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This page was generated on 2022-01-17 13:06:18 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 tokay2


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: 2022-01-16 01:55:05 -0500 (Sun, 16 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    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GeneAnswers
Version: 2.36.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAnswers.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeneAnswers_2.36.0.tar.gz
StartedAt: 2022-01-16 21:11:38 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 22:17:03 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 3925.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GeneAnswers.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAnswers.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GeneAnswers_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '2.36.0'
* 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 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 'C:/Users/biocbuild/bbs-3.14-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' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
getConceptTable            292.36   0.98  425.48
drawTable                  284.92   0.36  415.98
groupReport                284.72   0.54  412.50
geneAnswersReadable         52.38   0.47   52.84
GeneAnswers-class           32.00   2.33   36.28
geneAnswersConceptNet       30.83   0.11   30.93
geneAnswersConcepts         29.64   0.83   30.47
geneAnswersConceptRelation  29.05   0.50   29.55
geneAnswersBuilder          28.81   0.57   29.37
geneAnswersHomoMapping      29.09   0.29   29.39
geneAnswersChartPlots       29.17   0.03   29.21
getMultiLayerGraphIDs       28.78   0.21   28.98
geneAnswersHeatmap          28.11   0.39   28.52
buildNet                    27.79   0.15   27.94
geneAnswersSort             27.63   0.10   27.71
getConnectedGraph           26.32   0.28   26.59
GeneAnswers-package         25.51   0.75   26.28
getGOList                   19.75   1.52  225.86
getPATHList                  5.22   0.03    8.39
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
getConceptTable            331.73   0.37  487.39
groupReport                304.95   0.33  447.22
drawTable                  295.33   0.40  426.43
geneAnswersReadable         58.20   1.09   62.20
getConnectedGraph           28.75   0.18   28.92
geneAnswersBuilder          28.11   0.19   28.29
geneAnswersHeatmap          28.18   0.03   28.20
geneAnswersSort             28.05   0.02   28.06
getMultiLayerGraphIDs       27.97   0.05   28.13
geneAnswersChartPlots       27.45   0.03   27.49
GeneAnswers-class           26.60   0.61   27.21
geneAnswersConcepts         26.95   0.02   26.99
geneAnswersConceptNet       26.65   0.09   26.73
GeneAnswers-package         26.56   0.09   26.67
buildNet                    25.70   0.01   25.72
geneAnswersHomoMapping      25.37   0.06   25.44
geneAnswersConceptRelation  24.87   0.05   24.92
getGOList                   15.20   0.22   15.43
getPATHList                  5.58   0.01    8.75
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck/00check.log'
for details.



Installation output

GeneAnswers.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GeneAnswers_2.36.0.tar.gz && rm -rf GeneAnswers.buildbin-libdir && mkdir GeneAnswers.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneAnswers.buildbin-libdir GeneAnswers_2.36.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GeneAnswers_2.36.0.zip && rm GeneAnswers_2.36.0.tar.gz GeneAnswers_2.36.0.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
  5 32.6M    5 1782k    0     0  2911k      0  0:00:11 --:--:--  0:00:11 2912k
 20 32.6M   20 6763k    0     0  4193k      0  0:00:07  0:00:01  0:00:06 4192k
 41 32.6M   41 13.4M    0     0  5279k      0  0:00:06  0:00:02  0:00:04 5279k
 67 32.6M   67 22.0M    0     0  6243k      0  0:00:05  0:00:03  0:00:02 6243k
 88 32.6M   88 28.9M    0     0  6429k      0  0:00:05  0:00:04  0:00:01 6429k
100 32.6M  100 32.6M    0     0  6475k      0  0:00:05  0:00:05 --:--:-- 6955k

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  
    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'
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

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'
Warning: Package 'GeneAnswers' is deprecated and will be removed from
  Bioconductor version 3.15
* MD5 sums
packaged installation of 'GeneAnswers' as GeneAnswers_2.36.0.zip
* DONE (GeneAnswers)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GeneAnswers' successfully unpacked and MD5 sums checked

