BioC 2.13: CHECK report for GeneAnswers on perceval

Package: GeneAnswers

Version: 2.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneAnswers_2.4.0.tar.gz

StartedAt: 2014-04-05 01:26:15 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:41:36 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 921.4 seconds

RetCode: 0

Status:  OK

CheckDir: GeneAnswers.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/GeneAnswers.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneAnswers/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneAnswers’ version ‘2.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GeneAnswers’ can be installed ... [18s/19s] OK
* checking installed package size ... NOTE
  installed size is 35.2Mb
  sub-directories of 1Mb or more:
    data       1.0Mb
    doc        1.4Mb
    External  32.4Mb
* 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
* 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:
  ‘annotate’ ‘Biobase’ ‘Heatplus’ ‘igraph’ ‘MASS’ ‘RColorBrewer’ ‘XML’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘Heatplus’ ‘igraph’ ‘MASS’ ‘RColorBrewer’ ‘RCurl’ ‘RSQLite’
  ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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'.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘geneAnswers.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [11m/12m] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
geneAnswersReadable        88.056  5.853  95.634
GeneAnswers-class          54.485  4.152  61.282
getMultiLayerGraphIDs      43.688  3.020  47.236
geneAnswersHeatmap         40.441  2.692  43.942
geneAnswersHomoMapping     39.848  2.870  43.521
geneAnswersSort            39.081  2.341  42.318
GeneAnswers-package        37.832  3.191  43.993
getConnectedGraph          37.758  2.739  41.475
buildNet                   37.616  2.792  42.034
geneAnswersBuilder         37.164  2.798  41.872
geneAnswersConcepts        37.365  2.550  40.648
geneAnswersConceptRelation 36.808  2.584  40.041
geneAnswersChartPlots      35.976  2.600  39.664
geneAnswersConceptNet      33.404  2.639  36.986
getGOList                  21.784  2.273  24.660
* 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

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/GeneAnswers.Rcheck/00check.log’
for details.

* installing *source* package ‘GeneAnswers’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneAnswers)

name	user	system	elapsed
DO	0.859	0.046	0.923
DOLite	0.375	0.011	0.394
DOLiteTerm	0.008	0.003	0.011
DmIALite	0.089	0.018	0.114
GeneAnswers-class	54.485	4.152	61.282
GeneAnswers-package	37.832	3.191	43.993
HsIALite	0.260	0.021	0.291
MmIALite	0.021	0.019	0.041
RnIALite	0.010	0.013	0.022
buildNet	37.616	2.792	42.034
caBIO.PATHGenes	0.001	0.004	0.006
caBIO2entrez	0.001	0.003	0.004
categoryNet	0.002	0.003	0.005
chartPlots	0.030	0.014	0.067
drawTable	1.151	0.109	1.285
entrez2caBIO	0.002	0.004	0.008
geneAnnotationHeatmap	0.004	0.006	0.011
geneAnswersBuilder	37.164	2.798	41.872
geneAnswersChartPlots	35.976	2.600	39.664
geneAnswersConceptNet	33.404	2.639	36.986
geneAnswersConceptRelation	36.808	2.584	40.041
geneAnswersConcepts	37.365	2.550	40.648
geneAnswersHeatmap	40.441	2.692	43.942
geneAnswersHomoMapping	39.848	2.870	43.521
geneAnswersReadable	88.056	5.853	95.634
geneAnswersSort	39.081	2.341	42.318
geneConceptNet	0.003	0.004	0.006
getCategoryList	0.408	0.040	0.531
getCategoryTerms	0.109	0.011	0.120
getConceptTable	1.252	0.105	1.394
getConnectedGraph	37.758	2.739	41.475
getDOLiteTerms	0.010	0.007	0.017
getGOList	21.784	2.273	24.660
getHomoGeneIDs	0.400	0.032	0.453
getMultiLayerGraphIDs	43.688	3.020	47.236
getNextGOIDs	0.179	0.011	0.190
getPATHList	0.094	0.010	0.103
getPATHTerms	0.072	0.008	0.080
getREACTOMEPATHList	0.001	0.006	0.008
getREACTOMEPATHTerms	0.002	0.004	0.006
getSingleLayerGraphIDs	0.005	0.008	0.014
getSymbols	0.071	0.009	0.081
getTotalGeneNumber	0.266	0.053	0.320
getcaBIOPATHList	0.096	0.032	0.128
getcaBIOPATHTerms	0.002	0.003	0.005
groupReport	1.093	0.062	1.157
humanExpr	0.011	0.007	0.018
humanGeneInput	0.008	0.006	0.014
mouseExpr	0.009	0.008	0.017
mouseGeneInput	0.009	0.010	0.018
sampleGroupsData	0.158	0.057	0.217
searchEntrez	0.002	0.006	0.008
topCategory	0.121	0.031	0.151
topCategoryGenes	0.002	0.004	0.006
topDOLITE	0.002	0.003	0.006
topDOLITEGenes	0.002	0.004	0.006
topGO	0.003	0.004	0.006
topGOGenes	0.002	0.005	0.008
topPATH	0.002	0.003	0.005
topPATHGenes	0.002	0.003	0.006
topREACTOME.PATH	0.003	0.005	0.007
topREACTOME.PATHGenes	0.002	0.004	0.005
topcaBIO.PATH	0.002	0.004	0.006