Package: annotate

Version: 1.34.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.34.0.tar.gz

StartedAt: 2012-03-31 23:32:54 -0700 (Sat, 31 Mar 2012)

EndedAt: 2012-03-31 23:36:45 -0700 (Sat, 31 Mar 2012)

EllapsedTime: 230.6 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/annotate.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.34.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* 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
** installing vignettes
   '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	2.316	0.020	2.406
GO2heatmap	0.284	0.012	0.317
GOmnplot	0.112	0.012	0.142
HTMLPage-class	0	0	0
LL2homology	0.000	0.000	0.001
PMIDAmat	0.136	0.012	0.172
PWAmat	5.508	0.076	5.609
UniGeneQuery	0.004	0.000	0.002
accessionToUID	0.440	0.024	4.456
annPkgName	0	0	0
aqListGOIDs	0.372	0.036	0.442
blastSequences	1.064	0.032	82.038
buildChromLocation	1.052	0.012	1.083
buildPubMedAbst	0.068	0.004	0.678
chrCats	3.725	0.008	3.755
chromLocation-class	0.960	0.016	1.068
compatibleVersions	0.080	0.004	0.115
dropECode	0.080	0.012	0.114
entrezGeneByID	0	0	0
entrezGeneQuery	0	0	0
filterGOByOntology	0.076	0.008	0.094
findNeighbors	0.040	0.000	0.049
genbank	0.128	0.004	1.934
genelocator	0	0	0
getAnnMap	0.080	0.008	0.099
getEvidence	0.088	0.004	0.108
getGOTerm	0.108	0.000	0.117
getOntology	0.064	0.008	0.091
getPMInfo	0.824	0.016	1.465
getSYMBOL	0.192	0.004	0.227
getSeq4Acc	0.000	0.000	0.236
hasGOannote	0.040	0.004	0.052
hgByChroms	0.016	0.000	0.022
hgCLengths	0.000	0.000	0.007
hgu95Achroloc	0.076	0.000	0.087
hgu95Achrom	0.048	0.004	0.069
hgu95All	0.060	0.000	0.073
hgu95Asym	0.064	0.000	0.074
homoData-class	0.000	0.000	0.002
htmlpage	0.040	0.000	0.041
isValidkey	0	0	0
makeAnchor	0	0	0
neighborGeneFinder	0	0	0
organism	1.032	0.000	1.052
p2LL	0	0	0
pm.abstGrep	3.860	0.008	5.795
pm.getabst	4.004	0.012	5.895
pm.titles	3.789	0.000	5.420
pmAbst2HTML	0.064	0.012	0.670
pmid2MIAME	0	0	0
pmidQuery	0	0	0
probesByLL	1.256	0.004	1.281
pubMedAbst-class	0.068	0.004	0.764
pubmed	0.032	0.004	0.631
readGEOAnn	0	0	0
serializeEnv	0.000	0.000	0.002
setRepository	0.000	0.000	0.001
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.088	0.000	0.101