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### Running command:
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### /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_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/plrs.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.30.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: Package 'plrs' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/plrs.Rcheck/00install.out’ for details.
* 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: 0x7f8a99ae69a8>
<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, 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/plrs.Rcheck/00check.log’
for details.