Tests output


Example timings

GeneAnswers.Rcheck/examples_i386/GeneAnswers-Ex.timings

nameusersystemelapsed
DO0.390.000.39
DOLite0.040.000.05
DOLiteTerm000
DmIALite0.080.020.09
GeneAnswers-class32.00 2.3336.28
GeneAnswers-package25.51 0.7526.28
HsIALite0.220.000.22
MmIALite0.010.000.02
RnIALite0.000.020.01
buildNet27.79 0.1527.94
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.030.030.06
drawTable284.92 0.36415.98
entrez2caBIO000
geneAnnotationHeatmap000
geneAnswersBuilder28.81 0.5729.37
geneAnswersChartPlots29.17 0.0329.21
geneAnswersConceptNet30.83 0.1130.93
geneAnswersConceptRelation29.05 0.5029.55
geneAnswersConcepts29.64 0.8330.47
geneAnswersHeatmap28.11 0.3928.52
geneAnswersHomoMapping29.09 0.2929.39
geneAnswersReadable52.38 0.4752.84
geneAnswersSort27.63 0.1027.71
geneConceptNet000
getCategoryList0.150.000.79
getCategoryTerms000
getConceptTable292.36 0.98425.48
getConnectedGraph26.32 0.2826.59
getDOLiteTerms0.010.000.02
getGOList 19.75 1.52225.86
getHomoGeneIDs0.260.010.29
getListGIF000
getMultiLayerGraphIDs28.78 0.2128.98
getNextGOIDs0.080.000.08
getPATHList5.220.038.39
getPATHTerms0.340.000.55
getREACTOMEPATHList000
getREACTOMEPATHTerms000
getSingleLayerGraphIDs0.020.000.01
getSymbols0.020.000.02
getTotalGeneNumber0.480.000.50
getcaBIOPATHList000
getcaBIOPATHTerms000
groupReport284.72 0.54412.50
humanExpr0.010.000.01
humanGeneInput000
mouseExpr0.000.020.02
mouseGeneInput0.000.020.01
sampleGroupsData0.050.030.08
searchEntrez000
topCategory000
topCategoryGenes000
topDOLITE000
topDOLITEGenes000
topGO000
topGOGenes000
topPATH000
topPATHGenes000
topREACTOME.PATH000
topREACTOME.PATHGenes000
topcaBIO.PATH000

GeneAnswers.Rcheck/examples_x64/GeneAnswers-Ex.timings

nameusersystemelapsed
DO0.380.010.39
DOLite0.030.000.04
DOLiteTerm0.000.020.01
DmIALite0.060.000.06
GeneAnswers-class26.60 0.6127.21
GeneAnswers-package26.56 0.0926.67
HsIALite0.200.000.21
MmIALite0.020.000.01
RnIALite0.020.000.02
buildNet25.70 0.0125.72
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.010.040.04
drawTable295.33 0.40426.43
entrez2caBIO000
geneAnnotationHeatmap000
geneAnswersBuilder28.11 0.1928.29
geneAnswersChartPlots27.45 0.0327.49
geneAnswersConceptNet26.65 0.0926.73
geneAnswersConceptRelation24.87 0.0524.92
geneAnswersConcepts26.95 0.0226.99
geneAnswersHeatmap28.18 0.0328.20
geneAnswersHomoMapping25.37 0.0625.44
geneAnswersReadable58.20 1.0962.20
geneAnswersSort28.05 0.0228.06
geneConceptNet000
getCategoryList0.130.000.13
getCategoryTerms000
getConceptTable331.73 0.37487.39
getConnectedGraph28.75 0.1828.92
getDOLiteTerms0.000.010.02
getGOList15.20 0.2215.43
getHomoGeneIDs0.160.000.16
getListGIF000
getMultiLayerGraphIDs27.97 0.0528.13
getNextGOIDs0.10.00.1
getPATHList5.580.018.75
getPATHTerms0.370.000.59
getREACTOMEPATHList000
getREACTOMEPATHTerms000
getSingleLayerGraphIDs000
getSymbols0.030.000.03
getTotalGeneNumber0.310.000.31
getcaBIOPATHList000
getcaBIOPATHTerms000
groupReport304.95 0.33447.22
humanExpr0.020.000.01
humanGeneInput0.000.020.02
mouseExpr0.010.000.01
mouseGeneInput000
sampleGroupsData0.050.030.08
searchEntrez000
topCategory000
topCategoryGenes000
topDOLITE000
topDOLITEGenes000
topGO000
topGOGenes000
topPATH000
topPATHGenes000
topREACTOME.PATH000
topREACTOME.PATHGenes000
topcaBIO.PATH000