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CHECK report for Mirsynergy on machv2

This page was generated on 2020-10-17 11:58:58 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Mirsynergy PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1100/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mirsynergy 1.24.0
Yue Li
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Mirsynergy
Branch: RELEASE_3_11
Last Commit: a30de59
Last Changed Date: 2020-04-27 14:38:18 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: Mirsynergy
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Mirsynergy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Mirsynergy_1.24.0.tar.gz
StartedAt: 2020-10-17 03:08:04 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:09:35 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 91.4 seconds
RetCode: 1
Status:  ERROR 
CheckDir: Mirsynergy.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Mirsynergy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Mirsynergy_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Mirsynergy.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mirsynergy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mirsynergy’ version ‘1.24.0’
* 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 ‘Mirsynergy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Mirsynergy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mirsynergy
> ### Title: Detect synergistic miRNA regulatory modules by overlapping
> ###   neighbourhood expansion
> ### Aliases: mirsynergy
> ### Keywords: clustering microRNA
> 
> ### ** Examples
> 
> ##---- Should be DIRECTLY executable !! ----
> ##-- ==>  Define data, use random,
> ##--	or do  help(data=index)  for the standard data sets.
> ##
> # simulate N mRNA and M miRNA and their interaction matrices
> load(system.file("extdata/toy_modules.RData", package="Mirsynergy"))
> 
> # run mirsynergy clustering
> V <- mirsynergy(W, H, verbose=TRUE)
Discard row/column of all zeros in W

*Stage I. Cluster 18 miRNA:


Forming new module with seed: miRNA6
add: miRNA18; w.in: 0.655; w.bound: 1.535; new synergy: 0.106
add: miRNA8; w.in: 1.152; w.bound: 1.460; new synergy: 0.134
add: miRNA12; w.in: 2.072; w.bound: 0.540; new synergy: 0.195

Forming new module with seed: miRNA3
add: miRNA9; w.in: 0.735; w.bound: 0.484; new synergy: 0.141

Forming new module with seed: miRNA17
add: miRNA2; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195

Forming new module with seed: miRNA2
add: miRNA17; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195

Forming new module with seed: miRNA10
add: miRNA15; w.in: 0.304; w.bound: 0.532; new synergy: 0.063
add: miRNA14; w.in: 0.573; w.bound: 0.649; new synergy: 0.079
add: miRNA17; w.in: 0.796; w.bound: 1.120; new synergy: 0.080
add: miRNA2; w.in: 1.233; w.bound: 1.149; new synergy: 0.100

Forming new module with seed: miRNA16
add: miRNA20; w.in: 0.219; w.bound: 0.218; new synergy: 0.049
add: miRNA17; w.in: 0.373; w.bound: 0.827; new synergy: 0.052
add: miRNA2; w.in: 0.718; w.bound: 1.041; new synergy: 0.074
add: miRNA6; w.in: 1.032; w.bound: 2.376; new synergy: 0.077
add: miRNA18; w.in: 1.913; w.bound: 1.495; new synergy: 0.124
add: miRNA8; w.in: 2.410; w.bound: 1.420; new synergy: 0.135
add: miRNA12; w.in: 3.330; w.bound: 0.500; new synergy: 0.168

Forming new module with seed: miRNA1
add: miRNA19; w.in: 0.375; w.bound: 0.000; new synergy: 0.086

Forming new module with seed: miRNA7
add: miRNA15; w.in: 0.084; w.bound: 0.383; new synergy: 0.019
add: miRNA10; w.in: 0.453; w.bound: 0.398; new synergy: 0.066
add: miRNA14; w.in: 0.736; w.bound: 0.486; new synergy: 0.080
add: miRNA17; w.in: 0.959; w.bound: 0.957; new synergy: 0.080
add: miRNA2; w.in: 1.396; w.bound: 0.986; new synergy: 0.097

Forming new module with seed: miRNA11
add: miRNA3; w.in: 0.122; w.bound: 1.015; new synergy: 0.024
add: miRNA9; w.in: 0.863; w.bound: 0.356; new synergy: 0.120

Forming new module with seed: miRNA5

MRM before merging:
M1 (synergy=0.195232383222109): 
miRNA6 miRNA8 miRNA12 miRNA18 
M2 (synergy=0.14089190465843): 
miRNA3 miRNA9 
M3 (synergy=0.195232383222109): 
miRNA6 miRNA8 miRNA12 miRNA18 
M4 (synergy=0.195232383222109): 
miRNA6 miRNA8 miRNA12 miRNA18 
M5 (synergy=0.0995481886856942): 
miRNA2 miRNA10 miRNA14 miRNA15 miRNA17 
M6 (synergy=0.167919254849307): 
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20 
M7 (synergy=0.0857963527273969): 
miRNA1 miRNA19 
M8 (synergy=0.0970569736542555): 
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17 
M9 (synergy=0.119598648023761): 
miRNA3 miRNA9 miRNA11 
M10 (synergy=0): 
miRNA5 
Merge cluster threshold: overlap >= 0.80:


