Multiple platform build/check report for BioC 3.11 (small subset of software packages ONLY) - CHECK report for AnnotationDbi on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:AnnotationDbi.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings AnnotationDbi_1.49.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc-testing/meat/AnnotationDbi.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 ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.49.0’
* package encoding: UTF-8
* 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 ‘AnnotationDbi’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   6.0Mb
* 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 ... NOTE
createORGANISMSeeds: no visible global function definition for
  ‘makeAnnDbMapSeeds’
mapIds_base : .filter: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  makeAnnDbMapSeeds setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘AnnotationDbi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Bimap-envirAPI
> ### Title: Environment-like API for Bimap objects
> ### Aliases: Bimap-envirAPI ls ls,Bimap-method exists
> ###   exists,ANY,ANY,Bimap-method exists,ANY,Bimap,missing-method get
> ###   get,ANY,ANY,Bimap-method get,ANY,Bimap,missing-method [[,Bimap-method
> ###   $,Bimap-method mget mget,Bimap-method mget,ANY,Bimap-method eapply
> ###   eapply,Bimap-method contents,Bimap-method sample sample,Bimap-method
> ###   sample,environment-method
> ### Keywords: methods interface
> 
> ### ** Examples
> 
>   library(hgu95av2.db)
Loading required package: org.Hs.eg.db
>   x <- hgu95av2CHRLOC
> 
>   ls(x)[1:3]
[1] "1000_at"   "1001_at"   "1002_f_at"
>   exists(ls(x)[1], x)
[1] TRUE
>   exists("titi", x)
[1] FALSE
>   get(ls(x)[1], x)
       16        16        16 
-30116836 -30114104 -30114104 
>   x[[ls(x)[1]]]
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
AnnotationDbi
 --- call from context --- 
.doubleBracketSub(x, i, j, ...)
 --- call from argument --- 
!isS4(val) && is.na(val)
 --- R stacktrace ---
where 1: .doubleBracketSub(x, i, j, ...)
where 2: x[[ls(x)[1]]]
where 3: x[[ls(x)[1]]]

 --- value of length: 3 type: logical ---
   16    16    16 
FALSE FALSE FALSE 
 --- function from context --- 
function (x, i, j, ...) 
{
    subscripts <- list(...)
    if (!missing(i)) 
        subscripts$i <- i
    if (!missing(j)) 
        subscripts$j <- j
    if (length(subscripts) == 0) 
        stop("no index specified")
    i <- subscripts[[1]]
    if (length(i) < 1) 
        stop("attempt to select less than one element")
    if (length(i) > 1) 
        stop("attempt to select more than one element")
    if (!is.character(i) || is.na(i)) 
        stop("wrong argument for subsetting an object of class ", 
            sQuote(class(x)))
    val <- mget(i, envir = x, ifnotfound = NA)[[1]]
    if (!isS4(val) && is.na(val) && !(i %in% keys(x))) 
        val <- NULL
    val
}
<bytecode: 0x55968eb90e58>
<environment: namespace:AnnotationDbi>
 --- function search by body ---
Function .doubleBracketSub in namespace AnnotationDbi 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 ‘AnnotationDbi_unit_tests.R’
 ERROR
Running the tests in ‘tests/AnnotationDbi_unit_tests.R’ failed.
Last 13 lines of output:
          stop("attempt to select more than one element")
      if (!is.character(i) || is.na(i)) 
          stop("wrong argument for subsetting an object of class ", 
              sQuote(class(x)))
      val <- mget(i, envir = x, ifnotfound = NA)[[1]]
      if (!isS4(val) && is.na(val) && !(i %in% keys(x))) 
          val <- NULL
      val
  }
  <bytecode: 0x5586d4be7d98>
  <environment: namespace:AnnotationDbi>
   --- function search by body ---
  Function .doubleBracketSub in namespace AnnotationDbi has this body.
   ----------- END OF FAILURE REPORT -------------- 
  Fatal error: length > 1 in coercion to logical
* 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: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc-testing/meat/AnnotationDbi.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL AnnotationDbi
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc-testing/Rlibs’
* installing *source* package ‘AnnotationDbi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
** 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 (AnnotationDbi)

Tests output


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.

> require("AnnotationDbi") || stop("unable to load AnnotationDbi package")
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

[1] TRUE
> 
> AnnotationDbi:::.test()
Loading required package: org.Hs.eg.db

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
AnnotationDbi
 --- call from context --- 
.doubleBracketSub(x, i, j, ...)
 --- call from argument --- 
!isS4(val) && is.na(val)
 --- R stacktrace ---
where 1: .doubleBracketSub(x, i, j, ...)
where 2: x[[name]]
where 3: x[[name]]
where 4: map2$"1"
where 5: map2$"1"
where 6: func()
where 7: system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, classes, parentenv, handlers)
where 11: tryCatch(expr, error = function(e) {
    call <- conditionCall(e)
    if (!is.null(call)) {
        if (identical(call[[1L]], quote(doTryCatch))) 
            call <- sys.call(-4L)
        dcall <- deparse(call)[1L]
        prefix <- paste("Error in", dcall, ": ")
        LONG <- 75L
        sm <- strsplit(conditionMessage(e), "\n")[[1L]]
        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
        if (is.na(w)) 
            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
                type = "b")
        if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")
    }
    else prefix <- "Error : "
    msg <- paste0(prefix, conditionMessage(e), "\n")
    .Internal(seterrmessage(msg[1L]))
    if (!silent && isTRUE(getOption("show.error.messages"))) {
        cat(msg, file = outFile)
        .Internal(printDeferredWarnings())
    }
    invisible(structure(msg, class = "try-error", condition = e))
})
where 12: try(system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest))
where 13: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp, 
    tearDownFunc = .tearDown)
where 14: .sourceTestFile(testFile, testSuite$testFuncRegexp)
where 15: RUnit::runTestSuite(suite)
where 16: BiocGenerics:::testPackage("AnnotationDbi")
where 17: AnnotationDbi:::.test()

 --- value of length: 3 type: logical ---
[1] FALSE FALSE FALSE
 --- function from context --- 
function (x, i, j, ...) 
{
    subscripts <- list(...)
    if (!missing(i)) 
        subscripts$i <- i
    if (!missing(j)) 
        subscripts$j <- j
    if (length(subscripts) == 0) 
        stop("no index specified")
    i <- subscripts[[1]]
    if (length(i) < 1) 
        stop("attempt to select less than one element")
    if (length(i) > 1) 
        stop("attempt to select more than one element")
    if (!is.character(i) || is.na(i)) 
        stop("wrong argument for subsetting an object of class ", 
            sQuote(class(x)))
    val <- mget(i, envir = x, ifnotfound = NA)[[1]]
    if (!isS4(val) && is.na(val) && !(i %in% keys(x))) 
        val <- NULL
    val
}
<bytecode: 0x5586d4be7d98>
<environment: namespace:AnnotationDbi>
 --- function search by body ---
Function .doubleBracketSub in namespace AnnotationDbi has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical

name	user	system	elapsed
AnnDbObj-class	0.798	0.036	0.833
AnnDbPkg-checker	46.130	0.416	46.581
AnnotationDb-class	0.823	0.008	0.830
Bimap-direction	5.723	0.856	6.584

CHECK report for AnnotationDbi on malbec2

Summary

Command output

Installation output

Tests output

Example timings