Package: annotate

Version: 1.34.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.34.1.tar.gz

StartedAt: 2012-09-23 23:14:04 -0700 (Sun, 23 Sep 2012)

EndedAt: 2012-09-23 23:18:24 -0700 (Sun, 23 Sep 2012)

EllapsedTime: 260.3 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/annotate.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 sizes of PDF files under 'inst/doc' ... 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	3.452	0.072	3.526
GO2heatmap	0.376	0.031	0.408
GOmnplot	0.168	0.013	0.185
HTMLPage-class	0	0	0
LL2homology	0	0	0
PMIDAmat	0.223	0.019	0.282
PWAmat	7.028	0.165	7.197
UniGeneQuery	0.003	0.001	0.003
accessionToUID	0.311	0.028	4.488
annPkgName	0.000	0.000	0.001
aqListGOIDs	0.905	0.089	0.997
blastSequences	1.528	0.055	58.759
buildChromLocation	1.620	0.047	1.670
buildPubMedAbst	0.083	0.004	0.510
chrCats	6.070	0.559	6.638
chromLocation-class	1.508	0.050	1.559
compatibleVersions	0.087	0.014	0.103
dropECode	0.104	0.009	0.112
entrezGeneByID	0.000	0.000	0.001
entrezGeneQuery	0.000	0.000	0.001
filterGOByOntology	0.112	0.017	0.129
findNeighbors	0.048	0.009	0.097
genbank	0.158	0.016	1.979
genelocator	0	0	0
getAnnMap	0.139	0.040	0.179
getEvidence	0.105	0.012	0.116
getGOTerm	0.147	0.006	0.153
getOntology	0.165	0.015	0.181
getPMInfo	1.466	0.007	1.895
getSYMBOL	0.375	0.031	0.431
getSeq4Acc	0.001	0.000	0.233
hasGOannote	0.074	0.007	0.081
hgByChroms	0.029	0.002	0.030
hgCLengths	0.002	0.001	0.003
hgu95Achroloc	0.136	0.007	0.143
hgu95Achrom	0.120	0.007	0.127
hgu95All	0.126	0.007	0.133
hgu95Asym	0.158	0.007	0.165
homoData-class	0.003	0.001	0.004
htmlpage	0.043	0.003	0.073
isValidkey	0	0	0
makeAnchor	0.000	0.000	0.001
neighborGeneFinder	0.001	0.000	0.001
organism	2.330	0.051	2.385
p2LL	0	0	0
pm.abstGrep	6.260	0.056	7.823
pm.getabst	4.726	0.032	6.205
pm.titles	4.092	0.032	5.619
pmAbst2HTML	0.119	0.006	0.516
pmid2MIAME	0	0	0
pmidQuery	0.000	0.000	0.001
probesByLL	2.323	0.032	2.361
pubMedAbst-class	0.101	0.005	0.494
pubmed	0.047	0.005	0.453
readGEOAnn	0	0	0
serializeEnv	0.002	0.001	0.003
setRepository	0.001	0.000	0.001
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.126	0.006	0.131