MRM after merging/filtering:
M1 (density=3.45e-01; synergy=1.95e-01): 
miRNA6 miRNA8 miRNA12 miRNA18 
M2 (density=7.35e-01; synergy=1.41e-01): 
miRNA3 miRNA9 
M3 (density=9.31e-02; synergy=9.71e-02): 
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17 
M4 (density=1.19e-01; synergy=1.68e-01): 
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20 
M5 (density=3.75e-01; synergy=8.58e-02): 
miRNA1 miRNA19 
M6 (density=2.88e-01; synergy=1.2e-01): 
miRNA3 miRNA9 miRNA11 

Time elapsed for Stage I: 0.058

*Stage II. Grow MRM with mRNA:

 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
Mirsynergy
 --- call from context --- 
gencluster(V, W, H, alpha, density2.tol, verbose)
 --- call from argument --- 
if (class(H) != "dgCMatrix") H <- Matrix(as.matrix(H))
 --- R stacktrace ---
where 1: gencluster(V, W, H, alpha, density2.tol, verbose)
where 2: mirsynergy(W, H, verbose = TRUE)

 --- value of length: 2 type: logical ---
[1] TRUE TRUE
 --- function from context --- 
function (V, W, H, alpha, density.tol, verbose) 
{
    if (!isSymmetric(H)) {
        warning(paste("Gene-gene interaction must be symmetric!", 
            "Upper triangle matrix of H is used.", sep = "\n"))
        H[lower.tri(H)] <- t(H)[lower.tri(t(H))]
        diag(H) <- 0
    }
    if (class(H) != "dgCMatrix") 
        H <- Matrix(as.matrix(H))
    N <- as.numeric(nrow(H))
    M <- as.numeric(ncol(W))
    W2 <- rbind(cbind(H, W), cbind(t(W), Matrix(0, nrow = M, 
        ncol = M)))
    original.id <- rownames(W2)
    names(original.id) <- 1:nrow(W2)
    dimnames(W2) <- list(1:nrow(W2), 1:ncol(W2))
    w.sum <- as.numeric(apply(W2, 1, sum))
    tmp <- as.matrix(W2)
    n.list <- mclapply(as.numeric(rownames(W2)), function(i) as.numeric(which(tmp[i, 
        ] > 0)))
    V2 <- mclapply(V, function(v.t) {
        if (verbose) 
            message(sprintf("\nForming new module with seed: %s", 
                paste(original.id[v.t$v.in + N], collapse = ",")))
        v.t <- init_v(v.t, N, w.sum, n.list, alpha)
        mirID <- v.t$v.in
        v.t.old <- list()
        m <- length(v.t$v.in)
        while (!identical(v.t, v.t.old)) {
            v.t.old <- v.t
            v.t <- grow_v(v.t, W2, w.sum, n.list, alpha, verbose, 
                original.id, TRUE, N)
        }
        v.t$miRNA <- original.id[mirID]
        idx <- binary_search(v.t$v.in, N)
        v.t$mRNA <- original.id[v.t$v.in[1:idx]]
        v.t$v.in <- original.id[v.t$v.in]
        v.t$v.bound <- original.id[v.t$v.bound]
        v.t$card.m <- m
        v.t$card.t <- v.t$card
        v.t$card <- v.t$card.m + v.t$card.t
        v.t$density <- get_density2(v.t)
        v.t
    })
    V2[sapply(V2, function(v) v$density < density.tol)] <- NULL
    V2
}
<bytecode: 0x7fafc2b40e40>
<environment: namespace:Mirsynergy>
 --- function search by body ---
Function gencluster in namespace Mirsynergy has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
          v.t$card.m <- m
          v.t$card.t <- v.t$card
          v.t$card <- v.t$card.m + v.t$card.t
          v.t$density <- get_density2(v.t)
          v.t
      })
      V2[sapply(V2, function(v) v$density < density.tol)] <- NULL
      V2
  }
  <bytecode: 0x7fbefdab9d10>
  <environment: namespace:Mirsynergy>
   --- function search by body ---
  Function gencluster in namespace Mirsynergy 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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/Mirsynergy.Rcheck/00check.log’
for details.


