Package: annotate

Version: 1.60.1

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_1.60.1.tar.gz

StartedAt: 2019-04-15 22:20:40 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:23:51 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 190.9 seconds

RetCode: 0

Status:  OK

CheckDir: annotate.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.60.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/annotate.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.60.1’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        17.671  0.068  17.941
blastSequences  0.263  0.013  37.777
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL annotate
###
##############################################################################
##############################################################################


* 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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 -- Mon Apr 15 22:23:45 2019 
*********************************************** 
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 
  7.027   0.489   7.578 

name	user	system	elapsed
ACCNUMStats	2.496	0.058	2.617
GO2heatmap	0.156	0.009	0.167
GOmnplot	0.071	0.013	0.085
HTMLPage-class	0.000	0.000	0.001
LL2homology	0.001	0.000	0.001
PMIDAmat	0.139	0.005	0.145
PWAmat	2.515	0.061	2.612
UniGeneQuery	0.001	0.000	0.001
accessionToUID	0.342	0.035	4.528
annPkgName	0.001	0.001	0.001
aqListGOIDs	0.389	0.040	0.432
blastSequences	0.263	0.013	37.777
buildChromLocation	0.739	0.051	0.793
buildPubMedAbst	0.048	0.003	0.487
chrCats	17.671	0.068	17.941
chromLocation-class	0.609	0.030	0.642
compatibleVersions	0.036	0.002	0.038
dropECode	0.046	0.001	0.048
entrezGeneByID	0.001	0.000	0.002
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.126	0.011	0.137
findNeighbors	0.023	0.003	0.027
genbank	0.180	0.017	0.594
getAnnMap	0.040	0.010	0.052
getEvidence	0.068	0.003	0.071
getGOTerm	0.326	0.015	0.344
getOntology	0.045	0.002	0.047
getPMInfo	0.519	0.007	1.216
getSYMBOL	0.145	0.013	0.158
getSeq4Acc	0.013	0.002	0.272
hasGOannote	0.026	0.001	0.027
hgByChroms	0.017	0.004	0.021
hgCLengths	0.001	0.002	0.004
hgu95Achroloc	0.085	0.008	0.096
hgu95Achrom	0.050	0.007	0.056
hgu95All	0.070	0.007	0.078
hgu95Asym	0.069	0.005	0.077
homoData-class	0.003	0.000	0.002
htmlpage	0.028	0.001	0.030
isValidkey	0	0	0
makeAnchor	0.001	0.000	0.002
organism	0.721	0.031	0.761
p2LL	0	0	0
pm.abstGrep	1.230	0.051	2.269
pm.getabst	1.244	0.033	2.229
pm.titles	1.347	0.035	2.330
pmAbst2HTML	0.063	0.004	0.458
pmid2MIAME	0	0	0
pmidQuery	0.001	0.001	0.000
pubMedAbst-class	0.049	0.002	0.445
pubmed	0.028	0.002	0.420
readGEOAnn	0.001	0.001	0.000
serializeEnv	0.003	0.000	0.003
setRepository	0.002	0.000	0.003
updateSymbolsToValidKeys	0	0	0
usedChromGenes	0.104	0.016	0.123