BioC 2.12: CHECK report for annotate on pelham

Package: annotate

Version: 1.38.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.38.0.tar.gz

StartedAt: 2013-05-01 02:12:41 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 02:19:43 -0700 (Wed, 01 May 2013)

EllapsedTime: 421.8 seconds

RetCode: 0

Status: OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/annotate.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.38.0'
* 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 ... [16s/18s] 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 ... [122s/218s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        36.271  0.407  37.398
probesByLL     15.166  0.113  15.470
PWAmat         10.243  0.228  10.657
pm.abstGrep     9.183  0.130  10.612
pm.titles       8.495  0.081   9.992
pm.getabst      8.220  0.090   9.645
blastSequences  1.766  0.118  84.460
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'annotate_unit_tests.R' [18s/18s]
 [18s/18s] 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
** testing if installed package can be loaded
* DONE (annotate)

name	user	system	elapsed
ACCNUMStats	4.070	0.081	4.174
GO2heatmap	0.319	0.021	0.341
GOmnplot	0.157	0.017	0.177
HTMLPage-class	0.022	0.003	0.026
LL2homology	0.291	0.005	0.301
PMIDAmat	0.326	0.020	0.470
PWAmat	10.243	0.228	10.657
UniGeneQuery	0.007	0.006	0.013
accessionToUID	0.304	0.032	2.976
annPkgName	0.004	0.003	0.007
aqListGOIDs	1.167	0.114	1.543
blastSequences	1.766	0.118	84.460
buildChromLocation	3.209	0.073	3.351
buildPubMedAbst	0.158	0.013	0.721
chrCats	36.271	0.407	37.398
chromLocation-class	3.389	0.052	3.488
compatibleVersions	0.153	0.016	0.169
dropECode	0.183	0.020	0.205
entrezGeneByID	0.005	0.006	0.011
entrezGeneQuery	0.005	0.005	0.010
filterGOByOntology	0.229	0.030	0.358
findNeighbors	0.094	0.018	0.147
genbank	0.257	0.027	1.240
getAnnMap	0.129	0.033	0.238
getEvidence	0.125	0.012	0.137
getGOTerm	0.573	0.033	0.749
getOntology	0.117	0.013	0.130
getPMInfo	1.321	0.019	1.927
getSYMBOL	0.387	0.053	0.549
getSeq4Acc	0.005	0.005	0.346
hasGOannote	0.567	0.016	0.643
hgByChroms	0.027	0.024	0.052
hgCLengths	0.006	0.005	0.011
hgu95Achroloc	0.109	0.022	0.137
hgu95Achrom	0.092	0.022	0.114
hgu95All	0.111	0.017	0.130
hgu95Asym	0.101	0.015	0.120
homoData-class	0.009	0.007	0.015
htmlpage	0.099	0.029	0.129
isValidkey	0.005	0.009	0.014
makeAnchor	0.004	0.003	0.007
organism	3.347	0.056	3.448
p2LL	0.037	0.006	0.044
pm.abstGrep	9.183	0.130	10.612
pm.getabst	8.220	0.090	9.645
pm.titles	8.495	0.081	9.992
pmAbst2HTML	0.213	0.023	0.859
pmid2MIAME	0.003	0.004	0.008
pmidQuery	0.005	0.005	0.011
probesByLL	15.166	0.113	15.470
pubMedAbst-class	0.150	0.021	0.692
pubmed	0.067	0.010	0.680
readGEOAnn	0.003	0.004	0.008
serializeEnv	0.031	0.014	0.047
setRepository	0.039	0.024	0.064
updateSymbolsToValidKeys	0.032	0.011	0.044
usedChromGenes	0.153	0.031	0.188

Summary

Command output