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CHECK report for GeneAnswers on riesling1

This page was generated on 2021-05-13 12:13:00 -0400 (Thu, 13 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 704/2022HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneAnswers 2.33.0  (landing page)
Lei Huang and Gang Feng
Snapshot Date: 2021-05-12 14:50:04 -0400 (Wed, 12 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: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAnswers.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneAnswers_2.33.0.tar.gz
StartedAt: 2021-05-13 02:32:22 -0400 (Thu, 13 May 2021)
EndedAt: 2021-05-13 03:08:05 -0400 (Thu, 13 May 2021)
EllapsedTime: 2142.9 seconds
RetCode: 1
Status:   ERROR   
CheckDir: GeneAnswers.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAnswers.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneAnswers_2.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-bioc/meat/GeneAnswers.Rcheck'
* using R version 4.1.0 RC (2021-05-10 r80283)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... OK
* checking for portable file names ... 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 'D:/biocbuild/bbs-3.13-bioc/meat/GeneAnswers.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 34.7Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 binding for global variable
  'reactomePATHNAME2ID'
Undefined global functions or variables:
  count.mappedkeys getLDS reactomePATHNAME2ID 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 ...
** running examples for arch 'i386' ... 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
** running examples for arch 'x64' ... 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: 2 ERRORs, 2 WARNINGs, 5 NOTEs
See
  'D:/biocbuild/bbs-3.13-bioc/meat/GeneAnswers.Rcheck/00check.log'
for details.


Installation output

GeneAnswers.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GeneAnswers_2.33.0.tar.gz && rm -rf GeneAnswers.buildbin-libdir && mkdir GeneAnswers.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneAnswers.buildbin-libdir GeneAnswers_2.33.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GeneAnswers_2.33.0.zip && rm GeneAnswers_2.33.0.tar.gz GeneAnswers_2.33.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  6 32.6M    6 2006k    0     0  1925k      0  0:00:17  0:00:01  0:00:16 1925k
 18 32.6M   18 6062k    0     0  2991k      0  0:00:11  0:00:02  0:00:09 2989k
 37 32.6M   37 12.1M    0     0  4121k      0  0:00:08  0:00:03  0:00:05 4121k
 61 32.6M   61 20.2M    0     0  5141k      0  0:00:06  0:00:04  0:00:02 5139k
 92 32.6M   92 30.3M    0     0  6189k      0  0:00:05  0:00:05 --:--:-- 6218k
100 32.6M  100 32.6M    0     0  6395k      0  0:00:05  0:00:05 --:--:-- 7509k

install for i386

* 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
  converting help for package 'GeneAnswers'
    finding HTML links ... done
    DO                                      html  
    DOLite                                  html  
    DOLiteTerm                              html  
    DmIALite                                html  
    GeneAnswers-class                       html  
REDIRECT:topic	 class:GeneAnswers -> GeneAnswers-class.html [ FAIL ]
    GeneAnswers-package                     html  
    HsIALite                                html  
    MmIALite                                html  
    RnIALite                                html  
    buildNet                                html  
    caBIO.PATHGenes                         html  
    caBIO2entrez                            html  
    categoryNet                             html  
    chartPlots                              html  
    drawTable                               html  
    entrez2caBIO                            html  
    geneAnnotationHeatmap                   html  
    geneAnswersBuilder                      html  
    geneAnswersChartPlots                   html  
    geneAnswersConceptNet                   html  
    geneAnswersConceptRelation              html  
    geneAnswersConcepts                     html  
    geneAnswersHeatmap                      html  
    geneAnswersHomoMapping                  html  
    geneAnswersReadable                     html  
    geneAnswersSort                         html  
    geneConceptNet                          html  
    getCategoryList                         html  
    getCategoryTerms                        html  
    getConceptTable                         html  
    getConnectedGraph                       html  
    getDOLiteTerms                          html  
    getGOList                               html  
    getHomoGeneIDs                          html  
    getListGIF                              html  
    getMultiLayerGraphIDs                   html  
    getNextGOIDs                            html  
    getPATHList                             html  
    getPATHTerms                            html  
    getREACTOMEPATHList                     html  
    getREACTOMEPATHTerms                    html  
    getSingleLayerGraphIDs                  html  
    getSymbols                              html  
    getTotalGeneNumber                      html  
    getcaBIOPATHList                        html  
    getcaBIOPATHTerms                       html  
    groupReport                             html  
    humanExpr                               html  
    humanGeneInput                          html  
    mouseExpr                               html  
    mouseGeneInput                          html  
    sampleGroupsData                        html  
    searchEntrez                            html  
    topCategory                             html  
    topCategoryGenes                        html  
    topDOLITE                               html  
    topDOLITEGenes                          html  
    topGO                                   html  
    topGOGenes                              html  
    topPATH                                 html  
    topPATHGenes                            html  
    topREACTOME.PATH                        html  
    topREACTOME.PATHGenes                   html  
    topcaBIO.PATH                           html  
** 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

