BioC 2.8: CHECK report for annotate on pelham

Package: annotate

Version: 1.30.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.30.1.tar.gz

StartedAt: 2011-10-20 13:20:41 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 13:25:44 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 303.2 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 2.13.2 (2011-09-30)
* 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 '1.30.1'
* checking package namespace 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 sizes of PDF files under inst/doc ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: Rgraphviz
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'annotate' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (annotate)

name	user	system	elapsed
ACCNUMStats	3.774	0.064	3.921
GO2heatmap	0.365	0.022	0.387
GOmnplot	0.252	0.010	0.265
HTMLPage-class	0	0	0
LL2homology	0.004	0.002	0.004
PMIDAmat	0.289	0.020	0.434
PWAmat	5.854	0.216	6.168
UniGeneQuery	0.002	0.000	0.003
accessionToUID	0.742	0.029	3.809
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.721	0.075	0.812
blastSequences	5.194	0.073	100.795
buildChromLocation	2.047	0.089	2.494
buildPubMedAbst	0.138	0.006	0.991
chrCats	7.007	0.669	7.895
chromLocation-class	2.106	0.046	2.237
compatibleVersions	0.161	0.012	0.178
dropECode	0.125	0.008	0.139
entrezGeneByID	0	0	0
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.146	0.018	0.194
findNeighbors	0.004	0.001	0.005
genbank	0.177	0.015	1.221
genelocator	0.000	0.001	0.001
getAnnMap	0.198	0.043	0.315
getEvidence	0.319	0.009	0.340
getGOTerm	0.143	0.009	0.273
getOntology	0.121	0.009	0.130
getPMInfo	1.417	0.010	2.064
getSYMBOL	0.300	0.025	0.451
getSeq4Acc	0.001	0.000	0.176
hasGOannote	0.064	0.004	0.088
hgByChroms	0.017	0.001	0.018
hgCLengths	0.002	0.000	0.004
hgu95Achroloc	0.104	0.004	0.109
hgu95Achrom	0.099	0.005	0.105
hgu95All	0.115	0.006	0.128
hgu95Asym	0.103	0.005	0.124
homoData-class	0.004	0.001	0.003
htmlpage	0.059	0.003	0.083
isValidkey	0.000	0.000	0.001
makeAnchor	0.000	0.000	0.001
neighborGeneFinder	0.001	0.000	0.001
organism	2.100	0.045	2.283
p2LL	0	0	0
pm.abstGrep	21.320	0.124	23.002
pm.getabst	16.369	0.070	17.786
pm.titles	21.116	0.094	22.620
pmAbst2HTML	0.243	0.006	0.808
pmid2MIAME	0	0	0
pmidQuery	0.001	0.000	0.001
probesByLL	2.556	0.040	2.630
pubMedAbst-class	0.152	0.005	0.704
pubmed	0.068	0.005	0.687
readGEOAnn	0	0	0
serializeEnv	0.003	0.001	0.005
setRepository	0.001	0.001	0.002
updateSymbolsToValidKeys	0.000	0.000	0.001
usedChromGenes	0.138	0.006	0.144

Summary

Command output