BioC 2.12: CHECK report for annotate on lamb2

Package: annotate

Version: 1.37.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.37.3.tar.gz

StartedAt: 2013-01-16 00:31:49 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 00:40:59 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 549.9 seconds

RetCode: 0

Status: OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/annotate.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.37.3’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        28.938  0.008  28.966
probesByLL     11.145  0.012  11.171
PWAmat         11.017  0.124  11.143
pm.getabst      8.288  0.036   9.663
pm.titles       8.089  0.024   9.470
pm.abstGrep     8.053  0.004   9.547
blastSequences  1.892  0.032 148.837
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’
 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	2.960	0.044	3.008
GO2heatmap	0.288	0.004	0.291
GOmnplot	0.280	0.000	0.283
HTMLPage-class	0.016	0.000	0.019
LL2homology	0.016	0.004	0.020
PMIDAmat	0.252	0.012	0.322
PWAmat	11.017	0.124	11.143
UniGeneQuery	0.004	0.008	0.011
accessionToUID	0.260	0.012	4.678
annPkgName	0.004	0.004	0.005
aqListGOIDs	0.516	0.036	0.577
blastSequences	1.892	0.032	148.837
buildChromLocation	1.616	0.012	1.635
buildPubMedAbst	0.120	0.004	0.660
chrCats	28.938	0.008	28.966
chromLocation-class	1.564	0.004	1.570
compatibleVersions	0.112	0.004	0.114
dropECode	0.128	0.004	0.134
entrezGeneByID	0.384	0.000	0.386
entrezGeneQuery	0.004	0.000	0.007
filterGOByOntology	0.116	0.000	0.116
findNeighbors	0.064	0.004	0.091
genbank	0.204	0.004	2.089
getAnnMap	0.120	0.016	0.212
getEvidence	0.100	0.000	0.103
getGOTerm	0.148	0.008	0.334
getOntology	0.104	0.016	0.121
getPMInfo	1.040	0.000	1.667
getSYMBOL	0.260	0.024	0.295
getSeq4Acc	0.024	0.000	0.265
hasGOannote	0.048	0.004	0.051
hgByChroms	0.016	0.000	0.017
hgCLengths	0.024	0.000	0.020
hgu95Achroloc	0.080	0.004	0.083
hgu95Achrom	0.068	0.004	0.069
hgu95All	0.100	0.000	0.102
hgu95Asym	0.080	0.004	0.082
homoData-class	0.012	0.000	0.010
htmlpage	0.104	0.000	0.104
isValidkey	0.028	0.000	0.028
makeAnchor	0.004	0.000	0.004
organism	1.652	0.004	1.659
p2LL	0.004	0.000	0.003
pm.abstGrep	8.053	0.004	9.547
pm.getabst	8.288	0.036	9.663
pm.titles	8.089	0.024	9.470
pmAbst2HTML	0.200	0.008	0.722
pmid2MIAME	0.000	0.000	0.003
pmidQuery	0.016	0.000	0.020
probesByLL	11.145	0.012	11.171
pubMedAbst-class	0.124	0.000	0.671
pubmed	0.048	0.004	0.675
readGEOAnn	0.000	0.004	0.004
serializeEnv	0.028	0.000	0.029
setRepository	0.036	0.000	0.034
updateSymbolsToValidKeys	0.020	0.000	0.023
usedChromGenes	0.088	0.004	0.092

Summary

Command output