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CHECK report for Prize on merida1

This page was generated on 2021-01-19 11:58:09 -0500 (Tue, 19 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE Prize PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1385/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Prize 1.20.0
Daryanaz Dargahi
Snapshot Date: 2021-01-18 14:42:24 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/Prize
Branch: RELEASE_3_12
Last Commit: 278a85d
Last Changed Date: 2020-10-27 11:06:15 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  ERROR 
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: Prize
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Prize.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Prize_1.20.0.tar.gz
StartedAt: 2021-01-19 05:02:57 -0500 (Tue, 19 Jan 2021)
EndedAt: 2021-01-19 05:03:55 -0500 (Tue, 19 Jan 2021)
EllapsedTime: 58.2 seconds
RetCode: 1
Status:  ERROR 
CheckDir: Prize.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Prize.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Prize_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/Prize.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Prize/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Prize’ version ‘1.20.0’
* 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 ‘Prize’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'Prize' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/Prize.Rcheck/00install.out’ for details.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Prize-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AIJ
> ### Title: Aggregated individual judgements (AIJ) slot
> ### Aliases: AIJ aij Aij AIJ,ANY-method
> 
> ### ** Examples
> 
> mat <- matrix(nrow = 4, ncol = 1, data = NA)
> mat[,1] <- c(system.file('extdata','ind1.tsv',package = 'Prize'),
+             system.file('extdata','ind2.tsv',package = 'Prize'),
+             system.file('extdata','ind3.tsv',package = 'Prize'),
+             system.file('extdata','ind4.tsv',package = 'Prize'))
> rownames(mat) <- c('ind1','ind2','ind3', 'ind4')
> colnames(mat) <- c('individual_judgement')
> 
> # non-weighted aggregation
> res <- gaggregate(srcfile = mat, method = 'geometric', simulation = 500)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
Prize
 --- call from context --- 
gaggregate(srcfile = mat, method = "geometric", simulation = 500)
 --- call from argument --- 
if (class(srcfile) %in% c("matrix", "data.frame")) {
    x <- as.matrix(srcfile)
    judge <- dim(x)[1]
    ICRname <- as.character(rownames(x))
    if (dim(x)[2] > 1 && !all(is.na(x[, 2]))) {
        weights <- as.numeric(x[, 2])
        if (sum(as.numeric(weights)) != 1) {
            stop("Weights must add up to 1.")
        }
    }
    else {
        weights <- NULL
    }
    tmp <- list()
    if (file.exists(as.character(x[1, 1]))) {
        file <- read.delim(as.character(x[1, 1]), sep = "\t", 
            header = TRUE, row.names = 1)
        nRow <- dim(file)[1]
        nCol <- dim(file)[2]
        rname <- rownames(file)
        cname <- colnames(file)
    }
    else {
        stop(paste(as.character(x[1, 1]), " is missing.", sep = ""))
    }
    message(paste("Reading individual judgements.", sep = ""))
    for (i in seq_len(judge)) {
        if (file.exists(as.character(x[i, 1]))) {
            file <- read.delim(as.character(x[i, 1]), sep = "\t", 
                header = TRUE, row.names = 1)
            if (length(which(x == 0, arr.ind = TRUE)) > 0) {
                stop("Zero is not allowed in the matrix, infinite values are being created in the square matrix.")
            }
            if (dim(file)[1] != dim(file)[2]) {
                stop(paste(as.character(x[i, 1]), "is not a square/triangular matrix.", 
                  sep = " "))
            }
            if (!is.numeric(as.matrix(file))) {
                stop(paste(as.character(x[i, 1]), "is not a numeric matrix.", 
                  sep = " "))
            }
            if (dim(file)[1] != nRow || dim(file)[2] != nCol) {
                stop("Judgement matrices has different number of rows or columns.")
            }
            if (!all(rownames(file) == rname)) {
                stop("Judgement matrices have different orders.")
            }
            if (all(is.na(file[upper.tri(file)])) || all(is.na(file[lower.tri(file)]))) {
                out <- ahmatrix(file)
                file <- as.matrix(out@ahp_matrix)
            }
            tmp <- append(tmp, list(file))
        }
        else {
            stop(paste(as.character(x[i, 1]), " is missing.", 
                sep = ""))
        }
    }
} else {
    stop("'srcfile' must be a matrix/datafram that include the path to individual judgement matrices (PCM) and their weights (optional).")
}
 --- R stacktrace ---
where 1: gaggregate(srcfile = mat, method = "geometric", simulation = 500)

