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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: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch annotate_1.31.0.tar.gz
StartedAt: 2011-07-07 01:54:03 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 02:00:06 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 362.4 seconds
RetCode: 0
Status:  OK  
CheckDir: annotate.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/annotate.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 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
ACCNUMStats2.660.033.61
GO2heatmap0.300.010.55
GOmnplot0.280.000.28
HTMLPage-class000
LL2homology0.000.000.01
PMIDAmat0.260.000.89
PWAmat6.460.067.02
UniGeneQuery0.010.000.01
accessionToUID0.430.044.24
annPkgName000
aqListGOIDs0.460.065.20
blastSequences 3.82 0.0096.67
buildChromLocation1.780.031.89
buildPubMedAbst0.120.000.83
chrCats5.440.005.63
chromLocation-class1.460.001.55
compatibleVersions0.080.030.11
dropECode0.080.020.09
entrezGeneByID000
entrezGeneQuery000
filterGOByOntology0.160.000.16
findNeighbors0.010.000.02
genbank0.110.002.90
genelocator000
getAnnMap0.160.001.64
getEvidence0.070.010.09
getGOTerm0.130.020.86
getOntology0.080.000.08
getPMInfo1.10.01.9
getSYMBOL0.220.015.37
getSeq4Acc0.000.000.25
hasGOannote0.030.010.35
hgByChroms000
hgCLengths000
hgu95Achroloc0.090.000.09
hgu95Achrom0.060.000.07
hgu95All0.070.020.08
hgu95Asym0.060.000.06
homoData-class0.000.000.02
htmlpage0.030.000.05
isValidkey000
makeAnchor000
neighborGeneFinder000
organism1.470.001.48
p2LL000
pm.abstGrep21.25 0.0226.10
pm.getabst19.64 0.0423.57
pm.titles20.07 0.0823.18
pmAbst2HTML0.140.000.83
pmid2MIAME000
pmidQuery000
probesByLL1.610.021.62
pubMedAbst-class0.100.010.74
pubmed0.040.000.75
readGEOAnn000
serializeEnv000
setRepository000
updateSymbolsToValidKeys000
usedChromGenes0.090.000.10