BioC 3.5: CHECK report for annotate on malbec2

Package: annotate

Version: 1.54.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.54.0.tar.gz

StartedAt: 2017-08-15 21:07:23 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:09:46 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 142.9 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.54.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/annotate.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.54.0’
* 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 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        10.844  0.016  10.868
blastSequences  0.688  0.100  18.812
* 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	1.824	0.016	1.843
GO2heatmap	0.256	0.004	0.317
GOmnplot	0.096	0.008	0.108
HTMLPage-class	0.000	0.000	0.001
LL2homology	0.000	0.000	0.001
PMIDAmat	0.136	0.000	0.197
PWAmat	1.836	0.020	1.858
UniGeneQuery	0.004	0.000	0.002
accessionToUID	1.224	0.060	3.235
annPkgName	0.000	0.000	0.001
aqListGOIDs	0.244	0.008	0.251
blastSequences	0.688	0.100	18.812
buildChromLocation	2.036	0.004	2.089
buildPubMedAbst	0.224	0.012	0.742
chrCats	10.844	0.016	10.868
chromLocation-class	1.356	0.012	1.366
compatibleVersions	0.048	0.000	0.048
dropECode	0.044	0.000	0.041
entrezGeneByID	0	0	0
entrezGeneQuery	0.004	0.000	0.001
filterGOByOntology	0.060	0.008	0.070
findNeighbors	0.016	0.008	0.068
genbank	0.320	0.004	0.886
getAnnMap	0.048	0.000	0.234
getEvidence	0.112	0.000	0.115
getGOTerm	0.388	0.000	0.389
getOntology	0.052	0.004	0.056
getPMInfo	0.880	0.012	1.498
getSYMBOL	0.180	0.008	0.208
getSeq4Acc	0.084	0.004	0.430
hasGOannote	0.048	0.000	0.049
hgByChroms	0.020	0.004	0.023
hgCLengths	0.004	0.000	0.002
hgu95Achroloc	0.092	0.008	0.099
hgu95Achrom	0.072	0.008	0.083
hgu95All	0.076	0.004	0.084
hgu95Asym	0.088	0.008	0.097
homoData-class	0.004	0.000	0.003
htmlpage	0.512	0.000	0.515
isValidkey	0.000	0.000	0.001
makeAnchor	0.000	0.000	0.001
organism	1.548	0.000	1.549
p2LL	0.000	0.000	0.001
pm.abstGrep	1.148	0.008	2.292
pm.getabst	0.860	0.004	1.912
pm.titles	0.768	0.008	1.838
pmAbst2HTML	0.140	0.004	0.541
pmid2MIAME	0	0	0
pmidQuery	0	0	0
pubMedAbst-class	0.156	0.004	0.585
pubmed	0.084	0.004	0.520
readGEOAnn	0	0	0
serializeEnv	0.000	0.000	0.002
setRepository	0.004	0.000	0.002
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.076	0.000	0.076