CRAN Package Check Results for Package inpdfr

Last updated on 2018-10-20 09:55:01 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.6 7.18 86.31 93.49 ERROR
r-devel-linux-x86_64-debian-gcc 0.1.6 6.35 69.32 75.67 ERROR
r-devel-linux-x86_64-fedora-clang 0.1.6 109.46 ERROR
r-devel-linux-x86_64-fedora-gcc 0.1.6 105.78 ERROR
r-devel-windows-ix86+x86_64 0.1.6 16.00 99.00 115.00 OK
r-patched-linux-x86_64 0.1.6 5.57 68.77 74.34 OK
r-patched-solaris-x86 0.1.6 141.60 OK
r-release-linux-x86_64 0.1.6 5.58 68.83 74.41 OK
r-release-windows-ix86+x86_64 0.1.6 17.00 114.00 131.00 OK
r-release-osx-x86_64 0.1.6 OK
r-oldrel-windows-ix86+x86_64 0.1.6 9.00 115.00 124.00 OK
r-oldrel-osx-x86_64 0.1.6 OK

Check Details

Version: 0.1.6
Check: examples
Result: ERROR
    Running examples in ‘inpdfr-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: doMetacomMetacom
    > ### Title: Performs a metacomunity analysis.
    > ### Aliases: doMetacomMetacom
    >
    > ### ** Examples
    >
    > data("loremIpsum")
    > loremIpsum01 <- loremIpsum[1:100]
    > loremIpsum02 <- loremIpsum[101:200]
    > loremIpsum03 <- loremIpsum[201:300]
    > loremIpsum04 <- loremIpsum[301:400]
    > loremIpsum05 <- loremIpsum[401:500]
    > subDir <- "RESULTS"
    > dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
    > write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
    > write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
    > write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
    > write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
    > write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
    > wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"),
    + excludeSW = FALSE)
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    > file.remove(list.files(full.names = TRUE,
    + path = paste0(getwd(), "/RESULTS"), pattern = "loremIpsum"))
    [1] TRUE TRUE TRUE TRUE TRUE
    > doMetacomMetacom(wordF = wordOccuDF)
    Loading required package: metacom
    Loading required package: vegan
    Loading required package: permute
    Loading required package: lattice
    This is vegan 2.5-2
    Warning in IdentifyStructure(metaCom) : NAs introduced by coercion
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    inpdfr
     --- call from context ---
    IdentifyStructure(metaCom)
     --- call from argument ---
    if (as.numeric(t(metacom.obj$Coherence)[, 3]) >= 0.05) "Random" else if (as.numeric(t(metacom.obj$Coherence)[,
     1]) < as.numeric(t(metacom.obj$Coherence)[, 4]) & as.numeric(t(metacom.obj$Coherence)[,
     3]) < 0.05) "Checkerboard (negative coherence)" else if (as.numeric(t(metacom.obj$Coherence)[,
     1]) >= as.numeric(t(metacom.obj$Coherence)[, 4]) & as.numeric(t(metacom.obj$Coherence)[,
     3]) < 0.05) {
     print("Positive coherence...")
     if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (hyperdispersed"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (hyperdispersed)"
    }
     --- R stacktrace ---
    where 1: IdentifyStructure(metaCom)
    where 2: print(IdentifyStructure(metaCom))
    where 3: doTryCatch(return(expr), name, parentenv, handler)
    where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 5: tryCatchList(expr, classes, parentenv, handlers)
    where 6: 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 7: try(print(IdentifyStructure(metaCom)), silent = TRUE)
    where 8: doMetacomMetacom(wordF = wordOccuDF)
    
