BioC 2.12: CHECK report for annotate on george2

Package: annotate

Version: 1.37.4

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.37.4.tar.gz

StartedAt: 2013-03-24 23:57:41 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-25 00:05:28 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 466.5 seconds

RetCode: 0

Status: OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/annotate.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.37.4’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘annotate’ can be installed ... [20s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [127s/236s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        37.466  0.008  37.694
probesByLL     15.873  0.028  15.976
PWAmat         13.729  0.168  13.909
pm.titles      11.520  0.024  13.022
pm.abstGrep    10.361  0.028  11.662
pm.getabst      9.677  0.012  10.924
blastSequences  2.104  0.084  98.849
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [14s/14s]
 [15s/15s] OK
* checking for unstated dependencies in vignettes ... OK
* 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

* installing *source* package ‘annotate’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘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)

name	user	system	elapsed
ACCNUMStats	3.392	0.052	3.481
GO2heatmap	0.752	0.012	0.766
GOmnplot	0.212	0.016	0.230
HTMLPage-class	0.036	0.000	0.035
LL2homology	0.040	0.000	0.038
PMIDAmat	0.836	0.000	0.890
PWAmat	13.729	0.168	13.909
UniGeneQuery	0.004	0.012	0.014
accessionToUID	0.276	0.036	3.439
annPkgName	0.008	0.000	0.009
aqListGOIDs	0.648	0.052	0.701
blastSequences	2.104	0.084	98.849
buildChromLocation	1.749	0.012	1.760
buildPubMedAbst	0.140	0.008	0.667
chrCats	37.466	0.008	37.694
chromLocation-class	1.832	0.008	1.841
compatibleVersions	0.140	0.004	0.146
dropECode	0.164	0.000	0.165
entrezGeneByID	0.032	0.000	0.032
entrezGeneQuery	0.012	0.000	0.010
filterGOByOntology	0.120	0.016	0.137
findNeighbors	0.096	0.016	0.138
genbank	0.252	0.004	1.599
getAnnMap	0.192	0.024	0.561
getEvidence	0.124	0.004	0.130
getGOTerm	0.452	0.016	0.477
getOntology	0.144	0.008	0.151
getPMInfo	1.428	0.004	2.002
getSYMBOL	0.320	0.000	0.334
getSeq4Acc	0.008	0.000	0.244
hasGOannote	0.120	0.000	0.119
hgByChroms	0.020	0.000	0.022
hgCLengths	0.004	0.004	0.007
hgu95Achroloc	0.12	0.00	0.12
hgu95Achrom	0.072	0.004	0.072
hgu95All	0.076	0.004	0.081
hgu95Asym	0.104	0.000	0.104
homoData-class	0.044	0.000	0.042
htmlpage	0.128	0.000	0.129
isValidkey	0.008	0.000	0.008
makeAnchor	0.008	0.000	0.007
organism	1.528	0.004	1.532
p2LL	0.032	0.000	0.034
pm.abstGrep	10.361	0.028	11.662
pm.getabst	9.677	0.012	10.924
pm.titles	11.520	0.024	13.022
pmAbst2HTML	0.384	0.008	0.954
pmid2MIAME	0.004	0.000	0.003
pmidQuery	0.008	0.000	0.005
probesByLL	15.873	0.028	15.976
pubMedAbst-class	0.164	0.004	0.789
pubmed	0.068	0.004	0.660
readGEOAnn	0.012	0.000	0.010
serializeEnv	0.036	0.000	0.036
setRepository	0.040	0.000	0.041
updateSymbolsToValidKeys	0.028	0.000	0.031
usedChromGenes	0.140	0.004	0.149

Summary

Command output