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Package 31/479HostnameOS / ArchBUILDCHECKBUILD BIN
annotate 1.31.0
Biocore Team c/o BioC user list
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annotate
Last Changed Rev: 54802 / Revision: 56603
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: annotate
Version: 1.31.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.31.0.tar.gz
StartedAt: 2011-07-07 01:21:10 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 01:26:12 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 301.9 seconds
RetCode: 0
Status:  OK 
CheckDir: annotate.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/annotate.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* 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 '1.31.0'
* 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 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 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 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 tools::resaveRdaFiles() or R CMD build --resave-data
                     old_size new_size compress
  hgByChroms.rda         72Kb     51Kb       xz
  hgu95AProbLocs.rda    155Kb    110Kb    bzip2
  hgu95Achroloc.rda     126Kb     86Kb    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

annotate.Rcheck/00install.out:

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

** 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)

annotate.Rcheck/annotate-Ex.timings:

nameusersystemelapsed
ACCNUMStats3.9420.0724.067
GO2heatmap0.3900.0240.422
GOmnplot0.2650.0100.278
HTMLPage-class0.0000.0000.001
LL2homology0.0030.0010.004
PMIDAmat0.3010.0170.440
PWAmat6.2920.2206.579
UniGeneQuery0.0020.0000.003
accessionToUID0.6100.0183.903
annPkgName000
aqListGOIDs0.8720.0860.964
blastSequences 5.387 0.08680.366
buildChromLocation2.0700.0772.221
buildPubMedAbst0.1450.0060.723
chrCats7.3140.5738.066
chromLocation-class2.0300.0382.110
compatibleVersions0.1490.0100.160
dropECode0.1260.0070.134
entrezGeneByID0.0010.0000.001
entrezGeneQuery000
filterGOByOntology0.2220.0070.232
findNeighbors0.0030.0010.004
genbank0.1370.0101.046
genelocator0.0000.0000.001
getAnnMap0.1850.0370.358
getEvidence0.1370.0090.150
getGOTerm0.1510.0050.199
getOntology0.1240.0070.131
getPMInfo1.5280.0132.253
getSYMBOL0.2820.0210.397
getSeq4Acc0.0010.0010.171
hasGOannote0.0840.0030.088
hgByChroms0.0180.0010.019
hgCLengths0.0030.0010.003
hgu95Achroloc0.1120.0060.131
hgu95Achrom0.1000.0050.111
hgu95All0.1110.0060.135
hgu95Asym0.1060.0050.114
homoData-class0.0030.0000.004
htmlpage0.0820.0040.094
isValidkey000
makeAnchor0.0000.0000.001
neighborGeneFinder0.0000.0000.001
organism2.1630.0462.292
p2LL000
pm.abstGrep21.769 0.15024.246
pm.getabst20.978 0.11322.731
pm.titles17.909 0.16219.985
pmAbst2HTML0.1420.0070.702
pmid2MIAME000
pmidQuery000
probesByLL2.6350.0572.758
pubMedAbst-class0.1510.0070.721
pubmed0.0720.0070.711
readGEOAnn0.0000.0000.001
serializeEnv0.0030.0010.005
setRepository0.0020.0010.004
updateSymbolsToValidKeys0.0010.0000.001
usedChromGenes0.1480.0110.163