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CHECK report for plrs on machv2

This page was generated on 2020-10-17 11:59:13 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE plrs PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1325/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plrs 1.28.0
Gwenael G.R. Leday to
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/plrs
Branch: RELEASE_3_11
Last Commit: 74f1dbe
Last Changed Date: 2020-04-27 14:32:06 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: plrs
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:plrs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings plrs_1.28.0.tar.gz
StartedAt: 2020-10-17 03:59:25 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:00:55 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 90.3 seconds
RetCode: 1
Status:  ERROR 
CheckDir: plrs.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:plrs.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings plrs_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/plrs.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 ‘plrs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘plrs’ version ‘1.28.0’
* 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 ‘plrs’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' call to ‘mvtnorm’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': ‘CGHbase:::calls’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘plrs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plrs.series
> ### Title: Fit plrs models for a series of arrays.
> ### Aliases: plrs.series
> 
> ### ** Examples
> 
> 
> # Simulate data
> ngenes <- 10
> narray <- 48
> rna <- dnaseg <- dnacal <- matrix(NA, ngenes, narray)
> idx <- sample(1:4, ngenes, replace=TRUE, prob=rep(1/4,4))
> for(i in 1:ngenes){
+ 	Sim <- plrs.sim(n=narray, states=idx[i], sigma=0.5)
+ 	rna[i,] <- Sim$expr
+ 	dnaseg[i,] <- Sim$seg
+ 	dnacal[i,] <- Sim$cal
+ }
> 
> 
> # Screening procedure with linear model
> series <- plrs.series(expr = rna, cghseg = dnaseg, cghcall = NULL, control.select = NULL)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
plrs
 --- call from context --- 
plrs.series(expr = rna, cghseg = dnaseg, cghcall = NULL, control.select = NULL)
 --- call from argument --- 
if (class(expr) == "ExpressionSet") {
    expr <- exprs(expr)
}
 --- R stacktrace ---
where 1: plrs.series(expr = rna, cghseg = dnaseg, cghcall = NULL, control.select = NULL)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (expr, cghseg, cghcall = NULL, probloss = NULL, probnorm = NULL, 
    probgain = NULL, probamp = NULL, control.model = list(continuous = FALSE, 
        constr = TRUE, constr.slopes = 2, constr.intercepts = TRUE, 
        min.obs = 3, discard.obs = TRUE), control.select = list(crit = ifelse(control.model$constr, 
        "osaic", "aic")), control.test = list(testing = TRUE, 
        cb = FALSE, alpha = 0.05), control.output = list(save.models = FALSE, 
        save.plots = FALSE, plot.lin = FALSE, type = "jpeg")) 
{
    if (class(expr) == "ExpressionSet") {
        expr <- exprs(expr)
    }
    if (class(cghseg) == "cghSeg") {
        cghseg <- segmented(cghseg)
        cghcall <- NULL
    }
    if (class(cghseg) == "cghCall") {
        cghcall <- CGHbase:::calls(cghseg)
        if (sum(dim(cghcall) == c(0, 0)) != 0) {
            cghcall <- NULL
            probloss <- probnorm <- probgain <- probamp <- NULL
            cghseg <- segmented(cghseg)
        }
        else {
            probloss <- probloss(cghseg)
            probnorm <- probnorm(cghseg)
            probgain <- probgain(cghseg)
            probamp <- probamp(cghseg)
            cghseg <- segmented(cghseg)
        }
    }
    if (!(is.matrix(expr) & is.matrix(cghseg))) {
        stop("input data have to be in matrix format")
    }
    else {
        if (any(is.na(expr))) 
            stop("Missing values are not allowed in expr")
        if (!sum(dim(expr) == dim(cghseg)) == 2) 
            stop("dimensions of input data are not the same")
    }
    if (is.null(cghcall)) 
        cghcall <- matrix(0, nrow(expr), ncol(expr), dimnames = dimnames(expr))
