BioC 3.4: CHECK report for annotate on malbec1

Package: annotate

Version: 1.52.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.52.1.tar.gz

StartedAt: 2017-04-14 20:56:27 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 20:58:57 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 149.5 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.52.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/annotate.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.52.1’
* 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 ... 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        9.848  0.000   9.855
blastSequences 0.696  0.092  30.832
* 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	1.380	0.012	1.391
GO2heatmap	0.100	0.000	0.098
GOmnplot	0.048	0.000	0.049
HTMLPage-class	0	0	0
LL2homology	0	0	0
PMIDAmat	0.136	0.000	0.188
PWAmat	3.820	0.028	3.852
UniGeneQuery	0.000	0.000	0.002
accessionToUID	1.032	0.064	3.157
annPkgName	0.004	0.000	0.002
aqListGOIDs	0.440	0.012	0.451
blastSequences	0.696	0.092	30.832
buildChromLocation	1.356	0.008	1.383
buildPubMedAbst	0.124	0.000	0.657
chrCats	9.848	0.000	9.855
chromLocation-class	1.096	0.000	1.097
compatibleVersions	0.040	0.000	0.037
dropECode	0.040	0.000	0.039
entrezGeneByID	0.000	0.000	0.001
entrezGeneQuery	0.000	0.000	0.001
filterGOByOntology	0.060	0.004	0.063
findNeighbors	0.020	0.000	0.048
genbank	0.280	0.020	0.832
getAnnMap	0.032	0.016	0.169
getEvidence	0.048	0.000	0.050
getGOTerm	0.240	0.000	0.248
getOntology	0.048	0.004	0.053
getPMInfo	0.568	0.004	1.014
getSYMBOL	0.104	0.000	0.119
getSeq4Acc	0.112	0.004	0.409
hasGOannote	0.036	0.000	0.036
hgByChroms	0.024	0.000	0.022
hgCLengths	0.004	0.000	0.002
hgu95Achroloc	0.084	0.000	0.086
hgu95Achrom	0.064	0.004	0.065
hgu95All	0.056	0.000	0.056
hgu95Asym	0.052	0.004	0.057
homoData-class	0.000	0.000	0.002
htmlpage	0.02	0.00	0.02
isValidkey	0.004	0.000	0.001
makeAnchor	0	0	0
organism	1.448	0.000	1.450
p2LL	0.000	0.000	0.001
pm.abstGrep	0.964	0.012	2.006
pm.getabst	0.752	0.004	1.858
pm.titles	0.868	0.012	2.040
pmAbst2HTML	0.164	0.008	0.670
pmid2MIAME	0	0	0
pmidQuery	0.004	0.000	0.002
pubMedAbst-class	0.156	0.004	0.659
pubmed	0.112	0.008	0.538
readGEOAnn	0.000	0.000	0.001
serializeEnv	0.004	0.000	0.003
setRepository	0.004	0.000	0.004
updateSymbolsToValidKeys	0.004	0.000	0.001
usedChromGenes	0.116	0.004	0.119