Package: annotate

Version: 1.29.2

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.29.2.tar.gz

StartedAt: 2011-02-24 17:21:47 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 17:25:55 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 248.6 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/annotate.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.29.2’
* 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 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:
  GO hsahomology humanCHRLOC
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... 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 ...
** testing if installed package can be loaded

* DONE (annotate)

name	user	system	elapsed
ACCNUMStats	2.364	0.020	2.401
GO2heatmap	0.244	0.004	0.259
GOmnplot	0.152	0.012	0.165
HTMLPage-class	0	0	0
LL2homology	0.004	0.000	0.004
PMIDAmat	0.324	0.004	0.426
PWAmat	5.168	0.084	5.272
UniGeneQuery	0.004	0.000	0.002
accessionToUID	0.204	0.028	6.354
annPkgName	0	0	0
aqListGOIDs	0.492	0.028	0.534
blastSequences	2.816	0.032	72.836
buildChromLocation	1.280	0.004	1.287
buildPubMedAbst	0.128	0.000	1.303
chrCats	5.265	0.012	5.361
chromLocation-class	1.272	0.008	1.290
compatibleVersions	0.108	0.004	0.111
dropECode	0.092	0.008	0.098
entrezGeneByID	0.000	0.000	0.001
entrezGeneQuery	0	0	0
filterGOByOntology	0.004	0.000	0.003
findNeighbors	0.004	0.000	0.002
genbank	0.088	0.000	2.921
genelocator	0	0	0
getAnnMap	0.136	0.016	0.279
getEvidence	0.072	0.012	0.083
getGOTerm	0.140	0.000	0.196
getOntology	0.100	0.004	0.104
getPMInfo	1.228	0.000	2.092
getSYMBOL	0.196	0.016	0.271
getSeq4Acc	0.000	0.000	0.193
hasGOannote	0.052	0.000	0.049
hgByChroms	0.008	0.000	0.009
hgCLengths	0.000	0.000	0.002
hgu95Achroloc	0.068	0.004	0.074
hgu95Achrom	0.052	0.000	0.053
hgu95All	0.052	0.004	0.055
hgu95Asym	0.060	0.004	0.062
homoData-class	0.004	0.000	0.003
htmlpage	0.048	0.000	0.055
isValidkey	0	0	0
makeAnchor	0	0	0
neighborGeneFinder	0.000	0.000	0.001
organism	1.368	0.004	1.379
p2LL	0	0	0
pm.abstGrep	20.601	0.088	23.299
pm.getabst	20.438	0.040	23.591
pm.titles	20.197	0.048	25.900
pmAbst2HTML	0.156	0.000	0.877
pmid2MIAME	0.000	0.000	0.001
pmidQuery	0	0	0
probesByLL	1.768	0.016	1.928
pubMedAbst-class	0.096	0.000	0.658
pubmed	0.060	0.008	0.634
readGEOAnn	0	0	0
serializeEnv	0.000	0.000	0.002
setRepository	0.004	0.000	0.001
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.068	0.004	0.076