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This page was generated on 2021-10-22 12:04:01 -0400 (Fri, 22 Oct 2021).

CHECK results for GeneAnswers on nebbiolo2

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 713/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneAnswers 2.35.1  (landing page)
Lei Huang and Gang Feng
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/GeneAnswers
git_branch: master
git_last_commit: 9470a8d
git_last_commit_date: 2021-10-05 01:25:25 -0400 (Tue, 05 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    TIMEOUT    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: GeneAnswers
Version: 2.35.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GeneAnswers.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GeneAnswers_2.35.1.tar.gz
StartedAt: 2021-10-21 20:11:27 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 20:51:12 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 2385.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GeneAnswers.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GeneAnswers.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GeneAnswers_2.35.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘/home/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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
drawTable                  203.299  5.333 613.194
getConceptTable            200.301  5.021 611.584
groupReport                197.712  4.973 579.276
geneAnswersReadable         48.430  0.180  48.611
geneAnswersBuilder          44.336  0.566  51.953
GeneAnswers-class           30.834  1.083  31.919
geneAnswersConceptNet       30.451  0.056  30.507
geneAnswersConcepts         30.060  0.236  30.319
GeneAnswers-package         29.452  0.240  29.692
buildNet                    29.445  0.044  29.489
getMultiLayerGraphIDs       27.893  0.028  27.922
getConnectedGraph           26.950  0.180  27.130
geneAnswersConceptRelation  26.748  0.120  26.868
geneAnswersHeatmap          26.342  0.180  26.522
geneAnswersChartPlots       25.369  0.060  25.430
geneAnswersSort             25.184  0.104  25.288
geneAnswersHomoMapping      25.181  0.068  25.249
getGOList                   15.589  0.176  15.880
getPATHList                  3.761  0.076  10.328
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck/00check.log’
for details.



Installation output

GeneAnswers.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL GeneAnswers
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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
DO0.3090.0090.317
DOLite0.0220.0000.022
DOLiteTerm0.0020.0000.002
DmIALite0.0470.0040.051
GeneAnswers-class30.834 1.08331.919
GeneAnswers-package29.452 0.24029.692
HsIALite0.1820.0000.182
MmIALite0.0110.0000.011
RnIALite0.0050.0000.005
buildNet29.445 0.04429.489
caBIO.PATHGenes0.0010.0000.000
caBIO2entrez000
categoryNet000
chartPlots0.0670.0070.079
drawTable203.299 5.333613.194
entrez2caBIO0.0010.0000.001
geneAnnotationHeatmap0.0000.0030.003
geneAnswersBuilder44.336 0.56651.953
geneAnswersChartPlots25.369 0.06025.430
geneAnswersConceptNet30.451 0.05630.507
geneAnswersConceptRelation26.748 0.12026.868
geneAnswersConcepts30.060 0.23630.319
geneAnswersHeatmap26.342 0.18026.522
geneAnswersHomoMapping25.181 0.06825.249
geneAnswersReadable48.430 0.18048.611
geneAnswersSort25.184 0.10425.288
geneConceptNet000
getCategoryList0.1030.0040.108
getCategoryTerms000
getConceptTable200.301 5.021611.584
getConnectedGraph26.95 0.1827.13
getDOLiteTerms0.0040.0000.004
getGOList15.589 0.17615.880
getHomoGeneIDs0.1320.0040.137
getListGIF000
getMultiLayerGraphIDs27.893 0.02827.922
getNextGOIDs0.0720.0000.072
getPATHList 3.761 0.07610.328
getPATHTerms0.1950.0000.576
getREACTOMEPATHList000
getREACTOMEPATHTerms000
getSingleLayerGraphIDs0.0020.0000.002
getSymbols0.0300.0120.042
getTotalGeneNumber0.2380.0000.238
getcaBIOPATHList000
getcaBIOPATHTerms000
groupReport197.712 4.973579.276
humanExpr0.0060.0000.005
humanGeneInput0.0020.0000.003
mouseExpr0.0030.0000.004
mouseGeneInput0.0020.0000.003
sampleGroupsData0.0350.0160.050
searchEntrez000
topCategory000
topCategoryGenes000
topDOLITE000
topDOLITEGenes000
topGO000
topGOGenes000
topPATH000
topPATHGenes000
topREACTOME.PATH000
topREACTOME.PATHGenes000
topcaBIO.PATH000