BioC 2.7: CHECK report for annotate on pelham

Package: annotate

Version: 1.28.1

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.28.1.tar.gz

StartedAt: 2011-03-31 04:24:07 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 04:27:37 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 210.1 seconds

RetCode: 0

Status: OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/annotate.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* 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 ‘1.28.1’
* 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	3.906	0.085	4.085
GO2heatmap	0.389	0.025	0.423
GOmnplot	0.247	0.010	0.261
HTMLPage-class	0.001	0.000	0.000
LL2homology	0.004	0.001	0.006
PMIDAmat	0.380	0.019	0.483
PWAmat	5.560	0.199	5.814
UniGeneQuery	0.002	0.000	0.003
accessionToUID	0.568	0.056	6.191
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.800	0.098	0.915
buildChromLocation	1.994	0.071	2.092
buildPubMedAbst	0.141	0.006	0.750
chrCats	6.998	0.710	8.062
chromLocation-class	1.906	0.054	2.035
compatibleVersions	0.151	0.011	0.168
dropECode	0.126	0.009	0.138
entrezGeneByID	0.001	0.000	0.002
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.005	0.001	0.005
findNeighbors	0.005	0.001	0.006
genbank	0.109	0.009	1.069
genelocator	0.001	0.001	0.001
getAnnMap	0.197	0.042	0.418
getEvidence	0.117	0.008	0.127
getGOTerm	0.140	0.007	0.198
getOntology	0.108	0.007	0.120
getPMInfo	1.475	0.016	2.162
getSYMBOL	0.311	0.028	0.528
getSeq4Acc	0.005	0.001	0.200
hasGOannote	0.085	0.004	0.104
hgByChroms	0.018	0.001	0.024
hgCLengths	0.003	0.001	0.006
hgu95Achroloc	0.110	0.006	0.137
hgu95Achrom	0.097	0.005	0.133
hgu95All	0.105	0.006	0.143
hgu95Asym	0.106	0.007	0.132
homoData-class	0.004	0.001	0.009
htmlpage	0.086	0.004	0.126
isValidkey	0.001	0.000	0.000
makeAnchor	0.001	0.000	0.001
neighborGeneFinder	0.002	0.000	0.004
organism	2.170	0.074	3.052
p2LL	0.001	0.001	0.000
pm.abstGrep	19.827	0.138	24.177
pm.getabst	19.428	0.131	21.798
pm.titles	19.378	0.137	22.035
pmAbst2HTML	0.164	0.014	0.739
pmid2MIAME	0.000	0.000	0.001
pmidQuery	0.001	0.001	0.001
probesByLL	2.646	0.037	2.723
pubMedAbst-class	0.143	0.006	0.783
pubmed	0.068	0.006	1.274
readGEOAnn	0.000	0.001	0.001
serializeEnv	0.002	0.001	0.004
setRepository	0.005	0.001	0.005
updateSymbolsToValidKeys	0.000	0.000	0.001
usedChromGenes	0.126	0.006	0.134

Summary

Command output