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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: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings annotate_1.29.2.tar.gz
StartedAt: 2011-02-24 18:04:31 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 18:08:40 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 249.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: annotate.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/annotate.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 '1.29.2'
* 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 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' ... WARNING
Package vignettes without corresponding PDF:


D:/biocbld/bbs-2.8-bioc/meat/annotate.Rcheck/00_pkg_src/annotate/inst/doc/useHomology.Rnw
 SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/annotate.Rcheck/00check.log'
for details

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
ACCNUMStats2.830.045.15
GO2heatmap0.300.020.31
GOmnplot0.190.000.19
HTMLPage-class000
LL2homology000
PMIDAmat0.330.031.06
PWAmat5.920.035.95
UniGeneQuery000
accessionToUID0.330.027.97
annPkgName000
aqListGOIDs0.640.010.72
blastSequences 2.96 0.0373.86
buildChromLocation1.310.021.33
buildPubMedAbst0.080.020.75
chrCats4.990.015.17
chromLocation-class1.340.001.35
compatibleVersions0.110.000.11
dropECode0.110.000.11
entrezGeneByID0.020.000.01
entrezGeneQuery000
filterGOByOntology000
findNeighbors0.010.000.02
genbank0.10.01.8
genelocator000
getAnnMap0.140.020.76
getEvidence0.070.010.10
getGOTerm0.160.000.29
getOntology0.060.030.10
getPMInfo1.240.022.04
getSYMBOL0.170.030.55
getSeq4Acc0.000.000.19
hasGOannote0.030.020.04
hgByChroms0.020.000.02
hgCLengths000
hgu95Achroloc0.090.000.09
hgu95Achrom0.060.000.07
hgu95All0.070.000.06
hgu95Asym0.060.000.06
homoData-class0.010.000.02
htmlpage0.030.010.04
isValidkey000
makeAnchor000
neighborGeneFinder000
organism1.430.001.43
p2LL000
pm.abstGrep15.70 0.0019.93
pm.getabst16.56 0.0520.08
pm.titles15.57 0.0518.33
pmAbst2HTML0.130.000.92
pmid2MIAME000
pmidQuery000
probesByLL1.700.061.76
pubMedAbst-class0.110.000.75
pubmed0.060.002.05
readGEOAnn000
serializeEnv0.020.000.02
setRepository000
updateSymbolsToValidKeys000
usedChromGenes0.090.000.09