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: 2017-08-15 23:40:24 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:43:10 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 166.4 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 3.4.1 (2017-06-30)
* 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        12.790   0.04  13.203
blastSequences  0.241   0.01  24.454
* 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	2.455	0.035	2.570
GO2heatmap	0.262	0.010	0.278
GOmnplot	0.083	0.005	0.096
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.001	0.000	0.001
PMIDAmat	0.110	0.004	0.119
PWAmat	2.268	0.040	2.380
UniGeneQuery	0.001	0.000	0.001
accessionToUID	0.627	0.034	1.876
annPkgName	0.001	0.001	0.001
aqListGOIDs	0.496	0.018	0.525
blastSequences	0.241	0.010	24.454
buildChromLocation	2.802	0.042	2.920
buildPubMedAbst	0.091	0.003	0.435
chrCats	12.790	0.040	13.203
chromLocation-class	2.960	0.023	3.078
compatibleVersions	0.049	0.001	0.054
dropECode	0.056	0.001	0.057
entrezGeneByID	0.001	0.000	0.001
entrezGeneQuery	0.001	0.000	0.002
filterGOByOntology	0.101	0.004	0.106
findNeighbors	0.026	0.003	0.032
genbank	0.148	0.017	1.879
getAnnMap	0.036	0.011	0.049
getEvidence	0.083	0.004	0.088
getGOTerm	0.289	0.011	0.307
getOntology	0.042	0.002	0.044
getPMInfo	0.586	0.004	0.980
getSYMBOL	0.132	0.008	0.146
getSeq4Acc	0.009	0.001	0.258
hasGOannote	0.023	0.001	0.024
hgByChroms	0.015	0.004	0.024
hgCLengths	0.001	0.000	0.002
hgu95Achroloc	0.059	0.012	0.070
hgu95Achrom	0.045	0.009	0.055
hgu95All	0.064	0.008	0.072
hgu95Asym	0.060	0.010	0.072
homoData-class	0.002	0.000	0.003
htmlpage	0.414	0.003	0.421
isValidkey	0.001	0.000	0.001
makeAnchor	0.001	0.000	0.000
organism	2.531	0.007	2.628
p2LL	0.001	0.000	0.001
pm.abstGrep	0.696	0.029	1.586
pm.getabst	0.937	0.022	1.846
pm.titles	0.727	0.034	1.644
pmAbst2HTML	0.071	0.004	0.414
pmid2MIAME	0	0	0
pmidQuery	0	0	0
pubMedAbst-class	0.032	0.002	0.343
pubmed	0.021	0.002	0.355
readGEOAnn	0.000	0.000	0.001
serializeEnv	0.008	0.001	0.009
setRepository	0.004	0.000	0.004
updateSymbolsToValidKeys	0.001	0.001	0.000
usedChromGenes	0.072	0.007	0.086