Package: annotate

Version: 1.34.1

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.34.1.tar.gz

StartedAt: 2012-09-23 23:14:08 -0700 (Sun, 23 Sep 2012)

EndedAt: 2012-09-23 23:18:44 -0700 (Sun, 23 Sep 2012)

EllapsedTime: 276.6 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/annotate.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.34.1’
* 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	3.120	0.048	3.234
GO2heatmap	0.216	0.020	0.250
GOmnplot	0.160	0.000	0.163
HTMLPage-class	0	0	0
LL2homology	0.000	0.004	0.001
PMIDAmat	0.276	0.008	0.378
PWAmat	9.989	0.140	10.168
UniGeneQuery	0.004	0.000	0.003
accessionToUID	0.208	0.016	3.886
annPkgName	0.000	0.000	0.001
aqListGOIDs	0.468	0.036	0.508
blastSequences	1.440	0.064	68.267
buildChromLocation	1.304	0.000	1.304
buildPubMedAbst	0.084	0.000	0.593
chrCats	4.856	0.004	4.904
chromLocation-class	1.392	0.000	1.389
compatibleVersions	0.092	0.004	0.093
dropECode	0.100	0.000	0.104
entrezGeneByID	0	0	0
entrezGeneQuery	0.000	0.000	0.001
filterGOByOntology	0.076	0.008	0.087
findNeighbors	0.044	0.000	0.072
genbank	0.136	0.000	1.761
genelocator	0	0	0
getAnnMap	0.108	0.012	0.208
getEvidence	0.476	0.012	0.488
getGOTerm	0.132	0.008	0.233
getOntology	0.088	0.020	0.108
getPMInfo	0.956	0.008	1.608
getSYMBOL	0.244	0.004	0.313
getSeq4Acc	0.004	0.000	0.243
hasGOannote	0.044	0.004	0.051
hgByChroms	0.012	0.004	0.015
hgCLengths	0.000	0.004	0.002
hgu95Achroloc	0.080	0.000	0.079
hgu95Achrom	0.061	0.004	0.064
hgu95All	0.060	0.008	0.071
hgu95Asym	0.068	0.004	0.070
homoData-class	0.004	0.000	0.002
htmlpage	0.028	0.000	0.028
isValidkey	0	0	0
makeAnchor	0	0	0
neighborGeneFinder	0	0	0
organism	1.336	0.004	1.337
p2LL	0	0	0
pm.abstGrep	6.756	0.032	8.135
pm.getabst	5.428	0.048	7.023
pm.titles	6.165	0.008	7.657
pmAbst2HTML	0.096	0.004	0.619
pmid2MIAME	0	0	0
pmidQuery	0	0	0
probesByLL	1.724	0.000	1.724
pubMedAbst-class	0.092	0.000	0.681
pubmed	0.036	0.004	0.655
readGEOAnn	0.000	0.000	0.001
serializeEnv	0.004	0.000	0.002
setRepository	0.000	0.000	0.001
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.088	0.000	0.087