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This page was generated on 2021-08-02 12:05:12 -0400 (Mon, 02 Aug 2021).

CHECK results for GeneAnswers on merida1

To the developers/maintainers of the GeneAnswers package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneAnswers.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 697/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneAnswers 2.35.1  (landing page)
Lei Huang and Gang Feng
Snapshot Date: 2021-08-01 14:50:04 -0400 (Sun, 01 Aug 2021)
URL: https://git.bioconductor.org/packages/GeneAnswers
Branch: master
Last Commit: 187eb87
Last Changed Date: 2021-06-21 11:00:38 -0400 (Mon, 21 Jun 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    TIMEOUT  
riesling1Windows Server 2019 Standard / x64  OK    OK    TIMEOUT    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: GeneAnswers
Version: 2.35.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneAnswers.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneAnswers_2.35.1.tar.gz
StartedAt: 2021-08-02 02:34:34 -0400 (Mon, 02 Aug 2021)
EndedAt: 2021-08-02 03:09:15 -0400 (Mon, 02 Aug 2021)
EllapsedTime: 2081.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GeneAnswers.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneAnswers.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneAnswers_2.35.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck’
* using R version 4.1.0 RC (2021-05-16 r80304)
* 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 ‘2.35.1’
* 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 for sufficient/correct file permissions ... 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 ‘/Users/biocbuild/bbs-3.14-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, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck/00check.log’
for details.


Installation output

GeneAnswers.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/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’
Warning: Package 'GeneAnswers' is deprecated and will be removed from
  Bioconductor version 3.15
** 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’
Warning: Package 'GeneAnswers' is deprecated and will be removed from
  Bioconductor version 3.15
** testing if installed package keeps a record of temporary installation path
* DONE (GeneAnswers)

Tests output


Example timings

GeneAnswers.Rcheck/GeneAnswers-Ex.timings

nameusersystemelapsed
DO0.4010.0130.416
DOLite0.0570.0020.059
DOLiteTerm0.0030.0020.006
DmIALite0.0690.0030.072
GeneAnswers-class41.862 1.88743.963
GeneAnswers-package37.881 0.85338.799
HsIALite0.2600.0100.271
MmIALite0.0140.0070.021
RnIALite0.0070.0080.014
buildNet39.968 0.80040.827
caBIO.PATHGenes000
caBIO2entrez0.0000.0000.001
categoryNet0.0000.0000.001
chartPlots0.0600.0310.122
drawTable324.217 1.658646.539
entrez2caBIO0.0000.0010.001
geneAnnotationHeatmap0.0020.0000.002
geneAnswersBuilder39.879 0.63440.608
geneAnswersChartPlots37.751 0.88038.739
geneAnswersConceptNet38.043 0.54538.688
geneAnswersConceptRelation39.625 0.73740.436
geneAnswersConcepts41.891 0.58842.532
geneAnswersHeatmap39.730 0.61740.407
geneAnswersHomoMapping37.210 0.65037.913
geneAnswersReadable70.431 1.70672.244
geneAnswersSort36.175 0.51636.784
geneConceptNet0.0000.0000.001
getCategoryList0.1730.0140.189
getCategoryTerms000
getConceptTable330.062 1.688570.169
getConnectedGraph45.917 0.50061.570
getDOLiteTerms0.0080.0050.031
getGOList25.104 0.86937.045
getHomoGeneIDs0.3250.0110.692
getListGIF0.0010.0010.001
getMultiLayerGraphIDs43.185 0.77153.950
getNextGOIDs0.1220.0020.125
getPATHList 6.351 0.03112.101