BioC 3.4: CHECK report for annotate on morelia

Package: annotate

Version: 1.51.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.51.1.tar.gz

StartedAt: 2016-09-20 03:08:04 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:11:05 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 181.0 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 annotate_1.51.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/annotate.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.51.1’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘AnnotationDbi:::makeFlatBimapUsingSelect’
  See the note in ?`:::` about the use of this operator.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        10.252  0.100  10.421
accessionToUID  1.504  0.032   5.009
blastSequences  0.364  0.006  43.833
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’
 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
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-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	1.613	0.019	1.633
GO2heatmap	0.190	0.012	0.201
GOmnplot	0.098	0.005	0.103
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.001	0.000	0.001
PMIDAmat	0.148	0.005	0.350
PWAmat	2.891	0.056	2.949
UniGeneQuery	0.002	0.000	0.002
accessionToUID	1.504	0.032	5.009
annPkgName	0.001	0.000	0.000
aqListGOIDs	0.285	0.023	0.307
blastSequences	0.364	0.006	43.833
buildChromLocation	1.884	0.084	1.990
buildPubMedAbst	0.033	0.001	0.832
chrCats	10.252	0.100	10.421
chromLocation-class	1.783	0.014	1.797
compatibleVersions	0.041	0.001	0.041
dropECode	0.035	0.002	0.036
entrezGeneByID	0.000	0.000	0.001
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.068	0.005	0.073
findNeighbors	0.017	0.003	0.076
genbank	0.148	0.016	1.611
getAnnMap	0.032	0.010	0.234
getEvidence	0.036	0.001	0.038
getGOTerm	0.163	0.006	0.292
getOntology	0.045	0.002	0.046
getPMInfo	0.387	0.003	1.090
getSYMBOL	0.129	0.011	0.266
getSeq4Acc	0.013	0.001	0.524
hasGOannote	0.031	0.001	0.032
hgByChroms	0.017	0.004	0.020
hgCLengths	0.002	0.001	0.003
hgu95Achroloc	0.079	0.007	0.086
hgu95Achrom	0.067	0.009	0.077
hgu95All	0.076	0.007	0.083
hgu95Asym	0.049	0.006	0.055
homoData-class	0.002	0.000	0.002
htmlpage	0.019	0.001	0.020
isValidkey	0	0	0
makeAnchor	0.000	0.000	0.001
organism	1.940	0.027	1.967
p2LL	0	0	0
pm.abstGrep	0.725	0.023	2.279
pm.getabst	0.744	0.015	2.380
pm.titles	0.805	0.016	2.463
pmAbst2HTML	0.058	0.004	0.880
pmid2MIAME	0.001	0.000	0.001
pmidQuery	0.000	0.000	0.001
pubMedAbst-class	0.040	0.002	0.708
pubmed	0.019	0.002	0.752
readGEOAnn	0.001	0.000	0.000
serializeEnv	0.002	0.001	0.002
setRepository	0.003	0.000	0.004
updateSymbolsToValidKeys	0.000	0.000	0.001
usedChromGenes	0.098	0.017	0.116