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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: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings annotate_1.31.0.tar.gz
StartedAt: 2011-05-09 12:16:22 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 12:22:08 -0700 (Mon, 09 May 2011)
EllapsedTime: 346.3 seconds
RetCode: 0
Status:  OK  
CheckDir: annotate.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/annotate.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* 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 '1.31.0'
* 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
ACCNUMStats2.630.032.67
GO2heatmap0.230.030.27
GOmnplot0.230.000.24
HTMLPage-class0.020.000.01
LL2homology000
PMIDAmat0.170.020.35
PWAmat5.700.065.78
UniGeneQuery000
accessionToUID0.460.033.81
annPkgName000
aqListGOIDs0.590.030.64
blastSequences 3.52 0.0283.38
buildChromLocation1.790.012.14
buildPubMedAbst0.100.020.92
chrCats4.540.034.89
chromLocation-class1.520.031.58
compatibleVersions0.060.030.14
dropECode0.060.020.16
entrezGeneByID000
entrezGeneQuery000
filterGOByOntology0.160.010.21
findNeighbors0.000.000.04
genbank0.130.002.50
genelocator000
getAnnMap 0.14 0.0233.34
getEvidence0.060.000.06
getGOTerm0.100.003.39
getOntology0.080.000.08
getPMInfo1.180.002.09
getSYMBOL 0.18 0.0014.25
getSeq4Acc0.000.000.17
hasGOannote0.040.000.04
hgByChroms0.020.000.02
hgCLengths0.000.000.03
hgu95Achroloc0.080.000.31
hgu95Achrom0.070.000.09
hgu95All0.080.000.08
hgu95Asym0.080.000.32
homoData-class000
htmlpage0.030.000.04
isValidkey000
makeAnchor000
neighborGeneFinder000
organism1.520.001.57
p2LL000
pm.abstGrep15.57 0.0220.41
pm.getabst14.78 0.0318.72
pm.titles15.37 0.0019.34
pmAbst2HTML0.080.001.22
pmid2MIAME000
pmidQuery000
probesByLL1.750.001.78
pubMedAbst-class0.060.000.70
pubmed0.030.000.75
readGEOAnn000
serializeEnv000
setRepository000
updateSymbolsToValidKeys000
usedChromGenes0.110.020.13