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BioC 3.6: CHECK report for GeneAnswers on tokay1

This page was generated on 2017-08-16 13:28:40 -0400 (Wed, 16 Aug 2017).

Package 513/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneAnswers 2.19.0
Lei Huang and Gang Feng
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneAnswers
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneAnswers
Version: 2.19.0
Command: rm -rf GeneAnswers.buildbin-libdir GeneAnswers.Rcheck && mkdir GeneAnswers.buildbin-libdir GeneAnswers.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneAnswers.buildbin-libdir GeneAnswers_2.19.0.tar.gz >GeneAnswers.Rcheck\00install.out 2>&1 && cp GeneAnswers.Rcheck\00install.out GeneAnswers-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GeneAnswers.buildbin-libdir --install="check:GeneAnswers-install.out" --force-multiarch --no-vignettes --timings GeneAnswers_2.19.0.tar.gz
StartedAt: 2017-08-15 23:38:40 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:57:01 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 1101.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GeneAnswers.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GeneAnswers.buildbin-libdir GeneAnswers.Rcheck && mkdir GeneAnswers.buildbin-libdir GeneAnswers.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneAnswers.buildbin-libdir GeneAnswers_2.19.0.tar.gz >GeneAnswers.Rcheck\00install.out 2>&1 && cp GeneAnswers.Rcheck\00install.out GeneAnswers-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GeneAnswers.buildbin-libdir --install="check:GeneAnswers-install.out" --force-multiarch --no-vignettes --timings GeneAnswers_2.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GeneAnswers.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '2.19.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'igraph' '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::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers'
  Warning: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GeneAnswers.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 35.5Mb
  sub-directories of 1Mb or more:
    External  32.4Mb
    data       1.0Mb
    doc        1.6Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'Biobase' 'Heatplus' 'MASS' 'RColorBrewer' 'XML' 'igraph'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'GO.db' 'KEGG.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'.

.defaultHeatmapColors: no visible global function definition for 'rgb'
.drawHTMLtable: no visible global function definition for
  'colorRampPalette'
.heatmap.mds: no visible global function definition for
  'colorRampPalette'
buildNet: no visible global function definition for 'colorRampPalette'
chartPlots: no visible global function definition for 'x11'
chartPlots: no visible global function definition for 'rainbow'
drawTable: no visible global function definition for 'colorRampPalette'
drawTable: no visible global function definition for 'x11'
drawTable: no visible global function definition for 'dev.set'
drawTable: no visible global function definition for 'dev.prev'
geneAnnotationHeatmap: no visible global function definition for
  'colorRampPalette'
geneConceptNet: no visible global function definition for
  'colorRampPalette'
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'
groupReport: no visible global function definition for 'png'
groupReport: no visible global function definition for 'dev.off'
groupReport: no visible global function definition for 'rgb'
groupReport: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  col2rgb colorRampPalette count.mappedkeys dev.off dev.prev dev.set
  getLDS png rainbow reactomePATHNAME2ID rgb toTable useMart x11
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.off",
             "dev.prev", "dev.set", "png", "rainbow", "rgb", "x11")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
geneAnswersReadable        48.26   1.20   49.47
GeneAnswers-class          35.89   1.55   54.69
GeneAnswers-package        32.70   1.32   34.03
buildNet                   28.88   0.88   29.75
getMultiLayerGraphIDs      27.59   0.85   28.44
getConnectedGraph          27.10   0.95   28.06
geneAnswersSort            26.29   1.05   27.32
geneAnswersConceptNet      25.46   1.01   26.47
geneAnswersChartPlots      24.87   0.67   25.55
geneAnswersBuilder         24.14   0.77   24.92
geneAnswersConcepts        23.72   0.67   24.42
geneAnswersHeatmap         23.36   0.93   24.29
geneAnswersConceptRelation 23.01   1.08   24.09
geneAnswersHomoMapping     22.83   0.84   23.67
getGOList                  14.33   0.89  110.29
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
geneAnswersReadable        44.39   1.72   46.11
getMultiLayerGraphIDs      27.00   1.19   28.19
geneAnswersConceptRelation 25.74   1.35   27.07
geneAnswersConcepts        25.67   1.31   26.99
GeneAnswers-class          25.25   1.60   26.84
getConnectedGraph          24.61   1.20   25.81
geneAnswersHeatmap         24.23   0.89   25.12
geneAnswersSort            23.56   1.31   24.87
GeneAnswers-package        23.64   1.20   24.85
buildNet                   22.87   1.20   24.08
geneAnswersConceptNet      23.06   0.92   25.54
geneAnswersBuilder         22.30   1.34   23.64
geneAnswersChartPlots      22.08   1.00   23.17
geneAnswersHomoMapping     22.03   0.86   22.89
getGOList                  13.25   0.67   13.92
* 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: 1 WARNING, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GeneAnswers.Rcheck/00check.log'
for details.