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (srcfile, method = "geometric", simulation = 500) 
{
    if (class(srcfile) %in% c("matrix", "data.frame")) {
        x <- as.matrix(srcfile)
        judge <- dim(x)[1]
        ICRname <- as.character(rownames(x))
        if (dim(x)[2] > 1 && !all(is.na(x[, 2]))) {
            weights <- as.numeric(x[, 2])
            if (sum(as.numeric(weights)) != 1) {
                stop("Weights must add up to 1.")
            }
        }
        else {
            weights <- NULL
        }
        tmp <- list()
        if (file.exists(as.character(x[1, 1]))) {
            file <- read.delim(as.character(x[1, 1]), sep = "\t", 
                header = TRUE, row.names = 1)
            nRow <- dim(file)[1]
            nCol <- dim(file)[2]
            rname <- rownames(file)
            cname <- colnames(file)
        }
        else {
            stop(paste(as.character(x[1, 1]), " is missing.", 
                sep = ""))
        }
        message(paste("Reading individual judgements.", sep = ""))
        for (i in seq_len(judge)) {
            if (file.exists(as.character(x[i, 1]))) {
                file <- read.delim(as.character(x[i, 1]), sep = "\t", 
                  header = TRUE, row.names = 1)
                if (length(which(x == 0, arr.ind = TRUE)) > 0) {
                  stop("Zero is not allowed in the matrix, infinite values are being created in the square matrix.")
                }
                if (dim(file)[1] != dim(file)[2]) {
                  stop(paste(as.character(x[i, 1]), "is not a square/triangular matrix.", 
                    sep = " "))
                }
                if (!is.numeric(as.matrix(file))) {
                  stop(paste(as.character(x[i, 1]), "is not a numeric matrix.", 
                    sep = " "))
                }
                if (dim(file)[1] != nRow || dim(file)[2] != nCol) {
                  stop("Judgement matrices has different number of rows or columns.")
                }
                if (!all(rownames(file) == rname)) {
                  stop("Judgement matrices have different orders.")
                }
                if (all(is.na(file[upper.tri(file)])) || all(is.na(file[lower.tri(file)]))) {
                  out <- ahmatrix(file)
                  file <- as.matrix(out@ahp_matrix)
                }
                tmp <- append(tmp, list(file))
            }
            else {
                stop(paste(as.character(x[i, 1]), " is missing.", 
                  sep = ""))
            }
        }
    }
    else {
        stop("'srcfile' must be a matrix/datafram that include the path to individual judgement matrices (PCM) and their weights (optional).")
    }
    x <- tmp
    if (method == "geometric") {
        message(paste("Aggregating individual judgements with geometric mean (AIJ).", 
            sep = " "))
        if (is.null(weights)) {
            tmp <- x[[1]]
            iahp <- ahp(x[[1]], simulation = simulation)
            CR <- iahp@saaty_inconsistency
            IW <- iahp@weight
            for (i in seq(from = 2, to = judge)) {
                tmp <- tmp * x[[i]]
                iahp <- ahp(x[[i]], simulation = simulation)
                CR <- append(CR, iahp@saaty_inconsistency)
                IW <- rbind(IW, iahp@weight)
            }
            gmean <- tmp^(1/judge)
            names(CR) <- names(x)
            IW = rbind(IW, ahp(gmean, simulation = simulation)@weight)
            rownames(IW) <- append(rownames(srcfile), "Group judgement")
        }
        else {
            tmp <- x[[1]]^weights[1]
            iahp <- ahp(x[[1]], simulation = simulation)
            CR <- iahp@saaty_inconsistency
            IW <- iahp@weight
            for (i in seq(from = 2, to = judge)) {
                tmp <- tmp * (x[[i]]^weights[i])
                iahp <- ahp(x[[i]], simulation = simulation)
