BioC 2.8: CHECK report for annotate on pelham

Package: annotate

Version: 1.29.2

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.29.2.tar.gz

StartedAt: 2011-02-24 17:57:36 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:02:12 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 275.5 seconds

RetCode: 0

Status: OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/annotate.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.29.2’
* 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	3.877	0.070	3.984
GO2heatmap	0.409	0.025	0.436
GOmnplot	0.262	0.011	0.273
HTMLPage-class	0.000	0.001	0.001
LL2homology	0.004	0.001	0.006
PMIDAmat	0.306	0.021	0.463
PWAmat	5.719	0.198	5.945
UniGeneQuery	0.003	0.000	0.003
accessionToUID	0.319	0.032	3.446
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.880	0.127	1.055
blastSequences	4.188	0.062	79.758
buildChromLocation	2.043	0.058	2.122
buildPubMedAbst	0.152	0.008	0.721
chrCats	7.436	0.691	11.180
chromLocation-class	1.981	0.045	2.037
compatibleVersions	0.140	0.010	0.151
dropECode	0.124	0.007	0.132
entrezGeneByID	0.001	0.000	0.001
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.005	0.001	0.006
findNeighbors	0.005	0.001	0.006
genbank	0.111	0.011	1.069
genelocator	0.001	0.000	0.000
getAnnMap	0.195	0.041	0.604
getEvidence	0.116	0.008	0.124
getGOTerm	0.158	0.012	1.494
getOntology	0.110	0.006	0.115
getPMInfo	1.520	0.015	2.185
getSYMBOL	0.330	0.024	1.014
getSeq4Acc	0.005	0.001	0.184
hasGOannote	0.067	0.004	0.105
hgByChroms	0.017	0.001	0.019
hgCLengths	0.003	0.000	0.004
hgu95Achroloc	0.111	0.005	0.116
hgu95Achrom	0.099	0.006	0.106
hgu95All	0.105	0.006	0.111
hgu95Asym	0.107	0.006	0.113
homoData-class	0.024	0.001	0.025
htmlpage	0.081	0.003	0.091
isValidkey	0.001	0.001	0.001
makeAnchor	0.000	0.000	0.001
neighborGeneFinder	0.003	0.000	0.003
organism	2.105	0.046	2.167
p2LL	0.001	0.000	0.001
pm.abstGrep	19.277	0.231	22.239
pm.getabst	18.618	0.183	20.948
pm.titles	18.016	0.180	20.538
pmAbst2HTML	0.137	0.007	0.704
pmid2MIAME	0	0	0
pmidQuery	0.001	0.000	0.001
probesByLL	2.478	0.034	2.515
pubMedAbst-class	0.143	0.006	0.945
pubmed	0.068	0.006	0.715
readGEOAnn	0.000	0.000	0.001
serializeEnv	0.003	0.001	0.004
setRepository	0.004	0.000	0.005
updateSymbolsToValidKeys	0.000	0.001	0.000
usedChromGenes	0.127	0.005	0.132

Summary

Command output