Package: annotate

Version: 1.31.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.31.0.tar.gz

StartedAt: 2011-05-09 13:01:58 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:06:41 -0700 (Mon, 09 May 2011)

EllapsedTime: 283.5 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/annotate.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* 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 ‘1.31.0’
* 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 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
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	3.805	0.067	3.908
GO2heatmap	0.480	0.026	0.533
GOmnplot	0.268	0.017	0.285
HTMLPage-class	0.001	0.000	0.000
LL2homology	0.004	0.001	0.005
PMIDAmat	0.276	0.016	0.412
PWAmat	5.760	0.205	5.997
UniGeneQuery	0.003	0.000	0.003
accessionToUID	0.595	0.016	5.760
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.844	0.088	0.962
blastSequences	5.167	0.074	77.130
buildChromLocation	2.155	0.073	2.309
buildPubMedAbst	0.125	0.005	0.733
chrCats	6.822	0.550	7.472
chromLocation-class	1.959	0.035	2.021
compatibleVersions	0.144	0.010	0.168
dropECode	0.121	0.007	0.128
entrezGeneByID	0.001	0.000	0.002
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.234	0.007	0.241
findNeighbors	0.004	0.001	0.005
genbank	0.107	0.008	1.034
genelocator	0.000	0.000	0.001
getAnnMap	0.194	0.035	0.335
getEvidence	0.116	0.008	0.126
getGOTerm	0.314	0.009	0.422
getOntology	0.113	0.007	0.120
getPMInfo	1.376	0.009	2.030
getSYMBOL	0.290	0.020	0.384
getSeq4Acc	0.004	0.001	0.179
hasGOannote	0.064	0.003	0.067
hgByChroms	0.019	0.001	0.020
hgCLengths	0.002	0.001	0.003
hgu95Achroloc	0.111	0.005	0.116
hgu95Achrom	0.097	0.004	0.101
hgu95All	0.113	0.005	0.117
hgu95Asym	0.100	0.004	0.104
homoData-class	0.003	0.000	0.004
htmlpage	0.069	0.003	0.077
isValidkey	0.001	0.001	0.001
makeAnchor	0.001	0.000	0.001
neighborGeneFinder	0.002	0.001	0.002
organism	2.022	0.043	2.079
p2LL	0.000	0.000	0.001
pm.abstGrep	20.481	0.154	23.097
pm.getabst	18.779	0.109	20.587
pm.titles	19.930	0.157	22.186
pmAbst2HTML	0.188	0.013	1.175
pmid2MIAME	0	0	0
pmidQuery	0.001	0.000	0.000
probesByLL	2.659	0.044	2.721
pubMedAbst-class	0.143	0.006	0.706
pubmed	0.072	0.007	0.722
readGEOAnn	0.001	0.000	0.001
serializeEnv	0.003	0.001	0.004
setRepository	0.005	0.001	0.005
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.138	0.009	0.150