Package: annotate

Version: 1.26.1

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.26.1.tar.gz

StartedAt: 2010-10-04 15:51:49 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 15:54:32 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 162.7 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/annotate.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.26.1'
* 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 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (annotate)

name	user	system	elapsed
ACCNUMStats	2.472	0.036	2.508
GO2heatmap	0.216	0.004	0.221
GOmnplot	0.104	0.012	0.119
HTMLPage-class	0	0	0
LL2homology	0.004	0.000	0.003
PMIDAmat	0.280	0.008	0.333
PWAmat	5.388	0.072	5.460
UniGeneQuery	0.004	0.000	0.002
accessionToUID	0.472	0.024	4.463
annPkgName	0	0	0
aqListGOIDs	0.528	0.048	0.587
buildChromLocation	1.252	0.040	1.294
buildPubMedAbst	0.112	0.004	4.873
chrCats	5.217	0.032	5.252
chromLocation-class	1.208	0.008	1.217
compatibleVersions	0.124	0.004	0.136
dropECode	0.104	0.000	0.101
entrezGeneByID	0.004	0.000	0.000
entrezGeneQuery	0.000	0.000	0.001
filterGOByOntology	0.004	0.000	0.003
findNeighbors	0.000	0.000	0.002
genbank	0.068	0.004	0.864
genelocator	0	0	0
getAnnMap	0.148	0.004	0.262
getEvidence	0.088	0.008	0.095
getGOTerm	0.108	0.004	0.111
getOntology	0.092	0.004	0.096
getPMInfo	0.972	0.004	1.520
getSYMBOL	0.256	0.020	0.398
getSeq4Acc	0.000	0.000	0.411
hasGOannote	0.056	0.004	0.057
hgByChroms	0.012	0.000	0.010
hgCLengths	0.000	0.000	0.001
hgu95Achroloc	0.052	0.004	0.056
hgu95Achrom	0.048	0.000	0.048
hgu95All	0.052	0.000	0.052
hgu95Asym	0.052	0.000	0.053
homoData-class	0.004	0.000	0.003
htmlpage	0.048	0.000	0.046
isValidkey	0.000	0.000	0.001
makeAnchor	0.000	0.000	0.001
neighborGeneFinder	0.000	0.000	0.001
organism	1.248	0.000	1.249
p2LL	0	0	0
pm.abstGrep	18.521	0.080	19.947
pm.getabst	19.681	0.056	21.289
pm.titles	19.842	0.080	21.475
pmAbst2HTML	0.192	0.000	0.744
pmid2MIAME	0.000	0.000	0.001
pmidQuery	0.000	0.000	0.001
probesByLL	2.300	0.008	2.307
pubMedAbst-class	0.132	0.004	0.732
pubmed	0.060	0.000	0.674
readGEOAnn	0	0	0
serializeEnv	0.000	0.004	0.003
setRepository	0.000	0.000	0.005
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.120	0.000	0.116