Package: annotate

Version: 1.28.1

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.28.1.tar.gz

StartedAt: 2011-03-31 04:11:31 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 04:14:11 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 159.7 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/annotate.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘1.28.1’
* 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
  'openVignette()'. 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	2.316	0.024	2.338
GO2heatmap	0.316	0.004	0.341
GOmnplot	0.136	0.012	0.146
HTMLPage-class	0	0	0
LL2homology	0.000	0.000	0.003
PMIDAmat	0.280	0.012	0.364
PWAmat	4.764	0.064	4.836
UniGeneQuery	0.004	0.000	0.001
accessionToUID	0.312	0.044	5.225
annPkgName	0.004	0.000	0.000
aqListGOIDs	0.452	0.028	0.575
buildChromLocation	1.096	0.016	1.144
buildPubMedAbst	0.084	0.000	0.581
chrCats	4.837	0.020	4.954
chromLocation-class	1.068	0.004	1.074
compatibleVersions	0.096	0.000	0.097
dropECode	0.084	0.000	0.083
entrezGeneByID	0.000	0.004	0.001
entrezGeneQuery	0	0	0
filterGOByOntology	0.004	0.000	0.003
findNeighbors	0.004	0.000	0.002
genbank	0.068	0.000	1.192
genelocator	0	0	0
getAnnMap	0.136	0.008	0.564
getEvidence	0.072	0.004	0.076
getGOTerm	0.096	0.004	0.256
getOntology	0.072	0.004	0.077
getPMInfo	0.960	0.004	1.671
getSYMBOL	0.188	0.004	0.284
getSeq4Acc	0.000	0.000	0.185
hasGOannote	0.040	0.000	0.053
hgByChroms	0.008	0.000	0.009
hgCLengths	0.004	0.000	0.002
hgu95Achroloc	0.056	0.000	0.054
hgu95Achrom	0.048	0.000	0.048
hgu95All	0.048	0.000	0.050
hgu95Asym	0.048	0.000	0.050
homoData-class	0.000	0.000	0.003
htmlpage	0.044	0.000	0.042
isValidkey	0	0	0
makeAnchor	0.000	0.000	0.001
neighborGeneFinder	0.000	0.000	0.001
organism	1.116	0.004	1.119
p2LL	0	0	0
pm.abstGrep	19.069	0.236	21.665
pm.getabst	19.317	0.080	22.596
pm.titles	20.189	0.128	22.207
pmAbst2HTML	0.104	0.000	0.599
pmid2MIAME	0	0	0
pmidQuery	0	0	0
probesByLL	1.525	0.020	1.548
pubMedAbst-class	0.104	0.004	0.591
pubmed	0.040	0.004	0.612
readGEOAnn	0	0	0
serializeEnv	0.000	0.000	0.002
setRepository	0.000	0.004	0.002
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.064	0.000	0.063