     --- value of length: 2 type: logical ---
    [1] NA FALSE
     --- function from context ---
    function (metacom.obj)
    {
     if (as.numeric(t(metacom.obj$Coherence)[, 3]) >= 0.05)
     "Random"
     else if (as.numeric(t(metacom.obj$Coherence)[, 1]) < as.numeric(t(metacom.obj$Coherence)[,
     4]) & as.numeric(t(metacom.obj$Coherence)[, 3]) < 0.05)
     "Checkerboard (negative coherence)"
     else if (as.numeric(t(metacom.obj$Coherence)[, 1]) >= as.numeric(t(metacom.obj$Coherence)[,
     4]) & as.numeric(t(metacom.obj$Coherence)[, 3]) < 0.05) {
     print("Positive coherence...")
     if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) <= 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) <= 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (hyperdispersed"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) > 0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) > 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) > 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) >
     0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) >
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) >
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (hyperdispersed)"
     }
    }
    <bytecode: 0x9260358>
    <environment: namespace:inpdfr>
     --- function search by body ---
    Function IdentifyStructure in namespace inpdfr has this body.
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.6
Check: examples
Result: ERROR
    Running examples in ‘inpdfr-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: doMetacomMetacom
    > ### Title: Performs a metacomunity analysis.
    > ### Aliases: doMetacomMetacom
    >
    > ### ** Examples
    >
    > data("loremIpsum")
    > loremIpsum01 <- loremIpsum[1:100]
    > loremIpsum02 <- loremIpsum[101:200]
    > loremIpsum03 <- loremIpsum[201:300]
    > loremIpsum04 <- loremIpsum[301:400]
    > loremIpsum05 <- loremIpsum[401:500]
    > subDir <- "RESULTS"
    > dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
    > write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
    > write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
    > write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
    > write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
    > write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
    > wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"),
    + excludeSW = FALSE)
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    > file.remove(list.files(full.names = TRUE,
    + path = paste0(getwd(), "/RESULTS"), pattern = "loremIpsum"))
    [1] TRUE TRUE TRUE TRUE TRUE
    > doMetacomMetacom(wordF = wordOccuDF)
    Loading required package: metacom
    Loading required package: vegan
    Loading required package: permute
    Loading required package: lattice
    This is vegan 2.5-2
    Warning in IdentifyStructure(metaCom) : NAs introduced by coercion
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    inpdfr
     --- call from context ---
    IdentifyStructure(metaCom)
     --- call from argument ---
    if (as.numeric(t(metacom.obj$Coherence)[, 3]) >= 0.05) "Random" else if (as.numeric(t(metacom.obj$Coherence)[,
     1]) < as.numeric(t(metacom.obj$Coherence)[, 4]) & as.numeric(t(metacom.obj$Coherence)[,
     3]) < 0.05) "Checkerboard (negative coherence)" else if (as.numeric(t(metacom.obj$Coherence)[,
     1]) >= as.numeric(t(metacom.obj$Coherence)[, 4]) & as.numeric(t(metacom.obj$Coherence)[,
     3]) < 0.05) {
     print("Positive coherence...")
     if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (hyperdispersed"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (hyperdispersed)"
    }
     --- R stacktrace ---
    where 1: IdentifyStructure(metaCom)
    where 2: print(IdentifyStructure(metaCom))
    where 3: doTryCatch(return(expr), name, parentenv, handler)
    where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 5: tryCatchList(expr, classes, parentenv, handlers)
    where 6: 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 7: try(print(IdentifyStructure(metaCom)), silent = TRUE)
    where 8: doMetacomMetacom(wordF = wordOccuDF)
    