                CR <- append(CR, iahp@saaty_inconsistency)
                IW <- rbind(IW, iahp@weight)
            }
            gmean <- tmp
            names(CR) <- ICRname
            IW = rbind(IW, ahp(gmean, simulation = simulation)@weight)
            rownames(IW) <- append(rownames(srcfile), "Group judgement")
        }
        rmean <- gmean
        names(CR) <- ICRname
        message(paste("Computing group consistency ratio (GCR).", 
            sep = ""))
        GCR <- numeric()
        group_consistency_ratio <- numeric()
        if (simulation > 0) {
            GCR <- ahp(rmean, simulation = simulation)
            group_consistency_ratio <- GCR@saaty_inconsistency
        }
        message(paste("Computing consensus index (CI).", sep = ""))
        consensus_measure <- numeric()
        for (i in seq_len(judge)) {
            GCI <- 0
            for (j in seq_len(nRow)) {
                for (k in seq_len(nRow)) {
                  GCI <- GCI + (rmean[j, k] * x[[i]][k, j])
                }
            }
            GCI <- GCI/(nRow^2)
            consensus_measure <- append(consensus_measure, GCI)
        }
        names(consensus_measure) <- ICRname
        return(new("geoAggreg", AIJ = rmean, GCR = group_consistency_ratio, 
            CI = consensus_measure, ICR = CR, IP = IW))
    }
    else if (method == "arithmetic") {
        message(paste("Aggregating individual priorities with arithmetic mean (AIP).", 
            sep = " "))
        if (is.null(weights)) {
            temp <- ahp(x[[1]], simulation = simulation)
            tmp <- temp@weight
            CR <- temp@saaty_inconsistency
            IW <- temp@weight
            for (i in seq(from = 2, to = judge)) {
                temp <- ahp(x[[i]], simulation = simulation)
                tmp <- tmp + (temp@weight)
                CR <- append(CR, temp@saaty_inconsistency)
                IW <- rbind(IW, temp@weight)
            }
            tmp <- tmp/judge
            amean <- tmp
            names(CR) <- ICRname
            IW <- rbind(IW, amean)
            rownames(IW) <- append(rownames(srcfile), "Group judgement")
        }
        else {
            temp <- ahp(x[[1]], simulation = simulation)
            tmp <- temp@weight
            CR <- temp@saaty_inconsistency
            IW <- temp@weight
            tmp <- tmp * weights[1]
            for (i in seq(from = 2, to = judge)) {
                temp <- ahp(x[[i]], simulation = simulation)
                tmp <- tmp + (temp@weight * weights[i])
                CR <- append(CR, temp@saaty_inconsistency)
                IW <- rbind(IW, temp@weight)
            }
            amean <- tmp
            names(CR) <- ICRname
            IW <- rbind(IW, amean)
            rownames(IW) <- append(rownames(srcfile), "Group judgement")
        }
        rmean <- amean
        names(CR) <- ICRname
        return(new("ariAggreg", AIP = rmean, ICR = CR, IP = IW))
    }
    else {
        stop("Please choose one of the following methods: geometric, arithmetic")
    }
}
<bytecode: 0x7fe4274b3ed0>
<environment: namespace:Prize>
 --- function search by body ---
Function gaggregate in namespace Prize has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
          tmp <- t(1/(x))
          tmp[lower.tri(tmp)] <- 0
          tmp[!is.finite(tmp)] <- 0
          x <- x + tmp
          diag(x) <- 1
          x <- as.matrix(x)
      }
      return(new("ahmatrixObj", ahp_matrix = x))
  }
  <bytecode: 0x7fbfa9848560>
  <environment: namespace:Prize>
   --- function search by body ---
  Function ahmatrix in namespace Prize has this body.
   ----------- END OF FAILURE REPORT -------------- 
  Fatal error: the condition has length > 1
* 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, 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/Prize.Rcheck/00check.log’
for details.


