Package: annotate

Version: 1.32.3

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.32.3.tar.gz

StartedAt: 2012-03-23 23:05:12 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 23:09:35 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 262.3 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/annotate.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘1.32.3’
* 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 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	2.848	0.036	2.949
GO2heatmap	0.220	0.016	0.247
GOmnplot	0.144	0.012	0.167
HTMLPage-class	0	0	0
LL2homology	0.004	0.000	0.003
PMIDAmat	0.440	0.012	0.492
PWAmat	7.036	0.116	7.312
UniGeneQuery	0.000	0.000	0.002
accessionToUID	0.440	0.060	5.325
annPkgName	0.000	0.000	0.001
aqListGOIDs	0.468	0.024	0.492
blastSequences	1.265	0.032	73.951
buildChromLocation	1.656	0.024	1.772
buildPubMedAbst	0.100	0.004	0.637
chrCats	5.808	0.016	5.831
chromLocation-class	1.480	0.004	1.489
compatibleVersions	0.084	0.004	0.105
dropECode	0.072	0.008	0.080
entrezGeneByID	0	0	0
entrezGeneQuery	0.000	0.000	0.001
filterGOByOntology	0.084	0.000	0.084
findNeighbors	0.004	0.000	0.004
genbank	0.124	0.008	1.830
genelocator	0	0	0
getAnnMap	0.124	0.020	0.158
getEvidence	0.072	0.000	0.072
getGOTerm	0.116	0.008	0.124
getOntology	0.060	0.012	0.071
getPMInfo	1.180	0.004	1.780
getSYMBOL	0.232	0.012	0.260
getSeq4Acc	0.000	0.000	0.237
hasGOannote	0.048	0.004	0.050
hgByChroms	0.012	0.000	0.011
hgCLengths	0.004	0.000	0.002
hgu95Achroloc	0.068	0.008	0.075
hgu95Achrom	0.064	0.004	0.066
hgu95All	0.072	0.000	0.071
hgu95Asym	0.060	0.004	0.068
homoData-class	0.004	0.000	0.002
htmlpage	0.028	0.000	0.026
isValidkey	0	0	0
makeAnchor	0	0	0
neighborGeneFinder	0.004	0.000	0.001
organism	1.408	0.004	1.415
p2LL	0	0	0
pm.abstGrep	7.349	0.044	9.510
pm.getabst	5.700	0.020	7.361
pm.titles	6.469	0.024	8.035
pmAbst2HTML	0.092	0.004	0.605
pmid2MIAME	0	0	0
pmidQuery	0	0	0
probesByLL	1.624	0.008	1.634
pubMedAbst-class	0.084	0.000	0.596
pubmed	0.036	0.004	0.636
readGEOAnn	0	0	0
serializeEnv	0.000	0.000	0.002
setRepository	0.000	0.000	0.001
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.072	0.004	0.074