BioC 3.5: CHECK report for annotate on veracruz2

Package: annotate

Version: 1.54.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.54.0.tar.gz

StartedAt: 2017-10-18 00:24:46 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:27:29 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 163.3 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_1.54.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/annotate.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.54.0’
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        16.266  0.093  16.922
blastSequences  0.246  0.011  23.625
* 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: OK

* 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	2.562	0.049	2.685
GO2heatmap	0.247	0.009	0.261
GOmnplot	0.093	0.007	0.107
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.001	0.001	0.001
PMIDAmat	0.125	0.003	0.142
PWAmat	2.381	0.042	2.503
UniGeneQuery	0.002	0.000	0.003
accessionToUID	0.709	0.032	2.040
annPkgName	0.001	0.000	0.002
aqListGOIDs	0.350	0.020	0.373
blastSequences	0.246	0.011	23.625
buildChromLocation	0.686	0.022	0.720
buildPubMedAbst	0.105	0.002	0.467
chrCats	16.266	0.093	16.922
chromLocation-class	0.527	0.025	0.578
compatibleVersions	0.044	0.002	0.046
dropECode	0.050	0.001	0.051
entrezGeneByID	0.001	0.000	0.002
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.092	0.003	0.098
findNeighbors	0.020	0.002	0.025
genbank	0.121	0.013	0.594
getAnnMap	0.039	0.010	0.052
getEvidence	0.135	0.003	0.142
getGOTerm	0.254	0.007	0.278
getOntology	0.084	0.005	0.095
getPMInfo	0.613	0.006	0.986
getSYMBOL	0.140	0.011	0.163
getSeq4Acc	0.007	0.001	0.257
hasGOannote	0.021	0.001	0.023
hgByChroms	0.015	0.005	0.019
hgCLengths	0.002	0.001	0.003
hgu95Achroloc	0.052	0.008	0.062
hgu95Achrom	0.046	0.009	0.057
hgu95All	0.050	0.007	0.059
hgu95Asym	0.059	0.010	0.071
homoData-class	0.003	0.000	0.004
htmlpage	0.432	0.005	0.446
isValidkey	0.000	0.000	0.001
makeAnchor	0.001	0.000	0.000
organism	0.460	0.008	0.477
p2LL	0	0	0
pm.abstGrep	0.673	0.022	1.556
pm.getabst	0.922	0.020	1.934
pm.titles	0.761	0.020	1.644
pmAbst2HTML	0.105	0.003	0.479
pmid2MIAME	0.001	0.000	0.001
pmidQuery	0.001	0.000	0.002
pubMedAbst-class	0.032	0.001	0.382
pubmed	0.019	0.001	0.364
readGEOAnn	0.000	0.000	0.001
serializeEnv	0.002	0.000	0.003
setRepository	0.004	0.001	0.004
updateSymbolsToValidKeys	0.001	0.000	0.001
usedChromGenes	0.063	0.006	0.069