BioC 3.2: CHECK report for GeneAnswers on moscato1

Package: GeneAnswers

Version: 2.11.1

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_2.11.1.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_2.11.1.tar.gz

StartedAt: 2015-08-20 04:44:40 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 05:10:13 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 1533.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneAnswers.Rcheck

Warnings: 1

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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_2.11.1.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_2.11.1.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/GeneAnswers.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '2.11.1'
* 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 by 'igraph::spectrum' when loading 'GeneAnswers'
  Warning: replacing previous import 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' ... [12m] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
geneAnswersReadable        65.80   1.03   66.83
GeneAnswers-class          35.80   1.34   73.58
getMultiLayerGraphIDs      34.26   0.73   36.63
geneAnswersHeatmap         32.62   0.81   33.45
geneAnswersConceptRelation 32.21   0.87   33.09
geneAnswersConcepts        32.01   0.89   32.90
buildNet                   31.66   1.12   32.78
GeneAnswers-package        31.73   0.94   32.78
geneAnswersHomoMapping     31.23   0.80   32.04
geneAnswersConceptNet      31.27   0.55   31.85
geneAnswersSort            30.68   0.98   31.67
geneAnswersBuilder         30.39   0.83   31.22
getConnectedGraph          29.79   0.83   30.62
geneAnswersChartPlots      29.39   0.78   30.17
getGOList                  17.38   1.07  171.02
** running examples for arch 'x64' ... [542s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
geneAnswersReadable        68.96   1.36   70.36
GeneAnswers-class          37.75   1.39   39.14
getConnectedGraph          34.15   1.33   35.47
getMultiLayerGraphIDs      34.29   1.03   35.32
geneAnswersConceptRelation 33.66   1.15   34.82
geneAnswersSort            32.58   1.06   33.70
geneAnswersBuilder         32.65   0.82   33.48
geneAnswersConceptNet      32.35   1.06   33.42
geneAnswersHeatmap         32.59   0.80   33.38
geneAnswersHomoMapping     32.37   0.92   33.30
buildNet                   31.90   0.98   32.88
geneAnswersChartPlots      30.89   1.02   31.90
GeneAnswers-package        31.00   0.86   31.85
geneAnswersConcepts        29.72   0.73   30.47
getGOList                  18.19   0.65   18.84
* 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-3.2-bioc/meat/GeneAnswers.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'GeneAnswers' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'igraph::spectrum' when loading 'GeneAnswers'
Warning: replacing previous import 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 by 'igraph::spectrum' when loading 'GeneAnswers'
Warning: replacing previous import by 'igraph::decompose' when loading 'GeneAnswers'

install for x64

* installing *source* package 'GeneAnswers' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'igraph::decompose' when loading 'GeneAnswers'
Warning: replacing previous import by 'igraph::spectrum' when loading 'GeneAnswers'
* MD5 sums
packaged installation of 'GeneAnswers' as GeneAnswers_2.11.1.zip
* DONE (GeneAnswers)