     --- value of length: 2 type: logical ---
    [1] NA FALSE
     --- function from context ---
    function (metacom.obj)
    {
     if (as.numeric(t(metacom.obj$Coherence)[, 3]) >= 0.05)
     "Random"
     else if (as.numeric(t(metacom.obj$Coherence)[, 1]) < as.numeric(t(metacom.obj$Coherence)[,
     4]) & as.numeric(t(metacom.obj$Coherence)[, 3]) < 0.05)
     "Checkerboard (negative coherence)"
     else if (as.numeric(t(metacom.obj$Coherence)[, 1]) >= as.numeric(t(metacom.obj$Coherence)[,
     4]) & as.numeric(t(metacom.obj$Coherence)[, 3]) < 0.05) {
     print("Positive coherence...")
     if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) <= 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) <= 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (hyperdispersed"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) > 0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) > 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) > 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) >
     0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) >
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) >
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (hyperdispersed)"
     }
    }
    <bytecode: 0x559686a4f5e0>
    <environment: namespace:inpdfr>
     --- function search by body ---
    Function IdentifyStructure in namespace inpdfr has this body.
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.6
Check: examples
Result: ERROR
    Running examples in ‘inpdfr-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: doMetacomMetacom
    > ### Title: Performs a metacomunity analysis.
    > ### Aliases: doMetacomMetacom
    >
    > ### ** Examples
    >
    > data("loremIpsum")
    > loremIpsum01 <- loremIpsum[1:100]
    > loremIpsum02 <- loremIpsum[101:200]
    > loremIpsum03 <- loremIpsum[201:300]
    > loremIpsum04 <- loremIpsum[301:400]
    > loremIpsum05 <- loremIpsum[401:500]
    > subDir <- "RESULTS"
    > dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
    > write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
    > write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
    > write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
    > write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
    > write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
    > wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"),
    + excludeSW = FALSE)
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    > file.remove(list.files(full.names = TRUE,
    + path = paste0(getwd(), "/RESULTS"), pattern = "loremIpsum"))
    [1] TRUE TRUE TRUE TRUE TRUE
    > doMetacomMetacom(wordF = wordOccuDF)
    Loading required package: metacom
    Loading required package: vegan
    Loading required package: permute
    Loading required package: lattice
    This is vegan 2.5-2
    Warning in IdentifyStructure(metaCom) : NAs introduced by coercion
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    inpdfr
     --- call from context ---
    IdentifyStructure(metaCom)
     --- call from argument ---
    if (as.numeric(t(metacom.obj$Coherence)[, 3]) >= 0.05) "Random" else if (as.numeric(t(metacom.obj$Coherence)[,
     1]) < as.numeric(t(metacom.obj$Coherence)[, 4]) & as.numeric(t(metacom.obj$Coherence)[,
     3]) < 0.05) "Checkerboard (negative coherence)" else if (as.numeric(t(metacom.obj$Coherence)[,
     1]) >= as.numeric(t(metacom.obj$Coherence)[, 4]) & as.numeric(t(metacom.obj$Coherence)[,
     3]) < 0.05) {
     print("Positive coherence...")
     if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (hyperdispersed"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (hyperdispersed)"
    }
     --- R stacktrace ---
    where 1: IdentifyStructure(metaCom)
    where 2: print(IdentifyStructure(metaCom))
    where 3: doTryCatch(return(expr), name, parentenv, handler)
    where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 5: tryCatchList(expr, classes, parentenv, handlers)
    where 6: 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 7: try(print(IdentifyStructure(metaCom)), silent = TRUE)
    where 8: doMetacomMetacom(wordF = wordOccuDF)
    
