BioC 2.12: CHECK report for annotate on petty

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: 2013-03-25 01:07:09 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:14:43 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 454.7 seconds

RetCode: 0

Status: OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/annotate.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [15s/15s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [111s/291s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        36.389  0.689  37.100
probesByLL     12.645  0.050  12.702
pm.abstGrep     8.932  0.044  10.084
pm.getabst      8.757  0.053   9.905
pm.titles       8.277  0.054   9.533
PWAmat          6.992  0.213   7.218
blastSequences  2.360  0.112 171.040
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'annotate_unit_tests.R' [13s/13s]
 [14s/14s] 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	2.901	0.078	2.984
GO2heatmap	0.271	0.030	0.302
GOmnplot	0.165	0.020	0.187
HTMLPage-class	0.014	0.007	0.021
LL2homology	0.014	0.007	0.022
PMIDAmat	0.212	0.025	0.299
PWAmat	6.992	0.213	7.218
UniGeneQuery	0.019	0.009	0.029
accessionToUID	0.356	0.045	3.533
annPkgName	0.020	0.008	0.027
aqListGOIDs	0.847	0.113	0.962
blastSequences	2.360	0.112	171.040
buildChromLocation	2.134	0.072	2.209
buildPubMedAbst	0.166	0.014	0.715
chrCats	36.389	0.689	37.100
chromLocation-class	2.648	0.060	2.711
compatibleVersions	0.168	0.035	0.207
dropECode	0.183	0.029	0.215
entrezGeneByID	0.005	0.008	0.014
entrezGeneQuery	0.006	0.008	0.013
filterGOByOntology	0.204	0.033	0.240
findNeighbors	0.094	0.025	0.157
genbank	0.306	0.031	1.693
getAnnMap	0.173	0.046	0.264
getEvidence	0.173	0.027	0.203
getGOTerm	0.506	0.033	0.539
getOntology	0.160	0.033	0.193
getPMInfo	1.638	0.017	2.218
getSYMBOL	0.419	0.060	0.485
getSeq4Acc	0.005	0.006	0.294
hasGOannote	0.073	0.016	0.090
hgByChroms	0.037	0.012	0.088
hgCLengths	0.017	0.007	0.025
hgu95Achroloc	0.101	0.010	0.111
hgu95Achrom	0.086	0.010	0.096
hgu95All	0.102	0.011	0.112
hgu95Asym	0.125	0.014	0.140
homoData-class	0.025	0.008	0.033
htmlpage	0.090	0.028	0.118
isValidkey	0.019	0.009	0.029
makeAnchor	0.003	0.004	0.008
organism	1.833	0.041	1.878
p2LL	0.003	0.004	0.007
pm.abstGrep	8.932	0.044	10.084
pm.getabst	8.757	0.053	9.905
pm.titles	8.277	0.054	9.533
pmAbst2HTML	0.291	0.027	0.845
pmid2MIAME	0.002	0.004	0.006
pmidQuery	0.004	0.005	0.010
probesByLL	12.645	0.050	12.702
pubMedAbst-class	0.148	0.019	0.748
pubmed	0.067	0.015	0.669
readGEOAnn	0.003	0.005	0.008
serializeEnv	0.005	0.007	0.013
setRepository	0.042	0.023	0.065
updateSymbolsToValidKeys	0.016	0.010	0.026
usedChromGenes	0.159	0.014	0.173

Summary

Command output