failure: length > 1 in coercion to logical

[sneumann]

After the BioC build farm has enabled _R_CHECK_LENGTH_1_LOGIC2_
(see https://stat.ethz.ch/pipermail/bioc-devel/2020-January/016081.html for details)
we get a build error http://bioconductor.org/checkResults/devel/bioc-LATEST/CAMERA/malbec2-checksrc.html , see below for a copy.

Chances are good that the issue is here:

CAMERA/R/fct_findIsotopes.R

Line 95 in cbc9cdb

if(!is.infinite(ini) && length(ini) > 0){

So what's left is to figure how to safely fix this code.

Yours, Steffen

* checking examples ... ERROR
Running examples in ‘CAMERA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotate-methods
> ### Title: Automatic deconvolution/annotation of LC/ESI-MS data
> ### Aliases: annotate annotate,xcmsSet-method
> ### Keywords: methods
> 
> ### ** Examples
> 
>  library(CAMERA)
>  file <- system.file('mzdata/MM14.mzdata', package = "CAMERA")
>  xs   <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10))
Detecting mass traces at 30 ppm ... OK
Detecting chromatographic peaks in 456 regions of interest ... OK: 126 found.
>  xsa  <- annotate(xs)
Start grouping after retention time.
Created 14 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
 % finished: 20   ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
CAMERA
 --- call from context --- 
FUN(newX[, i], ...)
 --- call from argument --- 
!is.infinite(ini) && length(ini) > 0
 --- R stacktrace ---
where 1: FUN(newX[, i], ...)
where 2: apply(hits.iso[!hit, , drop = FALSE], 1, function(x) {
    if (!all(is.na(x))) {
        ini <- which(x > iso)
        if (!is.infinite(ini) && length(ini) > 0) {
            x[min(ini):ncol(hits.iso)] <- NA
        }
    }
    x
})
where 3: t(apply(hits.iso[!hit, , drop = FALSE], 1, function(x) {
    if (!all(is.na(x))) {
        ini <- which(x > iso)
        if (!is.infinite(ini) && length(ini) > 0) {
            x[min(ini):ncol(hits.iso)] <- NA
        }
    }
    x
}))
where 4: findIsotopesPspec(isomatrix, mz, ipeak, int, params)
where 5: findIsotopes(xa, maxcharge = maxcharge, maxiso = maxiso, ppm = ppm, 
    mzabs = mzabs, intval = intval, minfrac = minfrac)
where 6: findIsotopes(xa, maxcharge = maxcharge, maxiso = maxiso, ppm = ppm, 
    mzabs = mzabs, intval = intval, minfrac = minfrac)
where 7: annotate(xs)
where 8: annotate(xs)

 --- value of length: 2 type: logical ---
   2    3 
TRUE TRUE 
 --- function from context --- 
function (x) 
{
    if (!all(is.na(x))) {
        ini <- which(x > iso)
        if (!is.infinite(ini) && length(ini) > 0) {
            x[min(ini):ncol(hits.iso)] <- NA
        }
    }
    x
}
<bytecode: 0x55a4ac4776c0>
<environment: 0x55a4ac473030>
 --- function search by body ---
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical

[sneumann]

For the record, there are more cases of && that trigger errors in

CAMERA/R/xsAnnotate.R

Line 12 in 3e25fab

if(length(sampnames(xs)) > 1 && !nrow(xs@groups) > 0) {

and

CAMERA/R/pspec2metfrag.R

Line 18 in cbc9cdb

if(object@sample == 1 && length(sampnames(object@xcmsSet)) == 1){

Several cases now fixed in bc0e9fd