Installation output

Mirsynergy.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Mirsynergy
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘Mirsynergy’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Mirsynergy)

Tests output

Mirsynergy.Rcheck/tests/runTests.Rout.fail


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("Mirsynergy")

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Discard row/column of all zeros in W

*Stage I. Cluster 18 miRNA:


Forming new module with seed: miRNA6
add: miRNA18; w.in: 0.655; w.bound: 1.535; new synergy: 0.106
add: miRNA8; w.in: 1.152; w.bound: 1.460; new synergy: 0.134
add: miRNA12; w.in: 2.072; w.bound: 0.540; new synergy: 0.195

Forming new module with seed: miRNA3
add: miRNA9; w.in: 0.735; w.bound: 0.484; new synergy: 0.141

Forming new module with seed: miRNA17
add: miRNA2; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195

Forming new module with seed: miRNA2
add: miRNA17; w.in: 0.345; w.bound: 1.131; new synergy: 0.063
add: miRNA6; w.in: 0.659; w.bound: 2.466; new synergy: 0.072
add: miRNA18; w.in: 1.540; w.bound: 1.584; new synergy: 0.138
add: miRNA8; w.in: 2.037; w.bound: 1.510; new synergy: 0.150
add: miRNA12; w.in: 2.957; w.bound: 0.590; new synergy: 0.190
remove: miRNA17; w.in: 2.538; w.bound: 0.511; new synergy: 0.195
remove: miRNA2; w.in: 2.072; w.bound: 0.540; new synergy: 0.195

Forming new module with seed: miRNA10
add: miRNA15; w.in: 0.304; w.bound: 0.532; new synergy: 0.063
add: miRNA14; w.in: 0.573; w.bound: 0.649; new synergy: 0.079
add: miRNA17; w.in: 0.796; w.bound: 1.120; new synergy: 0.080
add: miRNA2; w.in: 1.233; w.bound: 1.149; new synergy: 0.100

Forming new module with seed: miRNA16
add: miRNA20; w.in: 0.219; w.bound: 0.218; new synergy: 0.049
add: miRNA17; w.in: 0.373; w.bound: 0.827; new synergy: 0.052
add: miRNA2; w.in: 0.718; w.bound: 1.041; new synergy: 0.074
add: miRNA6; w.in: 1.032; w.bound: 2.376; new synergy: 0.077
add: miRNA18; w.in: 1.913; w.bound: 1.495; new synergy: 0.124
add: miRNA8; w.in: 2.410; w.bound: 1.420; new synergy: 0.135
add: miRNA12; w.in: 3.330; w.bound: 0.500; new synergy: 0.168

Forming new module with seed: miRNA1
add: miRNA19; w.in: 0.375; w.bound: 0.000; new synergy: 0.086

Forming new module with seed: miRNA7
add: miRNA15; w.in: 0.084; w.bound: 0.383; new synergy: 0.019
add: miRNA10; w.in: 0.453; w.bound: 0.398; new synergy: 0.066
add: miRNA14; w.in: 0.736; w.bound: 0.486; new synergy: 0.080
add: miRNA17; w.in: 0.959; w.bound: 0.957; new synergy: 0.080
add: miRNA2; w.in: 1.396; w.bound: 0.986; new synergy: 0.097

Forming new module with seed: miRNA11
add: miRNA3; w.in: 0.122; w.bound: 1.015; new synergy: 0.024
add: miRNA9; w.in: 0.863; w.bound: 0.356; new synergy: 0.120

Forming new module with seed: miRNA5

MRM before merging:
M1 (synergy=0.195232383222109): 
miRNA6 miRNA8 miRNA12 miRNA18 
M2 (synergy=0.14089190465843): 
miRNA3 miRNA9 
M3 (synergy=0.195232383222109): 
miRNA6 miRNA8 miRNA12 miRNA18 
M4 (synergy=0.195232383222109): 
miRNA6 miRNA8 miRNA12 miRNA18 
M5 (synergy=0.0995481886856942): 
miRNA2 miRNA10 miRNA14 miRNA15 miRNA17 
M6 (synergy=0.167919254849307): 
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20 
M7 (synergy=0.0857963527273969): 
miRNA1 miRNA19 
M8 (synergy=0.0970569736542555): 
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17 
M9 (synergy=0.119598648023761): 
miRNA3 miRNA9 miRNA11 
M10 (synergy=0): 
miRNA5 
Merge cluster threshold: overlap >= 0.80:


MRM after merging/filtering:
M1 (density=3.45e-01; synergy=1.95e-01): 
miRNA6 miRNA8 miRNA12 miRNA18 
M2 (density=7.35e-01; synergy=1.41e-01): 
miRNA3 miRNA9 
M3 (density=9.31e-02; synergy=9.71e-02): 
miRNA2 miRNA7 miRNA10 miRNA14 miRNA15 miRNA17 
M4 (density=1.19e-01; synergy=1.68e-01): 
miRNA2 miRNA6 miRNA8 miRNA12 miRNA16 miRNA17 miRNA18 miRNA20 
M5 (density=3.75e-01; synergy=8.58e-02): 
miRNA1 miRNA19 
M6 (density=2.88e-01; synergy=1.2e-01): 
miRNA3 miRNA9 miRNA11 

