BioC 3.2: CHECK report for GeneAnswers on moscato1

Package: GeneAnswers

Version: 2.12.0

Command: rm -rf GeneAnswers.buildbin-libdir GeneAnswers.Rcheck && mkdir GeneAnswers.buildbin-libdir GeneAnswers.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneAnswers.buildbin-libdir GeneAnswers_2.12.0.tar.gz >GeneAnswers.Rcheck\00install.out 2>&1 && cp GeneAnswers.Rcheck\00install.out GeneAnswers-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GeneAnswers.buildbin-libdir --install="check:GeneAnswers-install.out" --force-multiarch --no-vignettes --timings GeneAnswers_2.12.0.tar.gz

StartedAt: 2016-04-23 02:35:49 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:15:52 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 2400.1 seconds

RetCode: None

Status:  TIMEOUT

CheckDir: GeneAnswers.Rcheck

Warnings: NA

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### Running command:
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###   rm -rf GeneAnswers.buildbin-libdir GeneAnswers.Rcheck && mkdir GeneAnswers.buildbin-libdir GeneAnswers.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneAnswers.buildbin-libdir GeneAnswers_2.12.0.tar.gz >GeneAnswers.Rcheck\00install.out 2>&1 && cp GeneAnswers.Rcheck\00install.out GeneAnswers-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GeneAnswers.buildbin-libdir --install="check:GeneAnswers-install.out" --force-multiarch --no-vignettes --timings GeneAnswers_2.12.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/GeneAnswers.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '2.12.0'
* 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-3.2-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'.

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'
* 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' ... [26m] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
geneAnswersReadable        56.94   0.89   57.84
GeneAnswers-class          38.50   1.52  604.58
GeneAnswers-package        37.15   1.28   38.43
geneAnswersConcepts        36.11   0.98   37.09
geneAnswersBuilder         36.13   0.80   36.93
geneAnswersChartPlots      35.67   0.99   36.69
geneAnswersConceptRelation 34.68   0.83   35.51
buildNet                   34.49   0.92   35.41
geneAnswersHomoMapping     34.25   1.15   35.40
getMultiLayerGraphIDs      33.76   1.09   38.46
geneAnswersHeatmap         33.39   1.03   34.42
geneAnswersConceptNet      32.98   0.80   34.07
geneAnswersSort            31.91   0.84   33.76
getConnectedGraph          31.16   0.91   32.07
getGOList                  13.40   0.91  422.93
getCategoryList             0.17   0.00    7.80
** running examples for arch 'x64' ... [10m] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
geneAnswersReadable        84.07   1.12   85.19
geneAnswersSort            39.28   1.05   40.41
getConnectedGraph          38.59   1.00   39.85
geneAnswersHomoMapping     38.45   0.92   39.38
geneAnswersHeatmap         38.34   0.85   39.19
GeneAnswers-package        38.00   1.10   39.11
getMultiLayerGraphIDs      37.66   0.96   38.62
geneAnswersConcepts        37.13   0.98   38.12
GeneAnswers-class          36.34   1.36   40.48
buildNet                   36.31   0.91   37.23
geneAnswersConceptRelation 34.94   1.01   35.99
geneAnswersBuilder         34.54   0.78   35.32
geneAnswersChartPlots      32.64   0.95   33.59
geneAnswersConceptNet      32.51   0.75   33.30
getGOList                  16.84   0.64   17.49
* 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 ...

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_2.12.0.zip
* DONE (GeneAnswers)