GeneAnswers.Rcheck/00install.out:


install for i386

* installing *source* package 'GeneAnswers' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers'
Warning: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers'
Warning: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers'

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_2.19.0.zip
* DONE (GeneAnswers)

GeneAnswers.Rcheck/examples_i386/GeneAnswers-Ex.timings:

nameusersystemelapsed
DO0.440.000.44
DOLite0.040.000.03
DOLiteTerm000
DmIALite0.080.000.08
GeneAnswers-class35.89 1.5554.69
GeneAnswers-package32.70 1.3234.03
HsIALite0.270.000.27
MmIALite0.010.010.03
RnIALite0.020.000.02
buildNet28.88 0.8829.75
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.040.030.10
drawTable0.640.000.65
entrez2caBIO000
geneAnnotationHeatmap0.020.000.01
geneAnswersBuilder24.14 0.7724.92
geneAnswersChartPlots24.87 0.6725.55
geneAnswersConceptNet25.46 1.0126.47
geneAnswersConceptRelation23.01 1.0824.09
geneAnswersConcepts23.72 0.6724.42
geneAnswersHeatmap23.36 0.9324.29
geneAnswersHomoMapping22.83 0.8423.67
geneAnswersReadable48.26 1.2049.47
geneAnswersSort26.29 1.0527.32
geneConceptNet000
getCategoryList0.310.000.43
getCategoryTerms0.060.000.06
getConceptTable0.720.050.76
getConnectedGraph27.10 0.9528.06
getDOLiteTerms0.000.020.02
getGOList 14.33 0.89110.29
getHomoGeneIDs0.300.010.32
getListGIF000
getMultiLayerGraphIDs27.59 0.8528.44
getNextGOIDs0.080.000.08
getPATHList0.030.000.03
getPATHTerms0.010.000.02
getREACTOMEPATHList000
getREACTOMEPATHTerms000
getSingleLayerGraphIDs0.020.000.01
getSymbols0.020.000.02
getTotalGeneNumber0.230.002.56
getcaBIOPATHList000
getcaBIOPATHTerms000
groupReport1.190.011.20
humanExpr0.010.000.02
humanGeneInput000
mouseExpr0.020.000.01
mouseGeneInput000
sampleGroupsData0.060.000.06
searchEntrez000
topCategory000
topCategoryGenes000
topDOLITE000
topDOLITEGenes000
topGO000
topGOGenes000
topPATH000
topPATHGenes000
topREACTOME.PATH000
topREACTOME.PATHGenes000
topcaBIO.PATH000

GeneAnswers.Rcheck/examples_x64/GeneAnswers-Ex.timings:

nameusersystemelapsed
DO0.390.000.39
DOLite0.030.000.03
DOLiteTerm0.000.010.02
DmIALite0.070.000.06
GeneAnswers-class25.25 1.6026.84
GeneAnswers-package23.64 1.2024.85
HsIALite0.180.000.18
MmIALite0.020.000.02
RnIALite0.020.000.01
buildNet22.87 1.2024.08
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.030.000.03
drawTable0.550.020.57
entrez2caBIO000
geneAnnotationHeatmap000
geneAnswersBuilder22.30 1.3423.64
geneAnswersChartPlots22.08 1.0023.17
geneAnswersConceptNet23.06 0.9225.54
geneAnswersConceptRelation25.74 1.3527.07
geneAnswersConcepts25.67 1.3126.99
geneAnswersHeatmap24.23 0.8925.12
geneAnswersHomoMapping22.03 0.8622.89
geneAnswersReadable44.39 1.7246.11
geneAnswersSort23.56 1.3124.87
geneConceptNet000
getCategoryList0.300.020.31
getCategoryTerms0.010.030.05
getConceptTable0.750.000.75
getConnectedGraph24.61 1.2025.81
getDOLiteTerms0.000.020.02
getGOList13.25 0.6713.92
getHomoGeneIDs0.280.010.29
getListGIF000
getMultiLayerGraphIDs27.00 1.1928.19
getNextGOIDs0.070.000.08
getPATHList0.030.000.03
getPATHTerms0.040.000.03
getREACTOMEPATHList000
getREACTOMEPATHTerms000
getSingleLayerGraphIDs000
getSymbols0.030.000.03
getTotalGeneNumber0.170.000.17
getcaBIOPATHList000
getcaBIOPATHTerms000
groupReport0.640.050.69
humanExpr0.000.010.01
humanGeneInput0.000.020.02
mouseExpr000
mouseGeneInput0.000.020.02
sampleGroupsData0.050.000.04
searchEntrez000
topCategory000
topCategoryGenes000
topDOLITE000
topDOLITEGenes000
topGO000
topGOGenes000
topPATH000
topPATHGenes000
topREACTOME.PATH000
topREACTOME.PATHGenes000
topcaBIO.PATH000