BioC 2.6: CHECK report for annotate on pelham

Package: annotate

Version: 1.26.1

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings annotate_1.26.1.tar.gz

StartedAt: 2010-10-04 15:48:21 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 15:51:30 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 188.7 seconds

RetCode: 0

Status: OK

CheckDir: annotate.Rcheck

Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/annotate.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.26.1'
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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
  'openVignette()'. 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)

name	user	system	elapsed
ACCNUMStats	4.007	0.082	4.782
GO2heatmap	0.318	0.019	0.446
GOmnplot	0.164	0.008	0.191
HTMLPage-class	0.000	0.000	0.001
LL2homology	0.004	0.001	0.005
PMIDAmat	0.301	0.017	0.431
PWAmat	5.330	0.170	6.168
UniGeneQuery	0.004	0.000	0.003
accessionToUID	0.331	0.014	4.029
annPkgName	0.000	0.001	0.001
aqListGOIDs	0.835	0.082	1.148
buildChromLocation	1.916	0.074	2.293
buildPubMedAbst	0.136	0.004	0.699
chrCats	7.599	0.588	9.579
chromLocation-class	1.905	0.052	2.681
compatibleVersions	0.144	0.009	0.183
dropECode	0.127	0.007	0.188
entrezGeneByID	0.001	0.000	0.002
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.004	0.001	0.005
findNeighbors	0.004	0.001	0.006
genbank	0.106	0.009	1.233
genelocator	0	0	0
getAnnMap	0.194	0.034	0.422
getEvidence	0.113	0.006	0.122
getGOTerm	0.174	0.007	0.286
getOntology	0.107	0.005	0.112
getPMInfo	1.520	0.011	2.282
getSYMBOL	0.317	0.019	0.424
getSeq4Acc	0.005	0.001	0.452
hasGOannote	0.066	0.003	0.071
hgByChroms	0.017	0.001	0.019
hgCLengths	0.002	0.001	0.003
hgu95Achroloc	0.103	0.005	0.108
hgu95Achrom	0.090	0.004	0.094
hgu95All	0.096	0.005	0.131
hgu95Asym	0.098	0.004	0.106
homoData-class	0.004	0.000	0.005
htmlpage	0.210	0.007	0.577
isValidkey	0.000	0.000	0.001
makeAnchor	0.001	0.000	0.001
neighborGeneFinder	0.002	0.000	0.002
organism	1.858	0.031	1.991
p2LL	0	0	0
pm.abstGrep	15.356	0.125	18.276
pm.getabst	17.419	0.083	19.973
pm.titles	15.227	0.081	17.375
pmAbst2HTML	0.202	0.006	0.755
pmid2MIAME	0.001	0.000	0.000
pmidQuery	0.001	0.000	0.001
probesByLL	2.733	0.040	2.785
pubMedAbst-class	0.131	0.004	0.697
pubmed	0.065	0.005	0.724
readGEOAnn	0.000	0.000	0.001
serializeEnv	0.002	0.001	0.004
setRepository	0.004	0.001	0.004
updateSymbolsToValidKeys	0.001	0.000	0.001
usedChromGenes	0.123	0.005	0.127

Summary

Command output