BioC 2.9: CHECK report for annotate on liverpool

Package: annotate

Version: 1.32.1

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch annotate_1.32.1.tar.gz

StartedAt: 2012-01-09 01:46:11 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 01:50:11 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 240.3 seconds

RetCode: 0

Status: OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/annotate.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.32.1'
* 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 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.

Unable to load common controls?!

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
* 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	2.45	0.02	2.63
GO2heatmap	0.22	0.01	0.24
GOmnplot	0.17	0.00	0.17
HTMLPage-class	0	0	0
LL2homology	0	0	0
PMIDAmat	0.17	0.00	0.28
PWAmat	5.19	0.06	5.25
UniGeneQuery	0.02	0.00	0.01
accessionToUID	0.45	0.00	5.85
annPkgName	0	0	0
aqListGOIDs	0.42	0.08	0.50
blastSequences	0.99	0.03	79.82
buildChromLocation	1.41	0.03	1.44
buildPubMedAbst	0.10	0.00	0.44
chrCats	4.45	0.02	4.52
chromLocation-class	1.23	0.00	1.24
compatibleVersions	0.06	0.02	0.07
dropECode	0.07	0.01	0.08
entrezGeneByID	0	0	0
entrezGeneQuery	0	0	0
filterGOByOntology	0.06	0.03	0.10
findNeighbors	0	0	0
genbank	0.09	0.00	1.62
genelocator	0	0	0
getAnnMap	0.10	0.02	0.91
getEvidence	0.07	0.00	0.08
getGOTerm	0.08	0.00	0.62
getOntology	0.05	0.00	0.05
getPMInfo	0.84	0.01	1.62
getSYMBOL	0.16	0.04	0.25
getSeq4Acc	0.00	0.00	0.25
hasGOannote	0.03	0.01	0.06
hgByChroms	0	0	0
hgCLengths	0.00	0.02	0.02
hgu95Achroloc	0.06	0.00	0.06
hgu95Achrom	0.08	0.00	0.08
hgu95All	0.08	0.00	0.07
hgu95Asym	0.07	0.00	0.08
homoData-class	0	0	0
htmlpage	0.03	0.00	0.03
isValidkey	0	0	0
makeAnchor	0	0	0
neighborGeneFinder	0	0	0
organism	1.19	0.00	1.19
p2LL	0	0	0
pm.abstGrep	4.42	0.01	6.70
pm.getabst	4.91	0.00	7.08
pm.titles	4.55	0.00	6.38
pmAbst2HTML	0.09	0.00	0.54
pmid2MIAME	0	0	0
pmidQuery	0	0	0
probesByLL	1.63	0.00	1.63
pubMedAbst-class	0.12	0.00	0.49
pubmed	0.05	0.00	0.76
readGEOAnn	0	0	0
serializeEnv	0	0	0
setRepository	0	0	0
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.11	0.00	0.11

Summary

Command output