BioC 2.13: CHECK report for annotate on zin1

Package: annotate

Version: 1.40.1

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.40.1.tar.gz

StartedAt: 2014-04-04 23:28:03 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:32:22 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 258.8 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/annotate.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.40.1’
* 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 ... [9s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘AnnotationDbi’ ‘Biobase’ ‘XML’
A package should be listed in only one of these fields.
* 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘GOusage.Rnw’, ‘annotate.Rnw’, ‘chromLoc.Rnw’, ‘prettyOutput.Rnw’,
  ‘query.Rnw’, ‘useDataPkgs.Rnw’, ‘useHomology.Rnw’, ‘useProbeInfo.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [66s/157s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        20.774  0.012  20.818
probesByLL      8.225  0.004   8.245
pm.getabst      5.749  0.020   6.932
PWAmat          5.400  0.052   5.459
pm.abstGrep     5.044  0.040   6.260
pm.titles       4.544  0.008   5.891
blastSequences  1.616  0.092  82.750
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [8s/8s]
 [8s/8s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/annotate.Rcheck/00check.log’
for details.

* 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	2.108	0.012	2.124
GO2heatmap	0.172	0.008	0.182
GOmnplot	0.104	0.000	0.103
HTMLPage-class	0.008	0.000	0.012
LL2homology	0.008	0.000	0.007
PMIDAmat	0.292	0.008	0.322
PWAmat	5.400	0.052	5.459
UniGeneQuery	0.000	0.000	0.003
accessionToUID	0.180	0.008	2.800
annPkgName	0.000	0.000	0.001
aqListGOIDs	0.376	0.024	0.400
blastSequences	1.616	0.092	82.750
buildChromLocation	1.068	0.012	1.083
buildPubMedAbst	0.076	0.000	0.776
chrCats	20.774	0.012	20.818
chromLocation-class	1.172	0.008	1.182
compatibleVersions	0.076	0.004	0.080
dropECode	0.076	0.016	0.089
entrezGeneByID	0.008	0.000	0.011
entrezGeneQuery	0.000	0.000	0.003
filterGOByOntology	0.072	0.000	0.073
findNeighbors	0.052	0.000	0.072
genbank	0.164	0.004	1.154
getAnnMap	0.068	0.020	0.170
getEvidence	0.084	0.000	0.082
getGOTerm	0.252	0.004	0.270
getOntology	0.072	0.004	0.075
getPMInfo	0.816	0.004	1.303
getSYMBOL	0.208	0.008	0.226
getSeq4Acc	0.004	0.000	0.177
hasGOannote	0.060	0.000	0.059
hgByChroms	0.024	0.000	0.027
hgCLengths	0.004	0.000	0.002
hgu95Achroloc	0.072	0.000	0.073
hgu95Achrom	0.068	0.004	0.071
hgu95All	0.076	0.000	0.076
hgu95Asym	0.076	0.000	0.078
homoData-class	0.004	0.000	0.005
htmlpage	0.088	0.000	0.086
isValidkey	0.004	0.000	0.001
makeAnchor	0.004	0.000	0.001
organism	1.224	0.012	1.237
p2LL	0.000	0.000	0.001
pm.abstGrep	5.044	0.040	6.260
pm.getabst	5.749	0.020	6.932
pm.titles	4.544	0.008	5.891
pmAbst2HTML	0.160	0.004	0.781
pmid2MIAME	0.000	0.000	0.002
pmidQuery	0.004	0.000	0.002
probesByLL	8.225	0.004	8.245
pubMedAbst-class	0.100	0.000	0.586
pubmed	0.056	0.000	0.526
readGEOAnn	0.004	0.000	0.001
serializeEnv	0.004	0.000	0.003
setRepository	0.028	0.000	0.028
updateSymbolsToValidKeys	0.012	0.000	0.013
usedChromGenes	0.084	0.000	0.084