    if (!is.matrix(cghcall)) {
        stop("input data have to be in matrix format")
    }
    else {
        if (!sum(dim(expr) == dim(cghcall)) == 2) 
            stop("dimensions of input data are not the same")
    }
    if (!is.list(control.model)) 
        stop("control.model is not a list")
    if (!"continuous" %in% names(control.model)) 
        control.model$continuous <- FALSE
    if (!"constr" %in% names(control.model)) 
        control.model$constr <- TRUE
    if (!"constr.slopes" %in% names(control.model)) 
        control.model$constr.slopes <- 2
    if (!"constr.intercepts" %in% names(control.model)) 
        control.model$constr.intercepts <- TRUE
    if (!"min.obs" %in% names(control.model)) 
        control.model$min.obs <- 3
    if (!"discard.obs" %in% names(control.model)) 
        control.model$discard.obs <- TRUE
    if (!is.list(control.select) & !is.null(control.select)) 
        stop("control.select is not a list")
    if (length(control.select) > 0) {
        if (!"crit" %in% names(control.select)) 
            control.select$crit <- ifelse(control.model$constr, 
                "osaic", "aic")
    }
    if (!is.list(control.test)) 
        stop("control.test is not a list")
    if (!"testing" %in% names(control.test)) 
        control.test$testing <- TRUE
    if (!"cb" %in% names(control.test)) 
        control.test$cb <- FALSE
    if (!"alpha" %in% names(control.test)) 
        control.test$alpha <- FALSE
    if (!control.test$testing & control.test$cb) 
        control.test$testing <- TRUE
    if (!is.list(control.output)) 
        stop("control.output is not a list")
    if (!"save.models" %in% names(control.output)) 
        control.output$save.models <- FALSE
    if (!"save.plots" %in% names(control.output)) 
        control.output$save.plots <- FALSE
    if (!"plot.lin" %in% names(control.output)) 
        control.output$plot.lin <- FALSE
    if (!"type" %in% names(control.output)) 
        control.output$type <- "jpeg"
    ngenes <- nrow(expr)
    est <- matrix(NA, ngenes, 8)
    nam1 <- colnames(est) <- c("theta0.0", "theta0.1", "theta1.0", 
        "theta1.1", "theta2.0", "theta2.1", "theta3.0", "theta3.1")
    rownames(est) <- paste("gene", 1:ngenes, sep = "")
    modelTypes <- matrix(F, ngenes, 4)
    colnames(modelTypes) <- c("Intercept", "Linear", "Piecewise level", 
        "Piecewise linear")
    rownames(modelTypes) <- rownames(est)
    Ieff <- Seff <- matrix(F, ngenes, 4)
    nam3 <- colnames(Ieff) <- colnames(Seff) <- c("Loss", "Norm.", 
        "Gain", "Ampl.")
    rownames(modelTypes) <- rownames(est)
    if (control.test$testing) {
        res.test <- matrix(NA, ngenes, 3, dimnames = list(rownames(est), 
            c("stat", "raw.pval", "BH.adj.pval")))
    }
    config <- matrix(NA, ngenes, 4)
    colnames(config) <- as.character(-1:2)
    rownames(config) <- rownames(est)
    if (control.output$save.plots) 
        dir.create("plrsSeriesPlots")
    if (control.output$save.models) 
        dir.create("plrsSeriesObjects")
    if (is.null(rownames(expr))) {
        lab <- 1:nrow(expr)
    }
    else {
        lab <- rownames(expr)
    }
    ind <- duplicated(lab)
    cp <- 1
    while (sum(ind) != 0) {
        lab[ind] <- paste(lab[ind], "_", cp, sep = "")
        ind <- duplicated(lab)
        if (sum(ind) != 0) 
            lab[ind] <- substr(lab[ind], 1, nchar(lab[ind]) - 
                2)
        cp <- cp + 1
    }
    if (ngenes > 100) {
        cat("In progress... \n\n")
        toprint <- round(quantile(1:ngenes, probs = seq(0, 1, 
            0.1))[-1])
        t <- proc.time()
        ct <- 1
    }
    for (x in 1:ngenes) {
        if (ngenes > 100) {
            if (x == toprint[ct]) {
                xx <- (proc.time() - t)[3]
                cat(names(toprint[ct]), " done (", toprint[ct], 
                  " genes),\t  ", "time elapsed = ", .convertToTime(xx), 
                  "\n", sep = "")
                ct <- ct + 1
            }
        }
        error <- try(model <- plrs(expr = expr[x, ], cghseg = cghseg[x, 
