Package: annotate

Version: 1.58.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:annotate.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annotate_1.58.0.tar.gz

StartedAt: 2018-10-16 19:51:30 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 19:54:37 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 186.8 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 --install=check:annotate.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings annotate_1.58.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/annotate.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.58.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        16.720  0.081  16.974
blastSequences  0.251  0.012  38.498
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL annotate
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘annotate’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (annotate)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("annotate")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: org.Hs.eg.db

'select()' returned 1:many mapping between keys and columns


RUNIT TEST PROTOCOL -- Tue Oct 16 19:54:30 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
annotate RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  7.188   0.516   7.739 

name	user	system	elapsed
ACCNUMStats	1.974	0.052	2.036
GO2heatmap	0.155	0.006	0.164
GOmnplot	0.044	0.003	0.049
HTMLPage-class	0.001	0.000	0.001
LL2homology	0.001	0.000	0.001
PMIDAmat	0.118	0.004	0.126
PWAmat	2.154	0.058	2.225
UniGeneQuery	0.002	0.000	0.002
accessionToUID	0.349	0.035	2.668
annPkgName	0.002	0.000	0.001
aqListGOIDs	0.379	0.043	0.424
blastSequences	0.251	0.012	38.498
buildChromLocation	0.754	0.053	0.821
buildPubMedAbst	0.052	0.002	0.559
chrCats	16.720	0.081	16.974
chromLocation-class	0.651	0.036	0.690
compatibleVersions	0.044	0.002	0.046
dropECode	0.045	0.001	0.046
entrezGeneByID	0.002	0.000	0.001
entrezGeneQuery	0.002	0.001	0.002
filterGOByOntology	0.128	0.008	0.140
findNeighbors	0.019	0.003	0.024
genbank	0.189	0.019	0.645
getAnnMap	0.044	0.011	0.057
getEvidence	0.072	0.002	0.074
getGOTerm	0.314	0.012	0.329
getOntology	0.049	0.002	0.051
getPMInfo	0.505	0.005	0.894
getSYMBOL	0.187	0.014	0.204
getSeq4Acc	0.012	0.002	0.258
hasGOannote	0.028	0.001	0.029
hgByChroms	0.021	0.004	0.026
hgCLengths	0.003	0.001	0.004
hgu95Achroloc	0.071	0.007	0.078
hgu95Achrom	0.067	0.006	0.079
hgu95All	0.072	0.007	0.079
hgu95Asym	0.084	0.008	0.094
homoData-class	0.003	0.000	0.004
htmlpage	0.034	0.001	0.036
isValidkey	0.001	0.001	0.002
makeAnchor	0.002	0.000	0.003
organism	0.688	0.024	0.718
p2LL	0.001	0.001	0.002
pm.abstGrep	1.074	0.041	2.160
pm.getabst	1.048	0.029	2.101
pm.titles	0.981	0.030	1.962
pmAbst2HTML	0.063	0.006	0.493
pmid2MIAME	0.001	0.000	0.002
pmidQuery	0.002	0.000	0.003
pubMedAbst-class	0.045	0.002	0.416
pubmed	0.030	0.003	0.413
readGEOAnn	0.002	0.000	0.002
serializeEnv	0.003	0.000	0.003
setRepository	0.006	0.001	0.007
updateSymbolsToValidKeys	0.002	0.000	0.002
usedChromGenes	0.114	0.010	0.124