Package: annotate

Version: 1.56.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.56.2.tar.gz

StartedAt: 2018-04-12 00:22:08 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:24:44 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 156.3 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.56.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/annotate.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.56.2’
* 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        12.699  0.071  12.902
blastSequences  0.227  0.011  20.343
* 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)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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 -- Thu Apr 12 00:24:39 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 
  5.347   0.249   5.653 

name	user	system	elapsed
ACCNUMStats	2.491	0.037	2.586
GO2heatmap	0.221	0.007	0.228
GOmnplot	0.078	0.006	0.085
HTMLPage-class	0.001	0.001	0.001
LL2homology	0.000	0.000	0.001
PMIDAmat	0.118	0.004	0.127
PWAmat	2.097	0.041	2.159
UniGeneQuery	0.003	0.000	0.003
accessionToUID	0.759	0.036	2.136
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.347	0.022	0.381
blastSequences	0.227	0.011	20.343
buildChromLocation	0.639	0.029	0.675
buildPubMedAbst	0.089	0.002	0.403
chrCats	12.699	0.071	12.902
chromLocation-class	0.458	0.017	0.478
compatibleVersions	0.040	0.001	0.042
dropECode	0.047	0.001	0.048
entrezGeneByID	0.001	0.000	0.001
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.084	0.005	0.089
findNeighbors	0.017	0.002	0.021
genbank	0.125	0.013	1.220
getAnnMap	0.034	0.009	0.057
getEvidence	0.096	0.004	0.101
getGOTerm	0.258	0.011	0.277
getOntology	0.031	0.002	0.035
getPMInfo	0.417	0.004	1.044
getSYMBOL	0.120	0.008	0.130
getSeq4Acc	0.007	0.001	0.269
hasGOannote	0.021	0.001	0.021
hgByChroms	0.011	0.001	0.012
hgCLengths	0.001	0.000	0.002
hgu95Achroloc	0.047	0.003	0.050
hgu95Achrom	0.040	0.004	0.045
hgu95All	0.046	0.004	0.049
hgu95Asym	0.044	0.003	0.048
homoData-class	0.002	0.000	0.002
htmlpage	0.415	0.003	0.424
isValidkey	0.001	0.000	0.001
makeAnchor	0.001	0.000	0.001
organism	0.418	0.015	0.435
p2LL	0.000	0.000	0.001
pm.abstGrep	0.781	0.035	1.813
pm.getabst	0.932	0.023	1.961
pm.titles	0.967	0.031	1.880
pmAbst2HTML	0.081	0.002	0.414
pmid2MIAME	0.000	0.001	0.001
pmidQuery	0.001	0.000	0.002
pubMedAbst-class	0.032	0.002	0.350
pubmed	0.016	0.002	1.370
readGEOAnn	0.001	0.000	0.000
serializeEnv	0.002	0.000	0.002
setRepository	0.003	0.001	0.003
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.067	0.005	0.072