Package: annotate

Version: 1.32.3

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.32.3.tar.gz

StartedAt: 2012-03-23 23:14:48 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 23:20:06 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 318.1 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 2.14.2 (2012-02-29)
* 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 '1.32.3'
* 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 ... NOTE
File 'annotate/R/zzz.R':
  .onLoad calls:
    require(Biobase)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                     old_size new_size compress
  hgByChroms.rda         72Kb     51Kb       xz
  hgu95AProbLocs.rda    155Kb    110Kb    bzip2
  hgu95Achroloc.rda     126Kb     87Kb    bzip2
  hgu95Achrom.rda        70Kb     41Kb    bzip2
  hgu95All.rda           94Kb     62Kb    bzip2
  hgu95Asym.rda         113Kb     70Kb    bzip2
* 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
** 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	4.156	0.084	4.286
GO2heatmap	0.375	0.029	0.405
GOmnplot	0.284	0.013	0.303
HTMLPage-class	0.000	0.000	0.001
LL2homology	0.003	0.001	0.005
PMIDAmat	0.471	0.019	0.531
PWAmat	6.256	0.270	6.624
UniGeneQuery	0.003	0.000	0.003
accessionToUID	0.754	0.045	5.348
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.746	0.083	0.832
blastSequences	1.798	0.055	83.959
buildChromLocation	2.193	0.053	2.871
buildPubMedAbst	0.154	0.006	0.688
chrCats	6.901	0.639	7.734
chromLocation-class	2.005	0.054	2.075
compatibleVersions	0.159	0.011	0.170
dropECode	0.118	0.007	0.125
entrezGeneByID	0.000	0.000	0.001
entrezGeneQuery	0.000	0.000	0.001
filterGOByOntology	0.140	0.018	0.161
findNeighbors	0.002	0.000	0.003
genbank	0.246	0.022	1.763
genelocator	0	0	0
getAnnMap	0.144	0.039	0.334
getEvidence	0.117	0.008	0.135
getGOTerm	0.128	0.008	0.245
getOntology	0.136	0.007	0.150
getPMInfo	1.386	0.008	1.792
getSYMBOL	0.264	0.019	0.285
getSeq4Acc	0.001	0.000	0.239
hasGOannote	0.062	0.004	0.093
hgByChroms	0.017	0.001	0.018
hgCLengths	0.002	0.001	0.002
hgu95Achroloc	0.114	0.005	0.120
hgu95Achrom	0.103	0.005	0.110
hgu95All	0.108	0.005	0.114
hgu95Asym	0.119	0.007	0.127
homoData-class	0.003	0.000	0.003
htmlpage	0.068	0.004	0.079
isValidkey	0	0	0
makeAnchor	0	0	0
neighborGeneFinder	0.001	0.001	0.001
organism	2.180	0.052	2.240
p2LL	0	0	0
pm.abstGrep	5.820	0.037	7.616
pm.getabst	5.287	0.032	6.866
pm.titles	6.001	0.033	8.047
pmAbst2HTML	0.144	0.006	0.527
pmid2MIAME	0	0	0
pmidQuery	0.001	0.000	0.000
probesByLL	2.582	0.031	2.625
pubMedAbst-class	0.127	0.003	0.501
pubmed	0.070	0.003	0.466
readGEOAnn	0	0	0
serializeEnv	0.002	0.001	0.003
setRepository	0.002	0.001	0.002
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.142	0.007	0.149