install for x64

* installing *source* package 'GeneAnswers' ...
** testing if installed package can be loaded
Warning: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers'
Warning: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers'
* MD5 sums
packaged installation of 'GeneAnswers' as GeneAnswers_2.33.0.zip
* DONE (GeneAnswers)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'GeneAnswers' successfully unpacked and MD5 sums checked

Tests output


Example timings

GeneAnswers.Rcheck/examples_i386/GeneAnswers-Ex.timings

nameusersystemelapsed
DO0.250.000.25
DOLite0.030.000.03
DOLiteTerm0.000.020.02
DmIALite0.030.010.05
GeneAnswers-class21.47 0.6922.30
GeneAnswers-package19.82 0.2220.05
HsIALite0.150.000.15
MmIALite0.020.000.02
RnIALite000
buildNet20.64 0.2120.86
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.020.000.02
drawTable133.46 0.20266.73
entrez2caBIO000
geneAnnotationHeatmap000
geneAnswersBuilder20.94 0.2021.14
geneAnswersChartPlots21.16 0.0021.17
geneAnswersConceptNet22.15 0.0222.18
geneAnswersConceptRelation24.60 0.0024.59
geneAnswersConcepts21.39 0.0321.42
geneAnswersHeatmap21.37 0.0321.41
geneAnswersHomoMapping19.82 0.0119.94
geneAnswersReadable37.29 0.1437.43
geneAnswersSort22.27 0.0222.29
geneConceptNet000
getCategoryList0.080.000.09
getCategoryTerms000
getConceptTable178.23 0.19330.33
getConnectedGraph30.42 0.3336.97
getDOLiteTerms0.000.010.01
getGOList13.64 0.4119.05
getHomoGeneIDs0.160.010.17
getListGIF000
getMultiLayerGraphIDs24.41 0.0525.16
getNextGOIDs0.080.000.08
getPATHList3.510.027.11

GeneAnswers.Rcheck/examples_x64/GeneAnswers-Ex.timings

nameusersystemelapsed
DO0.220.000.22
DOLite0.050.000.05
DOLiteTerm0.020.000.02
DmIALite0.060.000.06
GeneAnswers-class24.72 1.0525.76
GeneAnswers-package21.65 0.2521.91
HsIALite0.130.010.14
MmIALite0.020.000.02
RnIALite0.020.000.01
buildNet24.81 0.2725.10
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.000.030.05
drawTable150.89 0.20284.78
entrez2caBIO000
geneAnnotationHeatmap000
geneAnswersBuilder20.49 0.2820.76
geneAnswersChartPlots19.95 0.0219.98
geneAnswersConceptNet21.02 0.0321.06
geneAnswersConceptRelation21.08 0.0221.10
geneAnswersConcepts22.33 0.0322.36
geneAnswersHeatmap22.25 0.0322.29
geneAnswersHomoMapping22.19 0.0522.24
geneAnswersReadable38.56 0.2938.86
geneAnswersSort21.05 0.0021.07
geneConceptNet000
getCategoryList0.070.020.10
getCategoryTerms000
getConceptTable151.80 0.31279.13
getConnectedGraph20.07 0.1320.20
getDOLiteTerms0.020.000.02
getGOList10.56 0.1410.70
getHomoGeneIDs0.100.000.09
getListGIF000
getMultiLayerGraphIDs20.65 0.1120.78
getNextGOIDs0.050.000.05
getPATHList2.700.014.64