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This page was generated on 2022-01-14 13:05:12 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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 717/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneAnswers 2.36.0  (landing page)
Lei Huang and Gang Feng
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/GeneAnswers
git_branch: RELEASE_3_14
git_last_commit: ada47cb
git_last_commit_date: 2021-10-26 11:54:49 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    TIMEOUT  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    TIMEOUT    OK  

Summary

Package: GeneAnswers
Version: 2.36.0
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_2.36.0.tar.gz
StartedAt: 2022-01-13 07:40:29 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 08:20:30 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 2400.8 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: GeneAnswers.Rcheck
Warnings: NA

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_2.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.36.0’
* 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 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 ...

Installation output

GeneAnswers.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL GeneAnswers
###
##############################################################################
##############################################################################


* 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
DO0.3640.0120.376
DOLite0.0240.0000.024
DOLiteTerm0.0020.0000.003
DmIALite0.0550.0000.055
GeneAnswers-class40.997 1.36742.379
GeneAnswers-package32.828 2.00834.837
HsIALite0.1830.0020.185
MmIALite0.0110.0000.011
RnIALite0.0050.0000.006
buildNet31.035 0.08431.119
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.0700.0080.081
drawTable274.067 7.582651.314
entrez2caBIO000
geneAnnotationHeatmap0.0000.0020.002
geneAnswersBuilder37.428 0.27939.848
geneAnswersChartPlots36.275 0.09639.099
geneAnswersConceptNet27.729 0.22827.957
geneAnswersConceptRelation43.910 0.18350.719
geneAnswersConcepts51.294 0.20357.649
geneAnswersHeatmap32.995 0.10033.111
geneAnswersHomoMapping30.535 0.06430.600
geneAnswersReadable65.074 0.24965.323
geneAnswersSort29.428 0.16829.597
geneConceptNet000
getCategoryList0.1280.0040.135
getCategoryTerms000
getConceptTable269.066 7.132649.704
getConnectedGraph35.068 0.40235.471
getDOLiteTerms0.0040.0000.004
getGOList22.400 0.28923.685
getHomoGeneIDs0.1840.0060.190
getListGIF000
getMultiLayerGraphIDs42.667 0.18442.852
getNextGOIDs0.0650.0000.066
getPATHList 5.360 0.11212.787
getPATHTerms0.3210.0030.524
getREACTOMEPATHList000
getREACTOMEPATHTerms000
getSingleLayerGraphIDs0.0020.0000.002
getSymbols0.0210.0040.025
getTotalGeneNumber0.2580.0120.271
getcaBIOPATHList000
getcaBIOPATHTerms0.0010.0000.000