            ], cghcall = cghcall[x, ], probloss = probloss[x, 
            ], probnorm = probnorm[x, ], probgain = probgain[x, 
            ], probamp = probamp[x, ], continuous = control.model$continuous, 
            constr = control.model$constr, constr.slopes = control.model$constr.slopes, 
            constr.intercepts = control.model$constr.intercepts, 
            min.obs = control.model$min.obs, discard.obs = control.model$discard.obs), 
            T)
        if (!inherits(error, "try-error")) {
            vec <- as.vector(table(model@data$cghcall))
            config[x, colnames(config) %in% as.character(model@data$conf)] <- vec
            if (!is.null(control.select)) 
                model <- plrs.select(model, crit = control.select$crit)@model
            est[x, nam1 %in% names(coef(model))] <- coef(model)
            modelTypes[x, colnames(modelTypes) %in% model@type] <- TRUE
            tabb <- effects(model)
            indeff <- !is.na(tabb[, 2])
            Ieff[x, indeff] <- tabb[indeff, 2]
            Seff[x, indeff] <- tabb[indeff, 3]
            if (control.test$testing || control.test$cb) {
                model <- plrs.test(model)
                if (length(model@test) != 0) {
                  res.test[x, 1] <- model@test$stat
                  res.test[x, 2] <- model@test$pvalue
                  if (control.test$cb) {
                    model <- plrs.cb(model, alpha = 0.05)
                  }
                }
            }
            if (control.output$save.models) {
                save(model, file = paste("plrsSeriesObjects/gene_", 
                  lab[x], ".RData", sep = ""))
            }
            if (control.output$plot.lin || control.output$save.plots) {
                if (control.output$save.plots) {
                  if (control.output$type == "pdf") 
                    pdf(paste("plrsSeriesPlots/gene", lab[x], 
                      ".pdf", sep = ""))
                  if (control.output$type == "jpeg") 
                    jpeg(paste("plrsSeriesPlots/gene", lab[x], 
                      ".jpeg", sep = ""))
                }
                plot(model, lin = control.output$plot.lin)
                if (control.output$save.plots) 
                  dev.off()
            }
        }
    }
    est <- round(est, 8)
    general <- apply(config, 2, function(x) sum(!is.na(x)))
    tp <- matrix(NA, 4, 4)
    for (d in 1:ncol(config)) {
        if (general[d] != 0) 
            tp[, d] <- summary(config[, d])[c(1, 3, 4, 6)]
    }
    general <- rbind(general, tp)
    colnames(general) <- colnames(config)
    rownames(general) <- c("Nb genes", "Min. obs", "Median. obs", 
        "Mean. obs", "Max. obs")
    if (sum(general[1, ] != 0) == 1) {
        general <- t(as.matrix(general[1, ]))
        rownames(general) <- "Nb genes"
    }
    type.model <- as.matrix(colSums(modelTypes))
    rownames(type.model) <- c("Intercept", "Simple linear", "Piecewise level", 
        "Piecewise linear")
    colnames(type.model) <- "NbModels"
    if (control.test$testing) 
        res.test[, 3] <- p.adjust(res.test[, 2], method = "BH")
    else {
        res.test <- matrix(nrow = 0, ncol = 0)
    }
    cat("\n")
    out <- new("plrs.series", coefficients = est, effects = list(I = Ieff, 
        S = Seff), test = res.test, general = general, modelsType = list(summary = type.model, 
        all = modelTypes), call.arg = list(control.model = control.model, 
        control.select = control.select))
    return(out)
}
<bytecode: 0x7fe9c9bd2040>
<environment: namespace:plrs>
 --- function search by body ---
Function plrs.series in namespace plrs 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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/plrs.Rcheck/00check.log’
for details.


Installation output

plrs.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘plrs’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (plrs)

Tests output


Example timings

plrs.Rcheck/plrs-Ex.timings

nameusersystemelapsed
criteria0.2300.0160.246
modify.conf0.0040.0010.005
neveCN170.1900.0270.217
neveGE170.0620.0050.067
plrs0.0260.0140.039
plrs.cb1.8100.3982.322