* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/ALS.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 ‘ALS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ALS’ version ‘0.0.6’
* 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 ‘ALS’ can be installed ... 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 ... [6s/18s] 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 data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... ERROR
Running examples in ‘ALS-Ex.R’ failed
The error most likely occurred in:

> ### Name: als
> ### Title: alternating least squares multivariate curve resolution
> ###   (MCR-ALS)
> ### Aliases: als
> ### Keywords: optimize
> 
> ### ** Examples
> 
> ## load 2 matrix datasets into variables d1 and d2
> ## load starting values for elution profiles
> ## into variables Cstart1 and Cstart2
> ## load time labels as x, m/z values as x2
> data(multiex)
> 
> ## starting values for elution profiles
> matplot(x,Cstart1,type="l")
> matplot(x,Cstart2,type="l",add=TRUE)
> 
> ## using MCR-ALS, improve estimates for mass spectra S and the two
> ## matrices of elution profiles
> ## apply unimodality constraints to the elution profile estimates
> ## note that the starting estimates for S just contain a dummy matrix
> 
> test0 <- als(CList=list(Cstart1,Cstart2),S=matrix(1,nrow=400,ncol=2),
+ PsiList=list(d1,d2), x=x, x2=x2, uniC=TRUE, normS=0)
Initial RSS 3.039967e+13 
Iteration (opt. S): 1, RSS: 1.330703e+12, RD: 0.9562264
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
ALS
 --- call from context --- 
als(CList = list(Cstart1, Cstart2), S = matrix(1, nrow = 400, 
    ncol = 2), PsiList = list(d1, d2), x = x, x2 = x2, uniC = TRUE, 
    normS = 0)
 --- call from argument --- 
normS > S && (iter%%2 != b)
 --- R stacktrace ---
where 1: als(CList = list(Cstart1, Cstart2), S = matrix(1, nrow = 400, 
    ncol = 2), PsiList = list(d1, d2), x = x, x2 = x2, uniC = TRUE, 
    normS = 0)

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 --- function from context --- 
function (CList, PsiList, S = matrix(), WList = list(), thresh = 0.001, 
    maxiter = 100, forcemaxiter = FALSE, optS1st = TRUE, x = 1:nrow(CList[[1]]), 
    x2 = 1:nrow(S), baseline = FALSE, fixed = vector("list", 
        length(PsiList)), uniC = FALSE, uniS = FALSE, nonnegC = TRUE, 
    nonnegS = TRUE, normS = 0, closureC = list()) 
{
    RD <- 10^20
    PsiAll <- do.call("rbind", PsiList)
    resid <- vector("list", length(PsiList))
    if (length(WList) == 0) {
        WList <- vector("list", length(PsiList))
        for (i in 1:length(PsiList)) WList[[i]] <- matrix(1, 
            nrow(PsiList[[1]]), ncol(PsiList[[1]]))
    }
    W <- do.call("rbind", WList)
    for (i in 1:length(PsiList)) resid[[i]] <- matrix(0, nrow(PsiList[[i]]), 
        ncol(PsiList[[i]]))
    for (j in 1:length(PsiList)) {
        for (i in 1:nrow(PsiList[[j]])) {
            resid[[j]][i, ] <- PsiList[[j]][i, ] - CList[[j]][i, 
                ] %*% t(S * WList[[j]][i, ])
        }
    }
    initialrss <- oldrss <- sum(unlist(resid)^2)
    cat("Initial RSS", initialrss, "\n")
    iter <- 1
    b <- if (optS1st) 
        1
    else 0
    oneMore <- FALSE
    while (((RD > thresh || forcemaxiter) && maxiter >= iter) || 
        oneMore) {
        if (iter%%2 == b) 
            S <- getS(CList, PsiAll, S, W, baseline, uniS, nonnegS, 
                normS, x2)
        else CList <- getCList(S, PsiList, CList, WList, resid, 
            x, baseline, fixed, uniC, nonnegC, closureC)
        for (j in 1:length(PsiList)) {
            for (i in 1:nrow(PsiList[[j]])) {
                resid[[j]][i, ] <- PsiList[[j]][i, ] - CList[[j]][i, 
                  ] %*% t(S * WList[[j]][i, ])
            }
        }
        rss <- sum(unlist(resid)^2)
        RD <- ((oldrss - rss)/oldrss)
        oldrss <- rss
        typ <- if (iter%%2 == b) 
            "S"
        else "C"
        cat("Iteration (opt. ", typ, "): ", iter, ", RSS: ", 
            rss, ", RD: ", RD, "\n", sep = "")
        iter <- iter + 1
        oneMore <- (normS > S && (iter%%2 != b) && maxiter != 
            1) || (length(closureC) > 0 && (iter%%2 == b))
    }
    cat("Initial RSS / Final RSS =", initialrss, "/", rss, "=", 
        initialrss/rss, "\n")
    return(list(CList = CList, S = S, rss = rss, resid = resid, 
        iter = iter))
}
<bytecode: 0x4904e18>
<environment: namespace:ALS>
 --- function search by body ---
Function als in namespace ALS 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/ALS.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:44.44, 32.92 + 6.35