Time elapsed for Stage I: 0.040

*Stage II. Grow MRM with mRNA:

 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
Mirsynergy
 --- call from context --- 
gencluster(V, W, H, alpha, density2.tol, verbose)
 --- call from argument --- 
if (class(H) != "dgCMatrix") H <- Matrix(as.matrix(H))
 --- R stacktrace ---
where 1: gencluster(V, W, H, alpha, density2.tol, verbose)
where 2: mirsynergy(W, H, verbose = TRUE)
where 3: func()
where 4: system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest)
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 8: tryCatch(expr, error = function(e) {
    call <- conditionCall(e)
    if (!is.null(call)) {
        if (identical(call[[1L]], quote(doTryCatch))) 
            call <- sys.call(-4L)
        dcall <- deparse(call)[1L]
        prefix <- paste("Error in", dcall, ": ")
        LONG <- 75L
        sm <- strsplit(conditionMessage(e), "\n")[[1L]]
        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
        if (is.na(w)) 
            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
                type = "b")
        if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")
    }
    else prefix <- "Error : "
    msg <- paste0(prefix, conditionMessage(e), "\n")
    .Internal(seterrmessage(msg[1L]))
    if (!silent && isTRUE(getOption("show.error.messages"))) {
        cat(msg, file = outFile)
        .Internal(printDeferredWarnings())
    }
    invisible(structure(msg, class = "try-error", condition = e))
})
where 9: try(system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest))
where 10: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp, 
    tearDownFunc = .tearDown)
where 11: .sourceTestFile(testFile, testSuite$testFuncRegexp)
where 12: RUnit::runTestSuite(suite)
where 13: BiocGenerics:::testPackage("Mirsynergy")

 --- value of length: 2 type: logical ---
[1] TRUE TRUE
 --- function from context --- 
function (V, W, H, alpha, density.tol, verbose) 
{
    if (!isSymmetric(H)) {
        warning(paste("Gene-gene interaction must be symmetric!", 
            "Upper triangle matrix of H is used.", sep = "\n"))
        H[lower.tri(H)] <- t(H)[lower.tri(t(H))]
        diag(H) <- 0
    }
    if (class(H) != "dgCMatrix") 
        H <- Matrix(as.matrix(H))
    N <- as.numeric(nrow(H))
    M <- as.numeric(ncol(W))
    W2 <- rbind(cbind(H, W), cbind(t(W), Matrix(0, nrow = M, 
        ncol = M)))
    original.id <- rownames(W2)
    names(original.id) <- 1:nrow(W2)
    dimnames(W2) <- list(1:nrow(W2), 1:ncol(W2))
    w.sum <- as.numeric(apply(W2, 1, sum))
    tmp <- as.matrix(W2)
    n.list <- mclapply(as.numeric(rownames(W2)), function(i) as.numeric(which(tmp[i, 
        ] > 0)))
    V2 <- mclapply(V, function(v.t) {
        if (verbose) 
            message(sprintf("\nForming new module with seed: %s", 
                paste(original.id[v.t$v.in + N], collapse = ",")))
        v.t <- init_v(v.t, N, w.sum, n.list, alpha)
        mirID <- v.t$v.in
        v.t.old <- list()
        m <- length(v.t$v.in)
        while (!identical(v.t, v.t.old)) {
            v.t.old <- v.t
            v.t <- grow_v(v.t, W2, w.sum, n.list, alpha, verbose, 
                original.id, TRUE, N)
        }
        v.t$miRNA <- original.id[mirID]
        idx <- binary_search(v.t$v.in, N)
        v.t$mRNA <- original.id[v.t$v.in[1:idx]]
        v.t$v.in <- original.id[v.t$v.in]
        v.t$v.bound <- original.id[v.t$v.bound]
        v.t$card.m <- m
        v.t$card.t <- v.t$card
        v.t$card <- v.t$card.m + v.t$card.t
        v.t$density <- get_density2(v.t)
        v.t
    })
    V2[sapply(V2, function(v) v$density < density.tol)] <- NULL
    V2
}
<bytecode: 0x7fbefdab9d10>
<environment: namespace:Mirsynergy>
 --- function search by body ---
Function gencluster in namespace Mirsynergy has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1

Example timings

Mirsynergy.Rcheck/Mirsynergy-Ex.timings

nameusersystemelapsed