Installation output

Prize.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘Prize’ ...
** using staged installation
** R
** 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
Warning: Package 'Prize' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'Prize' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (Prize)

Tests output

Prize.Rcheck/tests/runTests.Rout.fail


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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("Prize")
Loading required package: shape
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
Prize
 --- call from context --- 
ahmatrix(ahmat)
 --- call from argument --- 
if (class(srcfile) %in% c("matrix", "data.frame")) {
    x <- as.matrix(srcfile)
} else {
    if (file.exists(srcfile)) {
        x <- read.delim(srcfile, sep = "\t", header = TRUE, row.names = 1)
    }
    else {
        stop("\"srcfile\" is missing.")
    }
}
 --- R stacktrace ---
where 1: ahmatrix(ahmat)
where 2: func()
where 3: system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest)
where 4: doTryCatch(return(expr), name, parentenv, handler)
where 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 6: tryCatchList(expr, classes, parentenv, handlers)
where 7: tryCatch(expr, error = function(e) {
    call <- conditionCall(e)
    if (!is.null(call)) {
        if (identical(call[[1L]], quote(doTryCatch))) 
            call <- sys.call(-4L)
        dcall <- deparse(call)[1L]
        prefix <- paste("Error in", dcall, ": ")
        LONG <- 75L
        sm <- strsplit(conditionMessage(e), "\n")[[1L]]
        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
        if (is.na(w)) 
            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
                type = "b")
        if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")
    }
    else prefix <- "Error : "
    msg <- paste0(prefix, conditionMessage(e), "\n")
    .Internal(seterrmessage(msg[1L]))
    if (!silent && isTRUE(getOption("show.error.messages"))) {
        cat(msg, file = outFile)
        .Internal(printDeferredWarnings())
    }
    invisible(structure(msg, class = "try-error", condition = e))
})
where 8: try(system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest))
where 9: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp, 
    tearDownFunc = .tearDown)
where 10: .sourceTestFile(testFile, testSuite$testFuncRegexp)
where 11: RUnit::runTestSuite(suite)
where 12: BiocGenerics:::testPackage("Prize")

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (x) 
{
    srcfile <- x
    if (class(srcfile) %in% c("matrix", "data.frame")) {
        x <- as.matrix(srcfile)
    }
    else {
        if (file.exists(srcfile)) {
            x <- read.delim(srcfile, sep = "\t", header = TRUE, 
                row.names = 1)
        }
        else {
            stop("\"srcfile\" is missing.")
        }
    }
    x <- as.matrix(x)
    if (length(which(x == 0, arr.ind = TRUE)) > 0) {
        stop("Zero is not allowed in the matrix, infinite values are being created in the square matrix.")
    }
    if (all(is.na(x[upper.tri(x)]))) {
        lower <- TRUE
        upper <- FALSE
        x[upper.tri(x, diag = TRUE)] = 0
    }
    else if (all(is.na(x[lower.tri(x)]))) {
        upper <- TRUE
        lower <- FALSE
        x[lower.tri(x, diag = TRUE)] = 0
    }
    else {
        stop("\"srcfile\" is not a triangular matrix.")
    }
    if (length(which(x == Inf, arr.ind = TRUE)) > 0 || length(which(is.na(x) == 
        TRUE, arr.ind = TRUE)) > 0) {
        stop("infinite or missing values in the triangular matrix")
    }
    if (upper == TRUE) {
        x[lower.tri(x)] <- 0
        tmp <- t(1/(x))
        tmp[upper.tri(tmp)] <- 0
        tmp[!is.finite(tmp)] <- 0
        x <- x + tmp
        diag(x) <- 1
        x <- as.matrix(x)
    }
    if (lower == TRUE) {
        x[upper.tri(x)] <- 0
        tmp <- t(1/(x))
        tmp[lower.tri(tmp)] <- 0
        tmp[!is.finite(tmp)] <- 0
        x <- x + tmp
        diag(x) <- 1
        x <- as.matrix(x)
    }
    return(new("ahmatrixObj", ahp_matrix = x))
}
<bytecode: 0x7fbfa9848560>
<environment: namespace:Prize>
 --- function search by body ---
Function ahmatrix in namespace Prize has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1

Example timings

Prize.Rcheck/Prize-Ex.timings

nameusersystemelapsed