BioC 2.8: CHECK report for annotate on lamb1

Package: annotate

Version: 1.30.1

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.30.1.tar.gz

StartedAt: 2011-10-20 11:37:06 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 11:41:25 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 259.2 seconds

RetCode: 0

Status: OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/annotate.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 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	2.448	0.020	2.465
GO2heatmap	0.244	0.012	0.258
GOmnplot	0.136	0.008	0.147
HTMLPage-class	0	0	0
LL2homology	0.004	0.000	0.004
PMIDAmat	0.332	0.000	0.333
PWAmat	6.592	0.088	6.685
UniGeneQuery	0.004	0.000	0.002
accessionToUID	0.532	0.060	4.336
annPkgName	0.000	0.000	0.001
aqListGOIDs	0.400	0.016	0.420
blastSequences	3.536	0.016	75.516
buildChromLocation	1.453	0.004	1.458
buildPubMedAbst	0.108	0.004	0.590
chrCats	5.160	0.004	5.162
chromLocation-class	1.284	0.004	1.303
compatibleVersions	0.084	0.008	0.091
dropECode	0.084	0.004	0.088
entrezGeneByID	0	0	0
entrezGeneQuery	0.000	0.000	0.001
filterGOByOntology	0.100	0.000	0.106
findNeighbors	0.004	0.000	0.003
genbank	0.116	0.000	1.119
genelocator	0	0	0
getAnnMap	0.156	0.008	0.244
getEvidence	0.076	0.012	0.087
getGOTerm	0.128	0.008	0.135
getOntology	0.076	0.004	0.090
getPMInfo	1.128	0.004	1.686
getSYMBOL	0.204	0.012	0.227
getSeq4Acc	0.000	0.000	0.172
hasGOannote	0.040	0.004	0.045
hgByChroms	0.012	0.000	0.010
hgCLengths	0.004	0.000	0.003
hgu95Achroloc	0.064	0.000	0.066
hgu95Achrom	0.052	0.004	0.058
hgu95All	0.064	0.000	0.066
hgu95Asym	0.060	0.000	0.062
homoData-class	0.004	0.000	0.003
htmlpage	0.072	0.000	0.072
isValidkey	0	0	0
makeAnchor	0	0	0
neighborGeneFinder	0.004	0.000	0.001
organism	1.428	0.012	1.460
p2LL	0	0	0
pm.abstGrep	27.326	0.092	29.947
pm.getabst	23.617	0.040	25.620
pm.titles	25.454	0.044	27.353
pmAbst2HTML	0.140	0.000	0.742
pmid2MIAME	0.000	0.000	0.001
pmidQuery	0	0	0
probesByLL	1.668	0.024	1.688
pubMedAbst-class	0.096	0.008	0.582
pubmed	0.048	0.000	0.606
readGEOAnn	0	0	0
serializeEnv	0.004	0.000	0.015
setRepository	0.004	0.000	0.002
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.072	0.000	0.076

Summary

Command output