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Package 31/462HostnameOS / ArchBUILDCHECKBUILD BIN
annotate 1.31.0
Biocore Team c/o BioC user list
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annotate
Last Changed Rev: 54802 / Revision: 55359
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 
pelham 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: 2011-05-09 13:01:58 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 13:06:41 -0700 (Mon, 09 May 2011)
EllapsedTime: 283.5 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) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* 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 ... OK
* 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
ACCNUMStats3.8050.0673.908
GO2heatmap0.4800.0260.533
GOmnplot0.2680.0170.285
HTMLPage-class0.0010.0000.000
LL2homology0.0040.0010.005
PMIDAmat0.2760.0160.412
PWAmat5.7600.2055.997
UniGeneQuery0.0030.0000.003
accessionToUID0.5950.0165.760
annPkgName0.0010.0000.001
aqListGOIDs0.8440.0880.962
blastSequences 5.167 0.07477.130
buildChromLocation2.1550.0732.309
buildPubMedAbst0.1250.0050.733
chrCats6.8220.5507.472
chromLocation-class1.9590.0352.021
compatibleVersions0.1440.0100.168
dropECode0.1210.0070.128
entrezGeneByID0.0010.0000.002
entrezGeneQuery0.0010.0000.001
filterGOByOntology0.2340.0070.241
findNeighbors0.0040.0010.005
genbank0.1070.0081.034
genelocator0.0000.0000.001
getAnnMap0.1940.0350.335
getEvidence0.1160.0080.126
getGOTerm0.3140.0090.422
getOntology0.1130.0070.120
getPMInfo1.3760.0092.030
getSYMBOL0.2900.0200.384
getSeq4Acc0.0040.0010.179
hasGOannote0.0640.0030.067
hgByChroms0.0190.0010.020
hgCLengths0.0020.0010.003
hgu95Achroloc0.1110.0050.116
hgu95Achrom0.0970.0040.101
hgu95All0.1130.0050.117
hgu95Asym0.1000.0040.104
homoData-class0.0030.0000.004
htmlpage0.0690.0030.077
isValidkey0.0010.0010.001
makeAnchor0.0010.0000.001
neighborGeneFinder0.0020.0010.002
organism2.0220.0432.079
p2LL0.0000.0000.001
pm.abstGrep20.481 0.15423.097
pm.getabst18.779 0.10920.587
pm.titles19.930 0.15722.186
pmAbst2HTML0.1880.0131.175
pmid2MIAME000
pmidQuery0.0010.0000.000
probesByLL2.6590.0442.721
pubMedAbst-class0.1430.0060.706
pubmed0.0720.0070.722
readGEOAnn0.0010.0000.001
serializeEnv0.0030.0010.004
setRepository0.0050.0010.005
updateSymbolsToValidKeys000
usedChromGenes0.1380.0090.150