CRAN Package Check Results for Package picante

Last updated on 2019-12-15 05:47:48 CET.

Check Details

Version: 1.8
Check: examples
Result: ERROR
    Running examples in 'picante-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: comdist
    > ### Title: Calculates inter-community mean pairwise distance
    > ### Aliases: comdist
    > ### Keywords: univar
    >
    > ### ** Examples
    >
    > data(phylocom)
    > comdist(phylocom$sample, cophenetic(phylocom$phylo), abundance.weighted=TRUE)
    [1] "Dropping taxa from the distance matrix because they are not present in the community data:"
    [1] "sp16" "sp23" "sp27" "sp28" "sp30" "sp31" "sp32"
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    picante
     --- call from context ---
    match.comm.dist(comm, dis)
     --- call from argument ---
    if (disclass == "dist") {
     res$dist <- as.dist(dis[colnames(comm), colnames(comm)])
    } else {
     res$dist <- dis[colnames(comm), colnames(comm)]
    }
     --- R stacktrace ---
    where 1: match.comm.dist(comm, dis)
    where 2: comdist(phylocom$sample, cophenetic(phylocom$phylo), abundance.weighted = TRUE)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (comm, dis)
    {
     res <- list()
     commtaxa <- colnames(comm)
     if (is.null(commtaxa)) {
     stop("Community data set lacks taxa (column) names, these are required to match distance matrix and community data")
     }
     disclass <- class(dis)
     dis <- as.matrix(dis)
     distaxa <- rownames(dis)
     if (is.null(distaxa)) {
     warning("Distance matrix lacks taxa names, these are required to match community and distance matrix. Data are returned unsorted. Assuming that distance matrix and community data taxa columns are in the same order!")
     if (disclass == "dist") {
     return(list(comm = comm, dist = as.dist(dis)))
     }
     else {
     return(list(comm = comm, dist = dis))
     }
     }
     if (!all(distaxa %in% commtaxa)) {
     print("Dropping taxa from the distance matrix because they are not present in the community data:")
     print(setdiff(distaxa, commtaxa))
     dis <- dis[intersect(distaxa, commtaxa), intersect(distaxa,
     commtaxa)]
     distaxa <- rownames(dis)
     }
     if (any(!(commtaxa %in% distaxa))) {
     print("Dropping taxa from the community because they are not present in the distance matrix:")
     print(setdiff(commtaxa, distaxa))
     res$comm <- comm[, intersect(commtaxa, distaxa)]
     }
     else {
     res$comm <- comm
     }
     if (disclass == "dist") {
     res$dist <- as.dist(dis[colnames(comm), colnames(comm)])
     }
     else {
     res$dist <- dis[colnames(comm), colnames(comm)]
     }
     return(res)
    }
    <bytecode: 0xbdfb7e8>
    <environment: namespace:picante>
     --- function search by body ---
    Function match.comm.dist in namespace picante has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (disclass == "dist") { : the condition has length > 1
    Calls: comdist -> match.comm.dist
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.8
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'picante-intro.Rnw' using Sweave
    Loading required package: ape
    Loading required package: vegan
    Loading required package: permute
    Loading required package: lattice
    This is vegan 2.5-6
    Loading required package: nlme
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    picante
     --- call from context ---
    match.comm.dist(comm, dis)
     --- call from argument ---
    if (disclass == "dist") {
     res$dist <- as.dist(dis[colnames(comm), colnames(comm)])
    } else {
     res$dist <- dis[colnames(comm), colnames(comm)]
    }
     --- R stacktrace ---
    where 1: match.comm.dist(comm, dis)
    where 2: comdist(comm, phydist)
    where 3: eval(expr, .GlobalEnv)
    where 4: eval(expr, .GlobalEnv)
    where 5: withVisible(eval(expr, .GlobalEnv))
    where 6: doTryCatch(return(expr), name, parentenv, handler)
    where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 8: tryCatchList(expr, classes, parentenv, handlers)
    where 9: 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 10: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
    where 11: evalFunc(ce, options)
    where 12: tryCatchList(expr, classes, parentenv, handlers)
    where 13: tryCatch(evalFunc(ce, options), finally = {
     cat("\n")
     sink()
    })
    where 14: driver$runcode(drobj, chunk, chunkopts)
    where 15: utils::Sweave(...)
    where 16: engine$weave(file, quiet = quiet, encoding = enc)
    where 17: doTryCatch(return(expr), name, parentenv, handler)
    where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 19: tryCatchList(expr, classes, parentenv, handlers)
    where 20: tryCatch({
     engine$weave(file, quiet = quiet, encoding = enc)
     setwd(startdir)
     output <- find_vignette_product(name, by = "weave", engine = engine)
     if (!have.makefile && vignette_is_tex(output)) {
     texi2pdf(file = output, clean = FALSE, quiet = quiet)
     output <- find_vignette_product(name, by = "texi2pdf",
     engine = engine)
     }
     outputs <- c(outputs, output)
    }, error = function(e) {
     thisOK <<- FALSE
     fails <<- c(fails, file)
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 21: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/picante.Rcheck/vign_test/picante",
     ser_elibs = "/tmp/Rtmp8d6emX/file4bb01be6c84d.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (comm, dis)
    {
     res <- list()
     commtaxa <- colnames(comm)
     if (is.null(commtaxa)) {
     stop("Community data set lacks taxa (column) names, these are required to match distance matrix and community data")
     }
     disclass <- class(dis)
     dis <- as.matrix(dis)
     distaxa <- rownames(dis)
     if (is.null(distaxa)) {
     warning("Distance matrix lacks taxa names, these are required to match community and distance matrix. Data are returned unsorted. Assuming that distance matrix and community data taxa columns are in the same order!")
     if (disclass == "dist") {
     return(list(comm = comm, dist = as.dist(dis)))
     }
     else {
     return(list(comm = comm, dist = dis))
     }
     }
     if (!all(distaxa %in% commtaxa)) {
     print("Dropping taxa from the distance matrix because they are not present in the community data:")
     print(setdiff(distaxa, commtaxa))
     dis <- dis[intersect(distaxa, commtaxa), intersect(distaxa,
     commtaxa)]
     distaxa <- rownames(dis)
     }
     if (any(!(commtaxa %in% distaxa))) {
     print("Dropping taxa from the community because they are not present in the distance matrix:")
     print(setdiff(commtaxa, distaxa))
     res$comm <- comm[, intersect(commtaxa, distaxa)]
     }
     else {
     res$comm <- comm
     }
     if (disclass == "dist") {
     res$dist <- as.dist(dis[colnames(comm), colnames(comm)])
     }
     else {
     res$dist <- dis[colnames(comm), colnames(comm)]
     }
     return(res)
    }
    <bytecode: 0xca48558>
    <environment: namespace:picante>
     --- function search by body ---
    Function match.comm.dist in namespace picante has this body.
     ----------- END OF FAILURE REPORT --------------
    
    Error: processing vignette 'picante-intro.Rnw' failed with diagnostics:
     chunk 13
    Error in if (disclass == "dist") { : the condition has length > 1
    
    --- failed re-building 'picante-intro.Rnw'
    
    SUMMARY: processing the following file failed:
     'picante-intro.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang