BioC 2.8: CHECK report for annotate on petty

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 14:54:11 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 14:58:09 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 238.2 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: ASCII
* 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	2.840	0.026	2.866
GO2heatmap	0.270	0.011	0.280
GOmnplot	0.178	0.005	0.183
HTMLPage-class	0	0	0
LL2homology	0.002	0.000	0.003
PMIDAmat	0.220	0.005	0.264
PWAmat	4.164	0.082	4.247
UniGeneQuery	0.001	0.000	0.002
accessionToUID	0.222	0.020	7.435
annPkgName	0.000	0.000	0.001
aqListGOIDs	0.622	0.057	0.680
blastSequences	3.164	0.052	82.426
buildChromLocation	1.535	0.017	1.552
buildPubMedAbst	0.108	0.007	1.045
chrCats	5.754	0.072	5.825
chromLocation-class	1.535	0.020	1.555
compatibleVersions	0.103	0.005	0.107
dropECode	0.090	0.004	0.095
entrezGeneByID	0.001	0.000	0.000
entrezGeneQuery	0.000	0.000	0.001
filterGOByOntology	0.002	0.001	0.003
findNeighbors	0.002	0.001	0.002
genbank	0.086	0.006	1.122
genelocator	0.000	0.000	0.001
getAnnMap	0.149	0.019	0.340
getEvidence	0.081	0.004	0.085
getGOTerm	0.136	0.004	0.138
getOntology	0.084	0.005	0.089
getPMInfo	1.211	0.008	1.856
getSYMBOL	0.236	0.014	0.341
getSeq4Acc	0.001	0.001	0.188
hasGOannote	0.046	0.002	0.048
hgByChroms	0.012	0.000	0.013
hgCLengths	0.003	0.001	0.003
hgu95Achroloc	0.078	0.001	0.080
hgu95Achrom	0.069	0.002	0.071
hgu95All	0.073	0.002	0.075
hgu95Asym	0.077	0.002	0.079
homoData-class	0.020	0.001	0.020
htmlpage	0.050	0.002	0.079
isValidkey	0.000	0.000	0.001
makeAnchor	0.001	0.000	0.001
neighborGeneFinder	0.000	0.001	0.001
organism	1.590	0.019	1.608
p2LL	0	0	0
pm.abstGrep	15.205	0.091	18.668
pm.getabst	15.551	0.072	19.108
pm.titles	14.639	0.058	16.389
pmAbst2HTML	0.179	0.004	0.759
pmid2MIAME	0	0	0
pmidQuery	0.001	0.000	0.001
probesByLL	2.103	0.012	2.115
pubMedAbst-class	0.090	0.002	1.528
pubmed	0.046	0.002	0.769
readGEOAnn	0.001	0.000	0.000
serializeEnv	0.002	0.000	0.002
setRepository	0.001	0.000	0.002
updateSymbolsToValidKeys	0.000	0.001	0.000
usedChromGenes	0.098	0.002	0.101

Summary

Command output