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BioC 3.4: CHECK report for GeneAnswers on moscato1

This page was generated on 2016-09-21 03:42:52 -0700 (Wed, 21 Sep 2016).

Package 464/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneAnswers 2.15.0
Lei Huang and Gang Feng
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneAnswers
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: GeneAnswers
Version: 2.15.0
Command: rm -rf GeneAnswers.buildbin-libdir GeneAnswers.Rcheck && mkdir GeneAnswers.buildbin-libdir GeneAnswers.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneAnswers.buildbin-libdir GeneAnswers_2.15.0.tar.gz >GeneAnswers.Rcheck\00install.out 2>&1 && cp GeneAnswers.Rcheck\00install.out GeneAnswers-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GeneAnswers.buildbin-libdir --install="check:GeneAnswers-install.out" --force-multiarch --no-vignettes --timings GeneAnswers_2.15.0.tar.gz
StartedAt: 2016-09-20 08:48:29 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:09:10 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 1240.3 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneAnswers.buildbin-libdir GeneAnswers_2.15.0.tar.gz >GeneAnswers.Rcheck\00install.out 2>&1 && cp GeneAnswers.Rcheck\00install.out GeneAnswers-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GeneAnswers.buildbin-libdir --install="check:GeneAnswers-install.out" --force-multiarch --no-vignettes --timings GeneAnswers_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/GeneAnswers.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '2.15.0'
* 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 'D:/biocbld/bbs-3.4-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        50.81   0.72   51.53
GeneAnswers-class          29.82   0.97   30.79
geneAnswersChartPlots      29.60   0.76   30.39
geneAnswersConceptRelation 28.36   0.96   29.33
geneAnswersSort            28.29   0.89   29.17
geneAnswersConceptNet      28.41   0.74   29.15
geneAnswersBuilder         27.50   0.73   28.24
getMultiLayerGraphIDs      27.51   0.72   28.22
geneAnswersHomoMapping     27.34   0.54   27.92
buildNet                   27.16   0.63   27.85
geneAnswersHeatmap         26.43   0.84   27.29
getConnectedGraph          26.42   0.76   27.22
GeneAnswers-package        25.98   0.76   26.74
geneAnswersConcepts        25.15   0.93   26.06
getGOList                  14.83   0.80  138.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
geneAnswersReadable        58.30   1.10   59.41
geneAnswersConcepts        33.60   1.08   34.68
GeneAnswers-class          33.10   1.39   34.51
getMultiLayerGraphIDs      31.60   0.83   32.43
geneAnswersHeatmap         30.79   0.62   36.73
geneAnswersSort            30.21   1.05   31.28
GeneAnswers-package        30.35   0.68   31.05
geneAnswersHomoMapping     30.11   0.91   31.02
buildNet                   29.59   0.75   30.36
geneAnswersConceptRelation 28.47   0.73   29.21
geneAnswersChartPlots      28.26   0.69   28.95
getConnectedGraph          27.89   0.68   28.63
geneAnswersBuilder         27.05   0.74   27.80
geneAnswersConceptNet      27.01   0.69   27.69
getGOList                  13.26   0.58   13.85
* 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
  'D:/biocbld/bbs-3.4-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_2.15.0.zip
* DONE (GeneAnswers)

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

nameusersystemelapsed
DO0.510.010.54
DOLite0.030.000.03
DOLiteTerm0.000.020.01
DmIALite0.10.00.1
GeneAnswers-class29.82 0.9730.79
GeneAnswers-package25.98 0.7626.74
HsIALite0.260.000.26
MmIALite0.020.020.03
RnIALite000
buildNet27.16 0.6327.85
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.020.000.02
drawTable0.820.030.85
entrez2caBIO000
geneAnnotationHeatmap0.010.000.01
geneAnswersBuilder27.50 0.7328.24
geneAnswersChartPlots29.60 0.7630.39
geneAnswersConceptNet28.41 0.7429.15
geneAnswersConceptRelation28.36 0.9629.33
geneAnswersConcepts25.15 0.9326.06
geneAnswersHeatmap26.43 0.8427.29
geneAnswersHomoMapping27.34 0.5427.92
geneAnswersReadable50.81 0.7251.53
geneAnswersSort28.29 0.8929.17
geneConceptNet000
getCategoryList0.100.000.21
getCategoryTerms0.030.000.03
getConceptTable0.860.001.37
getConnectedGraph26.42 0.7627.22
getDOLiteTerms000
getGOList 14.83 0.80138.68
getHomoGeneIDs0.230.060.30
getListGIF000
getMultiLayerGraphIDs27.51 0.7228.22
getNextGOIDs0.090.000.09
getPATHList0.030.000.03
getPATHTerms0.000.020.02
getREACTOMEPATHList000
getREACTOMEPATHTerms000
getSingleLayerGraphIDs000
getSymbols0.010.000.02
getTotalGeneNumber0.190.000.18
getcaBIOPATHList000
getcaBIOPATHTerms000
groupReport0.80.00.8
humanExpr000
humanGeneInput000
mouseExpr0.000.020.02
mouseGeneInput000
sampleGroupsData0.080.000.07
searchEntrez000
topCategory000
topCategoryGenes000
topDOLITE000
topDOLITEGenes000
topGO000
topGOGenes000
topPATH000
topPATHGenes000
topREACTOME.PATH000
topREACTOME.PATHGenes000
topcaBIO.PATH000

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

nameusersystemelapsed
DO0.540.000.55
DOLite0.020.020.03
DOLiteTerm0.010.000.02
DmIALite0.080.000.07
GeneAnswers-class33.10 1.3934.51
GeneAnswers-package30.35 0.6831.05
HsIALite0.220.000.21
MmIALite0.010.000.02
RnIALite0.000.020.01
buildNet29.59 0.7530.36
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.000.010.03
drawTable0.760.040.79
entrez2caBIO000
geneAnnotationHeatmap0.020.000.02
geneAnswersBuilder27.05 0.7427.80
geneAnswersChartPlots28.26 0.6928.95
geneAnswersConceptNet27.01 0.6927.69
geneAnswersConceptRelation28.47 0.7329.21
geneAnswersConcepts33.60 1.0834.68
geneAnswersHeatmap30.79 0.6236.73
geneAnswersHomoMapping30.11 0.9131.02
geneAnswersReadable58.30 1.1059.41
geneAnswersSort30.21 1.0531.28
geneConceptNet000
getCategoryList0.140.000.14
getCategoryTerms0.050.000.04
getConceptTable0.860.000.86
getConnectedGraph27.89 0.6828.63
getDOLiteTerms000
getGOList13.26 0.5813.85
getHomoGeneIDs0.410.000.41
getListGIF000
getMultiLayerGraphIDs31.60 0.8332.43
getNextGOIDs0.100.000.09
getPATHList0.030.000.03
getPATHTerms0.020.000.01
getREACTOMEPATHList000
getREACTOMEPATHTerms000
getSingleLayerGraphIDs000
getSymbols0.030.000.04
getTotalGeneNumber0.170.000.17
getcaBIOPATHList0.020.000.01
getcaBIOPATHTerms000
groupReport0.780.000.78
humanExpr0.010.000.02
humanGeneInput000
mouseExpr0.000.010.01
mouseGeneInput0.020.000.02
sampleGroupsData0.050.020.06
searchEntrez000
topCategory000
topCategoryGenes000
topDOLITE000
topDOLITEGenes000
topGO000
topGOGenes000
topPATH000
topPATHGenes000
topREACTOME.PATH000
topREACTOME.PATHGenes000
topcaBIO.PATH000