BioC 2.12: CHECK report for annotate on pelham

Package: annotate

Version: 1.37.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.37.4.tar.gz

StartedAt: 2013-03-24 02:14:31 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 02:22:06 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 455.1 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 beta (2013-03-21 r62346)
* 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 '1.37.4'
* 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 ... [17s/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 ... [119s/251s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        32.673  0.771  34.097
probesByLL     15.568  0.087  15.726
PWAmat         10.921  0.224  11.224
pm.titles       8.651  0.069   9.959
pm.abstGrep     8.565  0.081   9.838
pm.getabst      8.562  0.082   9.785
blastSequences  1.991  0.149 120.250
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'annotate_unit_tests.R' [15s/15s]
 [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	4.048	0.071	4.189
GO2heatmap	0.625	0.031	0.659
GOmnplot	0.226	0.018	0.248
HTMLPage-class	0.023	0.004	0.027
LL2homology	0.018	0.002	0.021
PMIDAmat	0.584	0.016	0.718
PWAmat	10.921	0.224	11.224
UniGeneQuery	0.007	0.008	0.026
accessionToUID	0.366	0.054	3.612
annPkgName	0.005	0.008	0.014
aqListGOIDs	0.763	0.118	1.117
blastSequences	1.991	0.149	120.250
buildChromLocation	3.206	0.090	3.297
buildPubMedAbst	0.145	0.018	0.700
chrCats	32.673	0.771	34.097
chromLocation-class	2.965	0.064	3.040
compatibleVersions	0.138	0.016	0.154
dropECode	0.165	0.016	0.183
entrezGeneByID	0.029	0.010	0.039
entrezGeneQuery	0.004	0.005	0.011
filterGOByOntology	0.130	0.023	0.240
findNeighbors	0.081	0.013	0.113
genbank	0.294	0.032	1.663
getAnnMap	0.166	0.036	0.284
getEvidence	0.209	0.024	0.234
getGOTerm	0.430	0.031	0.577
getOntology	0.119	0.013	0.133
getPMInfo	1.462	0.016	2.108
getSYMBOL	0.370	0.046	0.441
getSeq4Acc	0.006	0.004	0.250
hasGOannote	0.106	0.013	0.120
hgByChroms	0.026	0.017	0.043
hgCLengths	0.006	0.004	0.009
hgu95Achroloc	0.135	0.016	0.152
hgu95Achrom	0.095	0.018	0.115
hgu95All	0.107	0.019	0.127
hgu95Asym	0.129	0.022	0.151
homoData-class	0.038	0.010	0.049
htmlpage	0.121	0.030	0.152
isValidkey	0.005	0.009	0.014
makeAnchor	0.006	0.006	0.011
organism	3.343	0.067	3.435
p2LL	0.044	0.007	0.051
pm.abstGrep	8.565	0.081	9.838
pm.getabst	8.562	0.082	9.785
pm.titles	8.651	0.069	9.959
pmAbst2HTML	0.318	0.030	0.940
pmid2MIAME	0.003	0.005	0.007
pmidQuery	0.005	0.004	0.010
probesByLL	15.568	0.087	15.726
pubMedAbst-class	0.147	0.016	0.691
pubmed	0.067	0.016	0.624
readGEOAnn	0.003	0.005	0.007
serializeEnv	0.022	0.008	0.031
setRepository	0.028	0.018	0.046
updateSymbolsToValidKeys	0.021	0.009	0.030
usedChromGenes	0.149	0.022	0.242

Summary

Command output