name	user	system	elapsed
DO	0.75	0.00	0.75
DOLite	0.04	0.00	0.03
DOLiteTerm	0	0	0
DmIALite	0.15	0.00	0.16
GeneAnswers-class	35.80	1.34	73.58
GeneAnswers-package	31.73	0.94	32.78
HsIALite	0.33	0.00	0.33
MmIALite	0.03	0.00	0.03
RnIALite	0.01	0.00	0.02
buildNet	31.66	1.12	32.78
caBIO.PATHGenes	0	0	0
caBIO2entrez	0	0	0
categoryNet	0	0	0
chartPlots	0.01	0.01	0.03
drawTable	1.19	0.00	1.31
entrez2caBIO	0.01	0.00	0.01
geneAnnotationHeatmap	0	0	0
geneAnswersBuilder	30.39	0.83	31.22
geneAnswersChartPlots	29.39	0.78	30.17
geneAnswersConceptNet	31.27	0.55	31.85
geneAnswersConceptRelation	32.21	0.87	33.09
geneAnswersConcepts	32.01	0.89	32.90
geneAnswersHeatmap	32.62	0.81	33.45
geneAnswersHomoMapping	31.23	0.80	32.04
geneAnswersReadable	65.80	1.03	66.83
geneAnswersSort	30.68	0.98	31.67
geneConceptNet	0	0	0
getCategoryList	0.19	0.00	0.23
getCategoryTerms	0.06	0.00	0.06
getConceptTable	1.39	0.00	1.39
getConnectedGraph	29.79	0.83	30.62
getDOLiteTerms	0.02	0.00	0.02
getGOList	17.38	1.07	171.02
getHomoGeneIDs	0.36	0.02	0.37
getListGIF	0	0	0
getMultiLayerGraphIDs	34.26	0.73	36.63
getNextGOIDs	0.18	0.00	0.19
getPATHList	0.06	0.00	0.06
getPATHTerms	0.04	0.02	0.05
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0	0	0
getSingleLayerGraphIDs	0	0	0
getSymbols	0.04	0.00	0.05
getTotalGeneNumber	0.30	0.00	0.29
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0	0	0
groupReport	1.41	0.01	1.42
humanExpr	0.00	0.02	0.01
humanGeneInput	0.01	0.00	0.02
mouseExpr	0.02	0.00	0.01
mouseGeneInput	0	0	0
sampleGroupsData	0.06	0.04	0.11
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	0.60	0.04	0.64
DOLite	0.03	0.00	0.03
DOLiteTerm	0	0	0
DmIALite	0.08	0.00	0.08
GeneAnswers-class	37.75	1.39	39.14
GeneAnswers-package	31.00	0.86	31.85
HsIALite	0.36	0.03	0.39
MmIALite	0.01	0.00	0.02
RnIALite	0	0	0
buildNet	31.90	0.98	32.88
caBIO.PATHGenes	0.02	0.00	0.02
caBIO2entrez	0	0	0
categoryNet	0	0	0
chartPlots	0.01	0.02	0.03
drawTable	1.17	0.05	1.21
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0	0	0
geneAnswersBuilder	32.65	0.82	33.48
geneAnswersChartPlots	30.89	1.02	31.90
geneAnswersConceptNet	32.35	1.06	33.42
geneAnswersConceptRelation	33.66	1.15	34.82
geneAnswersConcepts	29.72	0.73	30.47
geneAnswersHeatmap	32.59	0.80	33.38
geneAnswersHomoMapping	32.37	0.92	33.30
geneAnswersReadable	68.96	1.36	70.36
geneAnswersSort	32.58	1.06	33.70
geneConceptNet	0	0	0
getCategoryList	0.33	0.00	0.33
getCategoryTerms	0.11	0.00	0.11
getConceptTable	1.40	0.01	1.42
getConnectedGraph	34.15	1.33	35.47
getDOLiteTerms	0.00	0.02	0.02
getGOList	18.19	0.65	18.84
getHomoGeneIDs	0.37	0.00	0.37
getListGIF	0	0	0
getMultiLayerGraphIDs	34.29	1.03	35.32
getNextGOIDs	0.17	0.00	0.17
getPATHList	0.05	0.00	0.05
getPATHTerms	0.06	0.00	0.06
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0	0	0
getSingleLayerGraphIDs	0.02	0.00	0.01
getSymbols	0.05	0.00	0.05
getTotalGeneNumber	0.24	0.00	0.24
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0	0	0
groupReport	1.23	0.00	1.23
humanExpr	0.02	0.00	0.01
humanGeneInput	0.02	0.00	0.02
mouseExpr	0.01	0.00	0.01
mouseGeneInput	0.02	0.00	0.02
sampleGroupsData	0.11	0.03	0.14
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	0.01	0.00	0.02
topcaBIO.PATH	0	0	0