     --- value of length: 2 type: logical ---
    [1] NA FALSE
     --- function from context ---
    function (metacom.obj)
    {
     if (as.numeric(t(metacom.obj$Coherence)[, 3]) >= 0.05)
     "Random"
     else if (as.numeric(t(metacom.obj$Coherence)[, 1]) < as.numeric(t(metacom.obj$Coherence)[,
     4]) & as.numeric(t(metacom.obj$Coherence)[, 3]) < 0.05)
     "Checkerboard (negative coherence)"
     else if (as.numeric(t(metacom.obj$Coherence)[, 1]) >= as.numeric(t(metacom.obj$Coherence)[,
     4]) & as.numeric(t(metacom.obj$Coherence)[, 3]) < 0.05) {
     print("Positive coherence...")
     if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) <= 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) <= 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (hyperdispersed"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) > 0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) > 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) > 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) >
     0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) >
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) >
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (hyperdispersed)"
     }
    }
    <bytecode: 0xa86da40>
    <environment: namespace:inpdfr>
     --- function search by body ---
    Function IdentifyStructure in namespace inpdfr has this body.
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1.6
Check: examples
Result: ERROR
    Running examples in ‘inpdfr-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: doMetacomMetacom
    > ### Title: Performs a metacomunity analysis.
    > ### Aliases: doMetacomMetacom
    >
    > ### ** Examples
    >
    > data("loremIpsum")
    > loremIpsum01 <- loremIpsum[1:100]
    > loremIpsum02 <- loremIpsum[101:200]
    > loremIpsum03 <- loremIpsum[201:300]
    > loremIpsum04 <- loremIpsum[301:400]
    > loremIpsum05 <- loremIpsum[401:500]
    > subDir <- "RESULTS"
    > dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
    > write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
    > write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
    > write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
    > write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
    > write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
    > wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"),
    + excludeSW = FALSE)
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    Warning in readChar(zz, file.info(filetxt)$size) :
     text connection used with readChar(), results may be incorrect
    Warning in tm_map.SimpleCorpus(corpus, tm::removePunctuation) :
     transformation drops documents
    > file.remove(list.files(full.names = TRUE,
    + path = paste0(getwd(), "/RESULTS"), pattern = "loremIpsum"))
    [1] TRUE TRUE TRUE TRUE TRUE
    > doMetacomMetacom(wordF = wordOccuDF)
    Loading required package: metacom
    Loading required package: vegan
    Loading required package: permute
    Loading required package: lattice
    This is vegan 2.5-2
    Warning in IdentifyStructure(metaCom) : NAs introduced by coercion
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    inpdfr
     --- call from context ---
    IdentifyStructure(metaCom)
     --- call from argument ---
    if (as.numeric(t(metacom.obj$Coherence)[, 3]) >= 0.05) "Random" else if (as.numeric(t(metacom.obj$Coherence)[,
     1]) < as.numeric(t(metacom.obj$Coherence)[, 4]) & as.numeric(t(metacom.obj$Coherence)[,
     3]) < 0.05) "Checkerboard (negative coherence)" else if (as.numeric(t(metacom.obj$Coherence)[,
     1]) >= as.numeric(t(metacom.obj$Coherence)[, 4]) & as.numeric(t(metacom.obj$Coherence)[,
     3]) < 0.05) {
     print("Positive coherence...")
     if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <= 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (hyperdispersed"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) > 0.05 &
     metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (hyperdispersed)"
    }
     --- R stacktrace ---
    where 1: IdentifyStructure(metaCom)
    where 2: print(IdentifyStructure(metaCom))
    where 3: doTryCatch(return(expr), name, parentenv, handler)
    where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 5: tryCatchList(expr, classes, parentenv, handlers)
    where 6: 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 7: try(print(IdentifyStructure(metaCom)), silent = TRUE)
    where 8: doMetacomMetacom(wordF = wordOccuDF)
    
     --- value of length: 2 type: logical ---
    [1] NA FALSE
     --- function from context ---
    function (metacom.obj)
    {
     if (as.numeric(t(metacom.obj$Coherence)[, 3]) >= 0.05)
     "Random"
     else if (as.numeric(t(metacom.obj$Coherence)[, 1]) < as.numeric(t(metacom.obj$Coherence)[,
     4]) & as.numeric(t(metacom.obj$Coherence)[, 3]) < 0.05)
     "Checkerboard (negative coherence)"
     else if (as.numeric(t(metacom.obj$Coherence)[, 1]) >= as.numeric(t(metacom.obj$Coherence)[,
     4]) & as.numeric(t(metacom.obj$Coherence)[, 3]) < 0.05) {
     print("Positive coherence...")
     if (as.numeric(t(metacom.obj$Turnover)[, 1]) >= as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) <= 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) <= 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) <=
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Nested (hyperdispersed"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) > 0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-clementsian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) > 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-gleasonian"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) >=
     as.numeric(t(metacom.obj$Turnover)[, 4]) & as.numeric(t(metacom.obj$Turnover)[,
     3]) > 0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-evenly spaced"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) >
     0.05 & metacom.obj$Boundary[, 1] >= 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (clumped)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) >
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] >= 0.05)
     "Quasi-nested (random)"
     else if (as.numeric(t(metacom.obj$Turnover)[, 1]) < as.numeric(t(metacom.obj$Turnover)[,
     4]) & as.numeric(t(metacom.obj$Turnover)[, 3]) >
     0.05 & metacom.obj$Boundary[, 1] < 0 & metacom.obj$Boundary[,
     2] < 0.05)
     "Quasi-nested (hyperdispersed)"
     }
    }
    <bytecode: 0x8dd51e0>
    <environment: namespace:inpdfr>
     --- function search by body ---
    Function IdentifyStructure in namespace inpdfr has this body.
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-fedora-gcc