Package: annotate

Version: 1.31.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.31.0.tar.gz

StartedAt: 2011-06-22 01:15:52 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 01:20:39 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 286.7 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/annotate.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.31.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘annotate’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... NOTE
‘library’ or ‘require’ calls not declared from:
  ‘hsahomology’ ‘humanCHRLOC’
* 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 examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘Rgraphviz’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘annotate’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘GOusage.Rnw’ 
   ‘annotate.Rnw’ 
   ‘chromLoc.Rnw’ 
   ‘prettyOutput.Rnw’ 
   ‘query.Rnw’ 
   ‘useDataPkgs.Rnw’ 
   ‘useHomology.Rnw’ 
   ‘useProbeInfo.Rnw’ 
** testing if installed package can be loaded

* DONE (annotate)

name	user	system	elapsed
ACCNUMStats	3.729	0.062	3.837
GO2heatmap	0.379	0.022	0.411
GOmnplot	0.312	0.009	0.322
HTMLPage-class	0	0	0
LL2homology	0.004	0.001	0.005
PMIDAmat	0.262	0.018	0.404
PWAmat	5.312	0.189	5.530
UniGeneQuery	0.002	0.000	0.003
accessionToUID	0.635	0.048	4.105
annPkgName	0.001	0.001	0.001
aqListGOIDs	0.834	0.076	0.921
blastSequences	5.210	0.068	78.415
buildChromLocation	1.931	0.056	2.146
buildPubMedAbst	0.141	0.006	0.777
chrCats	6.886	0.548	7.572
chromLocation-class	1.932	0.035	1.988
compatibleVersions	0.143	0.009	0.153
dropECode	0.139	0.008	0.148
entrezGeneByID	0.001	0.000	0.002
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.214	0.006	0.222
findNeighbors	0.004	0.000	0.005
genbank	0.108	0.008	1.135
genelocator	0.001	0.001	0.000
getAnnMap	0.198	0.036	0.355
getEvidence	0.113	0.007	0.121
getGOTerm	0.164	0.007	0.244
getOntology	0.116	0.006	0.127
getPMInfo	1.516	0.011	3.484
getSYMBOL	0.307	0.020	0.418
getSeq4Acc	0.005	0.001	0.185
hasGOannote	0.069	0.003	0.073
hgByChroms	0.019	0.001	0.021
hgCLengths	0.020	0.001	0.021
hgu95Achroloc	0.116	0.005	0.126
hgu95Achrom	0.098	0.004	0.103
hgu95All	0.103	0.004	0.107
hgu95Asym	0.107	0.005	0.113
homoData-class	0.004	0.000	0.004
htmlpage	0.071	0.003	0.083
isValidkey	0.001	0.000	0.000
makeAnchor	0.000	0.001	0.001
neighborGeneFinder	0.002	0.000	0.002
organism	2.219	0.033	2.295
p2LL	0	0	0
pm.abstGrep	20.124	0.160	22.392
pm.getabst	20.400	0.127	22.741
pm.titles	18.402	0.147	21.173
pmAbst2HTML	0.265	0.007	0.933
pmid2MIAME	0.001	0.000	0.001
pmidQuery	0.001	0.001	0.001
probesByLL	2.654	0.035	2.708
pubMedAbst-class	0.159	0.006	0.716
pubmed	0.076	0.006	0.777
readGEOAnn	0.001	0.000	0.000
serializeEnv	0.003	0.001	0.004
setRepository	0.004	0.000	0.005
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.139	0.006	0.145