BioC 2.14: CHECK report for annotate on morelia

Package: annotate

Version: 1.42.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.42.1.tar.gz

StartedAt: 2014-10-07 21:09:06 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:18:57 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 590.9 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.42.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/annotate.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.42.1’
* 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 ... [11s/11s] 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 ... NOTE
Unexported object imported by a ':::' call: ‘AnnotationDbi:::makeFlatBimapUsingSelect’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [63s/459s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        22.858  0.880  23.759
probesByLL      8.365  0.016   8.392
PWAmat          5.919  0.089   6.010
pm.titles       1.476  0.026   5.932
blastSequences  1.220  0.049 382.684
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [9s/9s]
 [9s/9s] 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
  ‘/Users/biocbuild/bbs-2.14-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	2.646	0.031	2.680
GO2heatmap	0.204	0.013	0.217
GOmnplot	0.234	0.009	0.242
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.001	0.000	0.001
PMIDAmat	0.187	0.009	0.195
PWAmat	5.919	0.089	6.010
UniGeneQuery	0.002	0.000	0.002
accessionToUID	0.238	0.015	3.741
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.542	0.040	0.584
blastSequences	1.220	0.049	382.684
buildChromLocation	2.564	0.038	2.604
buildPubMedAbst	0.080	0.002	0.502
chrCats	22.858	0.880	23.759
chromLocation-class	2.486	0.024	2.513
compatibleVersions	0.096	0.006	0.102
dropECode	0.081	0.004	0.084
entrezGeneByID	0.001	0.000	0.001
entrezGeneQuery	0.001	0.000	0.002
filterGOByOntology	0.101	0.006	0.106
findNeighbors	0.048	0.004	0.101
genbank	0.187	0.008	1.157
getAnnMap	0.110	0.013	0.234
getEvidence	0.107	0.007	0.113
getGOTerm	0.305	0.009	0.317
getOntology	0.097	0.004	0.101
getPMInfo	0.822	0.005	1.303
getSYMBOL	0.215	0.016	0.231
getSeq4Acc	0.003	0.001	0.185
hasGOannote	0.077	0.002	0.079
hgByChroms	0.017	0.005	0.023
hgCLengths	0.002	0.001	0.002
hgu95Achroloc	0.082	0.011	0.093
hgu95Achrom	0.069	0.011	0.081
hgu95All	0.080	0.011	0.091
hgu95Asym	0.083	0.010	0.094
homoData-class	0.005	0.001	0.005
htmlpage	0.034	0.001	0.035
isValidkey	0.001	0.000	0.001
makeAnchor	0.001	0.000	0.002
organism	2.230	0.034	2.265
p2LL	0.001	0.000	0.001
pm.abstGrep	1.280	0.025	2.559
pm.getabst	1.333	0.021	2.560
pm.titles	1.476	0.026	5.932
pmAbst2HTML	0.094	0.003	0.476
pmid2MIAME	0.001	0.000	0.001
pmidQuery	0.002	0.000	0.002
probesByLL	8.365	0.016	8.392
pubMedAbst-class	0.069	0.002	1.023
pubmed	0.048	0.002	0.514
readGEOAnn	0.000	0.000	0.001
serializeEnv	0.003	0.000	0.004
setRepository	0.004	0.000	0.004
updateSymbolsToValidKeys	0.000	0.000	0.001
usedChromGenes	0.103	0.008	0.110