Package: annotate

Version: 1.29.3

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.29.3.tar.gz

StartedAt: 2011-03-17 15:29:40 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 15:33:47 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 247.3 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) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.29.3'
* 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 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	2.842	0.024	2.867
GO2heatmap	0.288	0.012	0.299
GOmnplot	0.191	0.004	0.196
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.002	0.001	0.003
PMIDAmat	0.279	0.006	0.340
PWAmat	4.041	0.083	4.123
UniGeneQuery	0.002	0.000	0.002
accessionToUID	0.438	0.025	7.819
annPkgName	0.001	0.000	0.000
aqListGOIDs	0.623	0.047	0.671
blastSequences	3.943	0.029	83.921
buildChromLocation	1.876	0.051	1.926
buildPubMedAbst	0.108	0.004	1.033
chrCats	5.562	0.051	5.830
chromLocation-class	1.487	0.016	1.502
compatibleVersions	0.099	0.004	0.105
dropECode	0.085	0.003	0.088
entrezGeneByID	0.000	0.001	0.001
entrezGeneQuery	0	0	0
filterGOByOntology	0.170	0.003	0.173
findNeighbors	0.018	0.001	0.018
genbank	0.089	0.005	1.130
genelocator	0	0	0
getAnnMap	0.145	0.019	0.437
getEvidence	0.089	0.004	0.092
getGOTerm	0.127	0.004	0.162
getOntology	0.087	0.005	0.092
getPMInfo	1.200	0.015	3.799
getSYMBOL	0.187	0.011	1.367
getSeq4Acc	0.000	0.001	0.185
hasGOannote	0.055	0.003	0.058
hgByChroms	0.012	0.001	0.012
hgCLengths	0.003	0.000	0.003
hgu95Achroloc	0.076	0.001	0.078
hgu95Achrom	0.069	0.001	0.070
hgu95All	0.066	0.003	0.069
hgu95Asym	0.072	0.001	0.073
homoData-class	0.002	0.001	0.003
htmlpage	0.048	0.002	0.053
isValidkey	0.000	0.000	0.001
makeAnchor	0	0	0
neighborGeneFinder	0.000	0.000	0.001
organism	1.522	0.022	1.544
p2LL	0	0	0
pm.abstGrep	15.005	0.078	17.677
pm.getabst	15.125	0.167	19.330
pm.titles	13.544	0.174	16.530
pmAbst2HTML	0.212	0.011	0.849
pmid2MIAME	0.001	0.000	0.000
pmidQuery	0.001	0.000	0.000
probesByLL	2.070	0.006	2.076
pubMedAbst-class	0.112	0.002	0.741
pubmed	0.055	0.002	0.780
readGEOAnn	0	0	0
serializeEnv	0.002	0.000	0.002
setRepository	0.001	0.000	0.002
updateSymbolsToValidKeys	0.000	0.000	0.001
usedChromGenes	0.095	0.001	0.096