01 Mar 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: GeneAnswers
Version: 2.33.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneAnswers.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneAnswers_2.33.0.tar.gz
StartedAt: 2021-05-10 02:37:32 -0400 (Mon, 10 May 2021)
EndedAt: 2021-05-10 03:04:35 -0400 (Mon, 10 May 2021)
EllapsedTime: 1622.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GeneAnswers.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneAnswers.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneAnswers_2.33.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/GeneAnswers.Rcheck’
* using R version 4.1.0 alpha (2021-04-29 r80247)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneAnswers/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneAnswers’ version ‘2.33.0’
* 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 ... 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 ‘GeneAnswers’ can be installed ... WARNING
Found the following significant warnings:
  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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/GeneAnswers.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 34.2Mb
  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
* 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 global function definition for ‘toTable’
getTotalGeneNumber: no visible binding for global variable
  ‘reactomePATHNAME2ID’
Undefined global functions or variables:
  count.mappedkeys getLDS reactomePATHNAME2ID toTable 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GeneAnswers-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getPATHTerms
> ### Title: Get Pathway names of given KEGG IDs
> ### Aliases: getPATHTerms
> ### Keywords: methods
> 
> ### ** Examples
> 
> getPATHTerms(c('04916', '05221'))
Error in names(temp) <- sapply(temp, function(x) return(x$ENTRY)) : 
  attempt to set an attribute on NULL
Calls: getPATHTerms -> lapply -> queryKegg
Execution halted
* 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 ERROR, 2 WARNINGs, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/GeneAnswers.Rcheck/00check.log’
for details.


Installation output

GeneAnswers.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneAnswers
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘GeneAnswers’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’
Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’
Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’
Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’
** testing if installed package keeps a record of temporary installation path
* DONE (GeneAnswers)

Tests output


Example timings

GeneAnswers.Rcheck/GeneAnswers-Ex.timings

nameusersystemelapsed
DO0.4160.0080.424
DOLite0.0320.0030.035
DOLiteTerm0.0030.0020.005
DmIALite0.0870.0030.091
GeneAnswers-class39.725 1.91041.826
GeneAnswers-package38.211 1.04639.313
HsIALite0.2700.0080.278
MmIALite0.0160.0070.023
RnIALite0.0090.0080.018
buildNet37.835 0.82738.733
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.0630.0280.120
drawTable299.100 1.623426.192
entrez2caBIO0.0000.0000.001
geneAnnotationHeatmap0.0030.0010.003
geneAnswersBuilder37.452 0.61738.132
geneAnswersChartPlots36.897 0.46837.432
geneAnswersConceptNet35.876 0.73536.694
geneAnswersConceptRelation34.018 0.39234.457
geneAnswersConcepts33.829 0.60734.558
geneAnswersHeatmap32.710 0.68533.512
geneAnswersHomoMapping37.159 0.87038.663
geneAnswersReadable69.024 1.48870.738
geneAnswersSort34.633 0.60935.338
geneConceptNet0.0000.0000.001
getCategoryList0.1570.0220.181
getCategoryTerms000
getConceptTable313.282 0.941439.712
getConnectedGraph37.027 0.38837.437
getDOLiteTerms0.0060.0040.010
getGOList18.114 0.76619.180
getHomoGeneIDs0.1610.0040.165
getListGIF000
getMultiLayerGraphIDs35.765 0.54536.328
getNextGOIDs0.1220.0020.123
getPATHList6.3320.0349.397