name	user	system	elapsed
DO	0.57	0.00	0.56
DOLite	0.03	0.01	0.05
DOLiteTerm	0.01	0.00	0.02
DmIALite	0.08	0.00	0.07
GeneAnswers-class	38.50	1.52	604.58
GeneAnswers-package	37.15	1.28	38.43
HsIALite	0.37	0.03	0.41
MmIALite	0.02	0.01	0.03
RnIALite	0.01	0.00	0.02
buildNet	34.49	0.92	35.41
caBIO.PATHGenes	0	0	0
caBIO2entrez	0	0	0
categoryNet	0.02	0.00	0.02
chartPlots	0.01	0.02	0.03
drawTable	1.02	0.03	1.04
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0	0	0
geneAnswersBuilder	36.13	0.80	36.93
geneAnswersChartPlots	35.67	0.99	36.69
geneAnswersConceptNet	32.98	0.80	34.07
geneAnswersConceptRelation	34.68	0.83	35.51
geneAnswersConcepts	36.11	0.98	37.09
geneAnswersHeatmap	33.39	1.03	34.42
geneAnswersHomoMapping	34.25	1.15	35.40
geneAnswersReadable	56.94	0.89	57.84
geneAnswersSort	31.91	0.84	33.76
geneConceptNet	0	0	0
getCategoryList	0.17	0.00	7.80
getCategoryTerms	0.04	0.00	0.05
getConceptTable	0.88	0.00	0.87
getConnectedGraph	31.16	0.91	32.07
getDOLiteTerms	0.00	0.01	0.02
getGOList	13.40	0.91	422.93
getHomoGeneIDs	0.42	0.02	0.43
getListGIF	0	0	0
getMultiLayerGraphIDs	33.76	1.09	38.46
getNextGOIDs	0.16	0.00	0.15
getPATHList	0.08	0.00	0.08
getPATHTerms	0.04	0.00	0.05
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0	0	0
getSingleLayerGraphIDs	0	0	0
getSymbols	0.04	0.00	0.04
getTotalGeneNumber	0.35	0.00	0.35
getcaBIOPATHList	0.01	0.00	0.01
getcaBIOPATHTerms	0	0	0
groupReport	0.88	0.00	0.87
humanExpr	0.00	0.01	0.02
humanGeneInput	0.01	0.00	0.02
mouseExpr	0	0	0
mouseGeneInput	0.00	0.02	0.01
sampleGroupsData	0.07	0.01	0.08
searchEntrez	0	0	0
topCategory	0	0	0
topCategoryGenes	0	0	0
topDOLITE	0	0	0
topDOLITEGenes	0	0	0
topGO	0	0	0
topGOGenes	0	0	0
topPATH	0	0	0
topPATHGenes	0	0	0
topREACTOME.PATH	0	0	0
topREACTOME.PATHGenes	0	0	0
topcaBIO.PATH	0	0	0

name	user	system	elapsed
DO	0.67	0.00	1.67
DOLite	0.02	0.01	0.03
DOLiteTerm	0.00	0.02	0.02
DmIALite	0.07	0.00	0.08
GeneAnswers-class	36.34	1.36	40.48
GeneAnswers-package	38.00	1.10	39.11
HsIALite	0.22	0.04	0.24
MmIALite	0.02	0.00	0.02
RnIALite	0.00	0.01	0.02
buildNet	36.31	0.91	37.23
caBIO.PATHGenes	0	0	0
caBIO2entrez	0	0	0
categoryNet	0	0	0
chartPlots	0.02	0.01	0.03
drawTable	0.98	0.00	0.99
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0	0	0
geneAnswersBuilder	34.54	0.78	35.32
geneAnswersChartPlots	32.64	0.95	33.59
geneAnswersConceptNet	32.51	0.75	33.30
geneAnswersConceptRelation	34.94	1.01	35.99
geneAnswersConcepts	37.13	0.98	38.12
geneAnswersHeatmap	38.34	0.85	39.19
geneAnswersHomoMapping	38.45	0.92	39.38
geneAnswersReadable	84.07	1.12	85.19
geneAnswersSort	39.28	1.05	40.41
geneConceptNet	0	0	0
getCategoryList	0.28	0.00	0.28
getCategoryTerms	0.09	0.00	0.09
getConceptTable	1.05	0.01	1.06
getConnectedGraph	38.59	1.00	39.85
getDOLiteTerms	0.02	0.00	0.02
getGOList	16.84	0.64	17.49
getHomoGeneIDs	0.49	0.01	0.50
getListGIF	0	0	0
getMultiLayerGraphIDs	37.66	0.96	38.62
getNextGOIDs	0.11	0.00	0.90
getPATHList	0.05	0.00	0.05
getPATHTerms	0.03	0.00	0.03
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0	0	0
getSingleLayerGraphIDs	0	0	0
getSymbols	0.05	0.00	0.04
getTotalGeneNumber	0.2	0.0	0.2
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0	0	0
groupReport	0.84	0.00	0.84
humanExpr	0.00	0.01	0.02
humanGeneInput	0.00	0.02	0.02
mouseExpr	0.02	0.00	0.01
mouseGeneInput	0	0	0
sampleGroupsData	0.06	0.01	0.08
searchEntrez	0	0	0
topCategory	0	0	0
topCategoryGenes	0	0	0
topDOLITE	0	0	0
topDOLITEGenes	0	0	0
topGO	0	0	0
topGOGenes	0.09	0.00	0.09
topPATH	0	0	0
topPATHGenes	0	0	0
topREACTOME.PATH	0	0	0
topREACTOME.PATHGenes	0	0	0
topcaBIO.PATH	0	0	0