Package: annotate

Version: 1.65.0

Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings annotate_1.65.0.tar.gz

StartedAt: 2020-01-24 02:59:50 -0500 (Fri, 24 Jan 2020)

EndedAt: 2020-01-24 03:03:25 -0500 (Fri, 24 Jan 2020)

EllapsedTime: 215.0 seconds

RetCode: 1

Status:  ERROR

CheckDir: annotate.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:annotate.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings annotate_1.65.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc-testing/meat/annotate.Rcheck’
* using R Under development (unstable) (2019-12-14 r77569)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.65.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘annotate-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGOTerm
> ### Title: Functions to Access GO data.
> ### Aliases: getGOTerm getGOParents getGOChildren getGOOntology
> ### Keywords: manip
> 
> ### ** Examples
> 
>  library("GO.db")
> 
>  sG <- sample(keys(GO.db, "GOID"), 8)
> 
>  gT <- getGOTerm(sG)
>  gP <- getGOParents(sG)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
annotate
 --- call from context --- 
getGOParents(sG)
 --- call from argument --- 
(length(hasMF[[i]]) > 1) || !is.na(hasBP[[i]])
 --- R stacktrace ---
where 1: getGOParents(sG)

 --- value of length: 3 type: logical ---
                is_a                 is_a negatively_regulates 
                TRUE                 TRUE                 TRUE 
 --- function from context --- 
function (x) 
{
    if (!is.character(x)) 
        stop("need a character argument")
    if (length(x) == 0) 
        return(list())
    loadNamespace("GO.db")
    hasMF <- mget(x, envir = GO.db::GOMFPARENTS, ifnotfound = NA)
    hasBP <- mget(x, envir = GO.db::GOBPPARENTS, ifnotfound = NA)
    hasCC <- mget(x, envir = GO.db::GOCCPARENTS, ifnotfound = NA)
    lenx <- length(x)
    rval <- vector("list", length = lenx)
    names(rval) <- x
    rval <- vector("list", length = lenx)
    names(rval) <- x
    for (i in 1:lenx) {
        if ((length(hasMF[[i]]) > 1) || !is.na(hasMF[[i]])) 
            rval[[i]] <- list(Ontology = "MF", Parents = hasMF[[i]])
        else if ((length(hasMF[[i]]) > 1) || !is.na(hasBP[[i]])) 
            rval[[i]] <- list(Ontology = "BP", Parents = hasBP[[i]])
        else if ((length(hasMF[[i]]) > 1) || !is.na(hasCC[[i]])) 
            rval[[i]] <- list(Ontology = "CC", Parents = hasCC[[i]])
        else stop(paste(x[i], "is not a member of any ontology"))
    }
    return(rval)
}
<bytecode: 0x559d0f611390>
<environment: namespace:annotate>
 --- function search by body ---
Function getGOParents in namespace annotate has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical
* 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: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.11-bioc-testing/meat/annotate.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL annotate
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc-testing/Rlibs’
* installing *source* package ‘annotate’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (annotate)

R Under development (unstable) (2019-12-14 r77569) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, 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 -- Fri Jan 24 03:03:19 2020 
*********************************************** 
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 
  8.026   0.290   8.301 

name	user	system	elapsed
ACCNUMStats	1.942	0.036	1.977
GO2heatmap	0.174	0.012	0.186
GOmnplot	0.109	0.000	0.109
HTMLPage-class	0.001	0.000	0.000
LL2homology	0.001	0.000	0.000
PMIDAmat	0.148	0.000	0.147
PWAmat	2.358	0.016	2.374
UniGeneQuery	0.001	0.000	0.000
accessionToUID	0.712	0.016	3.481
annPkgName	0.001	0.000	0.001
aqListGOIDs	0.337	0.012	0.350
blastSequences	0.535	0.080	46.139
buildChromLocation	0.806	0.000	0.805
buildPubMedAbst	0.101	0.008	0.456
chrCats	19.023	0.004	19.038
chromLocation-class	0.855	0.000	0.855
compatibleVersions	0.06	0.00	0.06
dropECode	0.07	0.00	0.07
entrezGeneByID	0.001	0.000	0.001
entrezGeneQuery	0.001	0.000	0.001
filterGOByOntology	0.119	0.004	0.123
findNeighbors	0.032	0.000	0.032
genbank	0.337	0.008	1.401
getAnnMap	0.055	0.004	0.059
getEvidence	0.088	0.000	0.088