Package: annotate

Version: 1.31.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.31.0.tar.gz

StartedAt: 2011-07-06 23:26:27 -0700 (Wed, 06 Jul 2011)

EndedAt: 2011-07-06 23:30:44 -0700 (Wed, 06 Jul 2011)

EllapsedTime: 257.0 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/annotate.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘1.31.0’
* 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 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
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 ...
*** tangling vignette sources ...
   ‘GOusage.Rnw’ 
   ‘annotate.Rnw’ 
   ‘chromLoc.Rnw’ 
   ‘prettyOutput.Rnw’ 
   ‘query.Rnw’ 
   ‘useDataPkgs.Rnw’ 
   ‘useHomology.Rnw’ 
   ‘useProbeInfo.Rnw’ 
** testing if installed package can be loaded

* DONE (annotate)

name	user	system	elapsed
ACCNUMStats	2.236	0.040	2.353
GO2heatmap	0.216	0.004	0.221
GOmnplot	0.132	0.000	0.134
HTMLPage-class	0.000	0.000	0.001
LL2homology	0.000	0.000	0.004
PMIDAmat	0.200	0.000	0.201
PWAmat	6.880	0.120	7.091
UniGeneQuery	0.004	0.000	0.002
accessionToUID	0.368	0.052	4.631
annPkgName	0	0	0
aqListGOIDs	0.488	0.040	0.528
blastSequences	3.592	0.036	71.882
buildChromLocation	1.321	0.000	1.323
buildPubMedAbst	0.108	0.000	0.645
chrCats	5.108	0.008	5.215
chromLocation-class	1.668	0.004	1.734
compatibleVersions	0.092	0.008	0.109
dropECode	0.080	0.008	0.096
entrezGeneByID	0.000	0.000	0.001
entrezGeneQuery	0.000	0.000	0.001
filterGOByOntology	0.144	0.000	0.159
findNeighbors	0.004	0.000	0.003
genbank	0.072	0.004	1.048
genelocator	0	0	0
getAnnMap	0.144	0.008	0.192
getEvidence	0.076	0.004	0.083
getGOTerm	0.116	0.004	0.119
getOntology	0.068	0.008	0.077
getPMInfo	1.092	0.000	1.646
getSYMBOL	0.188	0.012	0.223
getSeq4Acc	0.000	0.000	0.169
hasGOannote	0.036	0.008	0.044
hgByChroms	0.008	0.000	0.010
hgCLengths	0.000	0.000	0.002
hgu95Achroloc	0.068	0.000	0.071
hgu95Achrom	0.06	0.00	0.06
hgu95All	0.056	0.008	0.061
hgu95Asym	0.060	0.004	0.063
homoData-class	0.004	0.000	0.003
htmlpage	0.068	0.000	0.067
isValidkey	0	0	0
makeAnchor	0	0	0
neighborGeneFinder	0.000	0.000	0.001
organism	1.740	0.008	1.746
p2LL	0.000	0.000	0.001
pm.abstGrep	23.774	0.060	25.692
pm.getabst	28.514	0.048	30.747
pm.titles	24.545	0.064	26.685
pmAbst2HTML	0.144	0.008	0.770
pmid2MIAME	0.004	0.000	0.000
pmidQuery	0	0	0
probesByLL	1.616	0.000	1.621
pubMedAbst-class	0.096	0.000	0.656
pubmed	0.040	0.004	0.595
readGEOAnn	0	0	0
serializeEnv	0.004	0.000	0.002
setRepository	0.000	0.000	0.002
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.08	0.00	0.08