* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/RGBM.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 ‘RGBM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RGBM’ version ‘1.0-8’
* 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 ‘RGBM’ can be installed ... [11s/28s] 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/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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... ERROR
Running examples in ‘RGBM-Ex.R’ failed
The error most likely occurred in:

> ### Name: RGBM
> ### Title: Regularized Gradient Boosting Machine for inferring GRN
> ### Aliases: RGBM
> 
> ### ** Examples
> 
> # load RGBM library
> library("RGBM")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
> cl <- makeCluster(2)
> # run network inference on a 100-by-100 dummy expression data.
> A = RGBM()
[1] "Identified colids for active tfs"
[1] "Identified list of active tfs for each gene"
[1] "Performed first step of model building"
[1] "Intermediate GRN and Variable Importance Curve in: /tmp/RtmpixnQiM/working_dir/RtmpoiBnBh"
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
RGBM
 --- call from context --- 
eval(xpr, envir = envir)
 --- call from argument --- 
(select_k + j) > (mink + 1) && select_k == 1 && temp == 0
 --- R stacktrace ---
where 1: eval(xpr, envir = envir)
where 2: eval(xpr, envir = envir)
where 3: doTryCatch(return(expr), name, parentenv, handler)
where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 5: tryCatchList(expr, classes, parentenv, handlers)
where 6: tryCatch(eval(xpr, envir = envir), error = function(e) e)
where 7: doTryCatch(return(expr), name, parentenv, handler)
where 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 9: tryCatchList(expr, classes, parentenv, handlers)
where 10: tryCatch({
    repeat {
        args <- nextElem(it)
        if (obj$verbose) {
            cat(sprintf("evaluation # %d:\n", i))
            print(args)
        }
        for (a in names(args)) assign(a, args[[a]], pos = envir, 
            inherits = FALSE)
        r <- tryCatch(eval(xpr, envir = envir), error = function(e) e)
        if (obj$verbose) {
            cat("result of evaluating expression:\n")
            print(r)
        }
        tryCatch(accumulator(list(r), i), error = function(e) {
            cat("error calling combine function:\n")
            print(e)
            NULL
        })
        i <- i + 1
    }
}, error = function(e) {
    if (!identical(conditionMessage(e), "StopIteration")) 
        stop(simpleError(conditionMessage(e), expr))
})
where 11: e$fun(obj, substitute(ex), parent.frame(), e$data)
where 12: foreach(i = 1:Actual_N, .combine = c, .inorder = TRUE) %dopar% 
    {
        target_id <- targets_to_consider[i]
        sorted_tf_impv <- importance_matrix[track_matrix[, target_id], 
            target_id]
        xcord <- c(1:TF)
        ref_v_y <- sorted_tf_impv[length(sorted_tf_impv)]
        ref_v_x <- TF/TF
        final_vector <- NULL
        if (mink == 0) {
            min_id = 1
        }
        else {
            min_id = mink
        }
        for (j in min_id:(TF - 2)) {
            ref_j_y <- sorted_tf_impv[j]
            ref_j_x <- j/TF
            temp <- c()
            for (k in ((j + 1):(TF - 1))) {
                ref_k_y <- sorted_tf_impv[k]
                ref_k_x <- k/TF
                a = c(ref_k_x - ref_j_x, ref_k_y - ref_j_y)
                b = c(ref_k_x - ref_v_x, ref_k_y - ref_v_y)
                norm_a <- sqrt(sum(a^2))
                norm_b <- sqrt(sum(b^2))
                numerator <- as.numeric(a %*% b)
                denominator <- (norm_a * norm_b)
                costheta <- numerator/denominator
                if (costheta <= -1) {
                  val <- acos(-1)
                }
                else {
                  val <- acos(costheta)
                }
                temp <- c(temp, pi - val)
            }
            select_value <- min(temp)
            select_k <- which.min(temp)
            if ((select_k + j) > (mink + 1)) {
                final_vector <- rbind(final_vector, cbind(j, 
                  (select_k + j), select_value))
            }
            if ((select_k + j) > (mink + 1) && select_k == 1 && 
                temp == 0) {
                break
            }
        }
        min_final_vector_id <- which.min(final_vector[, 3])
        ideal_k <- as.numeric(final_vector[min_final_vector_id, 
            1]) - 1
        ideal_k
    }
where 13: select_ideal_k(experimentid, mink, filepath, imagepath, adjacency_matrix_path)
where 14: regularized_GBM_step(E, A_first, K, tfs, targets, Ntfs, Ntargets, 
    lf, M, nu, s_f, experimentid, outputpath, sample_type, mink, 
    real)
where 15: RGBM()

 --- value of length: 5 type: logical ---
[1] FALSE FALSE FALSE FALSE FALSE
 --- function from context --- 
 --- function search by 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/RGBM.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:24.85, 46.70 + 7.15