* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/spftir.Rcheck’
* using R Under development (unstable) (2022-04-26 r82260)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘spftir/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spftir’ version ‘0.1.0’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘spftir’ can be installed ... [5s/16s] OK
* checking package 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [8s/26s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [3s/11s] ERROR
Running examples in ‘spftir-Ex.R’ failed
The error most likely occurred in:

> ### Name: spmblp
> ### Title: Polynomial Baseline Correction of a Matrix of Mid-infrared
> ###   Spectra
> ### Aliases: spmblp
> 
> ### ** Examples
> 
> data(spData)
> # Convert data frame to matrix
> spectra <- as.matrix(t(spData))
> # List of polynomial baseline components
> mblp <- spmblp(spectra, degree = 2, tol = 0.001, rep = 100)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
spftir
 --- call from context --- 
spmblp(spectra, degree = 2, tol = 0.001, rep = 100)
 --- call from argument --- 
missing(t) || (t == FALSE)
 --- R stacktrace ---
where 1: spmblp(spectra, degree = 2, tol = 0.001, rep = 100)

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 --- function from context --- 
function (spectra, degree = 2, tol = 0.001, rep = 100) 
{
    if (missing(spectra)) {
        stop("No spectral data provided")
    }
    if (missing(degree)) {
        stop("No degree value provided")
    }
    if (missing(tol)) {
        stop("No tolerance value provided")
    }
    if (missing(rep)) {
        stop("No maximum number of iterations provided")
    }
    if (spectra[1, 1] < spectra[1, dim(spectra)[2]]) {
        spectra <- t(apply(spectra, 1, rev))
    }
    dimnames(spectra) <- NULL
    t <- spectra[1, ]
    sp <- matrix(spectra[2:nrow(spectra), ], nrow = nrow(spectra) - 
        1, ncol = ncol(spectra))
    np <- dim(sp)
    baseline <- matrix(0, np[1], np[2])
    if (missing(t) || (t == FALSE)) 
        t <- 1:np[2]
    polx <- cbind(1/sqrt(np[2]), stats::poly(t, degree = degree))
    for (i in 1:np[1]) {
        ywork <- yold <- yorig <- sp[i, ]
        nrep <- 0
        repeat {
            nrep <- nrep + 1
            ypred <- polx %*% crossprod(polx, yold)
            ywork <- pmin(yorig, ypred)
            crit <- sum(abs((ywork - yold)/yold), na.rm = TRUE)
            if (crit < tol || nrep > rep) 
                break
            yold <- ywork
        }
        baseline[i, ] <- ypred
    }
    value <- list(original = rbind(t, sp), baseline = rbind(t, 
        baseline), corrected = rbind(t, sp - baseline))
    attr(value, "class") <- "spmblp"
    value
}
<bytecode: 0x49840f0>
<environment: namespace:spftir>
 --- function search by body ---
Function spmblp in namespace spftir has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/spftir.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:20.45, 35.92 + 5.94