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Package 25/436HostnameOS / ArchBUILDCHECKBUILD BIN
annotate 1.29.2
Biocore Team c/o BioC user list
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annotate
Last Changed Rev: 52541 / Revision: 53255
Last Changed Date: 2011-02-08 13:50:10 -0800 (Tue, 08 Feb 2011)
lamb2 Linux (openSUSE 11.2) / 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  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: annotate
Version: 1.29.2
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.29.2.tar.gz
StartedAt: 2011-02-24 17:21:47 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 17:25:55 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 248.6 seconds
RetCode: 0
Status:  OK 
CheckDir: annotate.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/annotate.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.29.2’
* 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 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:
  GO hsahomology humanCHRLOC
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... 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 ...
** testing if installed package can be loaded

* DONE (annotate)

annotate.Rcheck/annotate-Ex.timings:

nameusersystemelapsed
ACCNUMStats2.3640.0202.401
GO2heatmap0.2440.0040.259
GOmnplot0.1520.0120.165
HTMLPage-class000
LL2homology0.0040.0000.004
PMIDAmat0.3240.0040.426
PWAmat5.1680.0845.272
UniGeneQuery0.0040.0000.002
accessionToUID0.2040.0286.354
annPkgName000
aqListGOIDs0.4920.0280.534
blastSequences 2.816 0.03272.836
buildChromLocation1.2800.0041.287
buildPubMedAbst0.1280.0001.303
chrCats5.2650.0125.361
chromLocation-class1.2720.0081.290
compatibleVersions0.1080.0040.111
dropECode0.0920.0080.098
entrezGeneByID0.0000.0000.001
entrezGeneQuery000
filterGOByOntology0.0040.0000.003
findNeighbors0.0040.0000.002
genbank0.0880.0002.921
genelocator000
getAnnMap0.1360.0160.279
getEvidence0.0720.0120.083
getGOTerm0.1400.0000.196
getOntology0.1000.0040.104
getPMInfo1.2280.0002.092
getSYMBOL0.1960.0160.271
getSeq4Acc0.0000.0000.193
hasGOannote0.0520.0000.049
hgByChroms0.0080.0000.009
hgCLengths0.0000.0000.002
hgu95Achroloc0.0680.0040.074
hgu95Achrom0.0520.0000.053
hgu95All0.0520.0040.055
hgu95Asym0.0600.0040.062
homoData-class0.0040.0000.003
htmlpage0.0480.0000.055
isValidkey000
makeAnchor000
neighborGeneFinder0.0000.0000.001
organism1.3680.0041.379
p2LL000
pm.abstGrep20.601 0.08823.299
pm.getabst20.438 0.04023.591
pm.titles20.197 0.04825.900
pmAbst2HTML0.1560.0000.877
pmid2MIAME0.0000.0000.001
pmidQuery000
probesByLL1.7680.0161.928
pubMedAbst-class0.0960.0000.658
pubmed0.0600.0080.634
readGEOAnn000
serializeEnv0.0000.0000.002
setRepository0.0040.0000.001
updateSymbolsToValidKeys000
usedChromGenes0.0680.0040.076