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This page was generated on 2021-10-22 12:04:58 -0400 (Fri, 22 Oct 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 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: /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: 2021-10-22 04:05:29 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 04:41:42 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 2173.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GeneAnswers.Rcheck
Warnings: 2

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 4.1.1 Patched (2021-08-22 r80813)
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
drawTable                  347.016  1.496 468.290
groupReport                321.107  1.440 442.941
getConceptTable            309.491  1.450 437.445
geneAnswersReadable         69.645  1.579  71.349
GeneAnswers-class           41.819  1.794  43.732
geneAnswersConceptNet       40.111  0.872  41.051
geneAnswersChartPlots       39.776  1.020  40.893
GeneAnswers-package         39.279  0.954  40.295
geneAnswersBuilder          38.981  0.719  39.783
buildNet                    38.692  0.771  39.542
geneAnswersConceptRelation  38.867  0.533  39.478
geneAnswersConcepts         37.985  0.785  38.847
geneAnswersHomoMapping      37.421  0.647  38.206
getConnectedGraph           36.293  0.600  36.948
geneAnswersSort             35.541  0.507  36.104
getMultiLayerGraphIDs       35.251  0.516  35.807
geneAnswersHeatmap          34.603  0.983  35.730
getGOList                   19.172  1.073  21.715
getPATHList                  6.072  0.029   9.569
* 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
  ‘/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
DO0.5840.0140.599
DOLite0.0390.0030.043
DOLiteTerm0.0030.0030.006
DmIALite0.0860.0020.088
GeneAnswers-class41.819 1.79443.732
GeneAnswers-package39.279 0.95440.295
HsIALite0.2560.0040.261
MmIALite0.0150.0020.017
RnIALite0.0090.0020.011
buildNet38.692 0.77139.542
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.1010.0750.214
drawTable347.016 1.496468.290
entrez2caBIO000
geneAnnotationHeatmap0.0020.0000.002
geneAnswersBuilder38.981 0.71939.783
geneAnswersChartPlots39.776 1.02040.893
geneAnswersConceptNet40.111 0.87241.051
geneAnswersConceptRelation38.867 0.53339.478
geneAnswersConcepts37.985 0.78538.847
geneAnswersHeatmap34.603 0.98335.730
geneAnswersHomoMapping37.421 0.64738.206
geneAnswersReadable69.645 1.57971.349
geneAnswersSort35.541 0.50736.104
geneConceptNet000
getCategoryList0.1700.0100.181
getCategoryTerms000
getConceptTable309.491 1.450437.445
getConnectedGraph36.293 0.60036.948
getDOLiteTerms0.0050.0040.008
getGOList19.172 1.07321.715
getHomoGeneIDs0.2220.0060.229
getListGIF000
getMultiLayerGraphIDs35.251 0.51635.807
getNextGOIDs0.2150.0170.232
getPATHList6.0720.0299.569
getPATHTerms0.3580.0010.554
getREACTOMEPATHList0.0000.0000.001
getREACTOMEPATHTerms000
getSingleLayerGraphIDs0.0020.0010.003
getSymbols0.0320.0010.033
getTotalGeneNumber0.4700.0070.477
getcaBIOPATHList0.0000.0000.001
getcaBIOPATHTerms000
groupReport321.107 1.440442.941
humanExpr0.0060.0030.010
humanGeneInput0.0040.0030.006
mouseExpr0.0050.0030.008
mouseGeneInput0.0040.0040.007
sampleGroupsData0.0690.0390.109
searchEntrez000
topCategory000
topCategoryGenes000
topDOLITE0.0000.0000.001
topDOLITEGenes000
topGO000
topGOGenes000
topPATH0.0000.0000.001
topPATHGenes0.0000.0010.000
topREACTOME.PATH000
topREACTOME.PATHGenes0.0010.0000.000
topcaBIO.PATH000