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Package 31/467HostnameOS / ArchBUILDCHECKBUILD BIN
annotate 1.30.1
Biocore Team c/o BioC user list
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/annotate
Last Changed Rev: 57663 / Revision: 59457
Last Changed Date: 2011-08-25 10:31:40 -0700 (Thu, 25 Aug 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: annotate
Version: 1.30.1
Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch annotate_1.30.1.tar.gz
StartedAt: 2011-10-20 12:55:41 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 13:00:04 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 263.0 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 2.13.2 (2011-09-30)
* 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 '1.30.1'
* checking package namespace 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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' ... WARNING
Package vignette(s) without corresponding PDF:
   GOusage.Rnw
   annotate.Rnw
   chromLoc.Rnw
   prettyOutput.Rnw
   query.Rnw
   useDataPkgs.Rnw
   useHomology.Rnw
   useProbeInfo.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (annotate)

annotate.Rcheck/annotate-Ex.timings:

nameusersystemelapsed
ACCNUMStats2.470.012.55
GO2heatmap0.260.021.43
GOmnplot0.130.030.16
HTMLPage-class000
LL2homology000
PMIDAmat0.280.000.53
PWAmat5.440.065.55
UniGeneQuery000
accessionToUID0.510.054.98
annPkgName000
aqListGOIDs0.50.00.5
blastSequences 3.92 0.0098.44
buildChromLocation1.60.01.6
buildPubMedAbst0.110.000.75
chrCats5.010.035.28
chromLocation-class1.310.001.32
compatibleVersions0.080.020.09
dropECode0.090.000.09
entrezGeneByID000
entrezGeneQuery000
filterGOByOntology0.110.000.14
findNeighbors000
genbank0.110.001.80
genelocator000
getAnnMap0.140.020.98
getEvidence0.110.000.11
getGOTerm0.150.000.57
getOntology0.080.000.08
getPMInfo1.130.001.88
getSYMBOL0.250.000.43
getSeq4Acc0.000.000.18
hasGOannote0.040.000.06
hgByChroms0.020.000.01
hgCLengths000
hgu95Achroloc0.080.000.08
hgu95Achrom0.060.000.06
hgu95All0.080.000.08
hgu95Asym0.060.000.07
homoData-class000
htmlpage0.060.000.06
isValidkey000
makeAnchor000
neighborGeneFinder000
organism1.390.011.40
p2LL000
pm.abstGrep20.12 0.0321.92
pm.getabst16.08 0.0418.16
pm.titles14.21 0.0715.97
pmAbst2HTML0.390.001.20
pmid2MIAME000
pmidQuery000
probesByLL1.450.001.45
pubMedAbst-class0.070.000.72
pubmed0.030.000.81
readGEOAnn000
serializeEnv0.020.000.02
setRepository000
updateSymbolsToValidKeys000
usedChromGenes0.080.000.07