BioC 3.5: CHECK report for annotate on oaxaca

Package: annotate

Version: 1.53.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.53.1.tar.gz

StartedAt: 2017-03-03 23:03:16 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:06:39 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 203.4 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_1.53.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/annotate.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.53.1’
* 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 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        12.570  0.020  12.659
blastSequences  0.753  0.011  26.432
* 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	2.563	0.025	2.590
GO2heatmap	0.354	0.013	0.367
GOmnplot	0.095	0.008	0.103
HTMLPage-class	0.000	0.000	0.001
LL2homology	0.001	0.000	0.001
PMIDAmat	0.280	0.004	0.456
PWAmat	1.927	0.049	1.977
UniGeneQuery	0.001	0.000	0.002
accessionToUID	0.896	0.030	4.324
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.416	0.027	0.498
blastSequences	0.753	0.011	26.432
buildChromLocation	3.088	0.036	3.153
buildPubMedAbst	0.130	0.002	0.740
chrCats	12.570	0.020	12.659
chromLocation-class	2.610	0.034	2.644
compatibleVersions	0.051	0.002	0.053
dropECode	0.057	0.002	0.091
entrezGeneByID	0.001	0.000	0.002
entrezGeneQuery	0.001	0.000	0.002
filterGOByOntology	0.125	0.005	0.130
findNeighbors	0.019	0.003	0.542
genbank	0.153	0.010	1.300
getAnnMap	0.045	0.012	0.201
getEvidence	0.105	0.001	0.106
getGOTerm	0.394	0.010	0.648
getOntology	0.054	0.001	0.056
getPMInfo	0.813	0.004	1.532
getSYMBOL	0.156	0.013	0.422
getSeq4Acc	0.013	0.001	0.530
hasGOannote	0.030	0.001	0.056
hgByChroms	0.016	0.004	0.019
hgCLengths	0.002	0.001	0.002
hgu95Achroloc	0.084	0.009	0.093
hgu95Achrom	0.074	0.010	0.084
hgu95All	0.081	0.011	0.090
hgu95Asym	0.088	0.009	0.097
homoData-class	0.003	0.000	0.003
htmlpage	0.724	0.004	0.729
isValidkey	0.001	0.000	0.000
makeAnchor	0.001	0.000	0.001
organism	3.077	0.015	3.093
p2LL	0.001	0.000	0.000
pm.abstGrep	1.142	0.028	2.742
pm.getabst	0.747	0.016	2.336
pm.titles	0.791	0.017	2.326
pmAbst2HTML	0.121	0.003	0.739
pmid2MIAME	0	0	0
pmidQuery	0.002	0.001	0.001
pubMedAbst-class	0.035	0.001	0.630
pubmed	0.019	0.002	0.746
readGEOAnn	0	0	0
serializeEnv	0.002	0.000	0.001
setRepository	0.004	0.000	0.004
updateSymbolsToValidKeys	0.001	0.000	0.001
usedChromGenes	0.077	0.007	0.085