##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:LINC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings LINC_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/LINC.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 ‘LINC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LINC’ version ‘1.16.0’
* 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 ‘LINC’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  sysdata.rda    449Kb    297Kb       xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘LINC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: linc-methods
> ### Title: Compute A Correlation Matrix of Co-expressed Coding And
> ###   Non-Coding Genes
> ### Aliases: linc-methods linc,data.frame,ANY-method
> ###   linc,ExpressionSet,ANY-method linc,LINCmatrix,missing-method
> ###   linc,matrix,ANY-method linc
> ### Keywords: methods linc
> 
> ### ** Examples
> 
> data(BRAIN_EXPR)
> 
> # call 'linc' with no further arguments
> crbl_matrix <- linc(cerebellum, codingGenes = pcgenes_crbl)
linc: gene system(s) assumed:
ENTREZID
Warning in linc(cerebellum, codingGenes = pcgenes_crbl) :
  single outliers and high sample variance were detected
by ESD and ANOVA; statistical correction is recommended
linc: Correlation function with 'everything' called
linc: Computation of correlation matrix started
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
LINC
 --- call from context --- 
linc(cerebellum, codingGenes = pcgenes_crbl)
 --- call from argument --- 
if (class(out_cormatrix) == "try-error") stop(errorm12)
 --- R stacktrace ---
where 1: linc(cerebellum, codingGenes = pcgenes_crbl)
where 2: linc(cerebellum, codingGenes = pcgenes_crbl)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
Method Definition:

function (object, codingGenes = NULL, corMethod = "spearman", 
    batchGroups = NULL, nsv = 1, rmPC = NULL, outlier = NULL, 
    userFun = NULL, verbose = TRUE) 
{
    errorm00 <- paste("Assignment of protein-coding genes", "in 'codingGenes' is required")
    errorm01 <- paste("'codingGenes' must have the same", "length as 'nrow(object)'")
    errorm02 <- paste("'corMethod' needs to be 'pearson',", "'kendall' or 'spearman'")
    errorm03 <- "A numeric matrix is required as input"
    errorm04 <- "Size or content of matrix insufficient"
    errorm05 <- "Gene names as 'rownames(object)' required"
    errorm06 <- paste("'batchGroups' need to be of the", "same length as the columns")
    errorm07 <- paste("Not allowed to use the same name", "for every entry in 'batchGroups'")
    errorm08 <- paste("unable to use 'rmPC' as an index", "vector for the removal of pcs")
    errorm09 <- paste("'outlier' needs to be 'zscore',", "or 'esd'")
    errorm10 <- paste("'codingGenes' needs to be a gene", "annotation or a logical vector")
    errorm11 <- paste("Error in argument 'codingGenes',", "not enough protein-coding genes")
    errorm12 <- paste("unable to compute correlation matrix:", 
        "1. check input for infinite values / NAs", "2. check user-defined correlation function", 
        sep = "\n")
    errorm13 <- "computation of cor. matrix lnc vs lnc failed"
    warnim01 <- "Input 'object' contains infinite values"
    warnim02 <- "'linc' was unable to identify a gene system"
    warnim03 <- paste("single outliers and high sample variance were detected", 
        "by ESD and ANOVA; statistical correction is recommended", 
        sep = "\n")
    warnim04 <- paste("Subsequent use of sva and removal of", 
        "principle components is not intended")
    warnim05 <- paste("correlation matrix contains infinite", 
        "or missing values; converted to 0")
    inform01 <- quote(paste("linc: removed ", infrm, "rows contaning only infinite values"))
    inform02 <- quote(paste("removed", length(obvar[obvar == 
        0]), "zero variance genes from input"))
    inform22 <- "removed genes with duplicated names"
    inform03 <- "linc: gene system(s) assumed:"
    inform04 <- "linc: correction by sva was called"
    inform05 <- "linc: remove principle components"
    inform06 <- quote(paste("linc: The outlier method '", ol_promise, 
        "' was called"))
    inform07 <- quote(paste("linc: Correlation function", " with '", 
        cor_use, "' called", sep = ""))
    inform08 <- paste("linc: Computation of correlation", "matrix started")
    store <- new.env(parent = emptyenv())
    out_history <- new.env(parent = emptyenv())
    if (is.null(codingGenes)) 
        stop(errorm00)
    if (length(codingGenes) != nrow(object)) 
        stop(errorm01)
    pc_promise <- codingGenes
    if (class(verbose) != "logical") {
        verbose <- TRUE
    }
    else {
        if (!any(verbose)) 
            verbose <- FALSE
        if (any(verbose)) 
            verbose <- TRUE
    }
    if (!verbose) 
        message <- function(x) x
    cM_promise <- try(match.arg(corMethod, c("pearson", "kendall", 
        "spearman")), silent = TRUE)
    if (class(cM_promise) == "try-error") 
        stop(errorm02)
    if (!is.null(userFun)) 
        cor_Method <- "user-defined"
    if (!is.numeric(object)) 
        stop(errorm03)
    if (!all(is.finite(object))) {
        warning(warnim01)
        mobject <- object[apply(object, 1, function(x) {
            any(is.finite(x))
        }), ]
        pcobject <- object
        rownames(pcobject) <- pc_promise
        pcobject <- pcobject[apply(pcobject, 1, function(x) {
            any(is.finite(x))
        }), ]
        infrm <- nrow(object) - nrow(mobject)
        if (infrm != 0) {
            message(inform01)
            object <- mobject
            pc_promise <- rownames(pcobject)
        }
    }
    obvar <- apply(object, 1, var)
    if (is.element(0, obvar)) {
        object <- object[obvar != 0, ]
        pc_promise <- pc_promise[obvar != 0]
        message(eval(inform02))
    }
    if (any(duplicated(rownames(object)))) {
        pc_promise <- pc_promise[!duplicated(rownames(object))]
        object <- object[(!duplicated(rownames(object))), ]
        message(inform22)
    }
    out_object <- object
    object <- object[!is.na(rownames(object)), ]
    pc_promise <- pc_promise[!is.na(pc_promise)]
    if (!all(dim(object) > 5)) 
        stop(errorm04)
    colnum <- ncol(object)
    gN_promise <- rownames(object)
    if (is.null(gN_promise)) 
        stop(errorm05)
    gD_promise <- try(identifyGenes(gN_promise), silent = TRUE)
    if (class(gD_promise) == "try-error" | length(gD_promise) == 
        0) {
        warning(warnim02)
        out_history$gene_system <- NA
    }
    else {
        out_history$gene_system <- gD_promise
        message(inform03)
        sapply(gD_promise, function(x) message(x))
    }
    if (!is.null(batchGroups)) {
        if (length(batchGroups) != colnum) 
            stop(errorm06)
        if (1 == length(unique(batchGroups))) 
            stop(errorm07)
        store$SVA <- TRUE
        message(inform04)
        if (length(nsv) == 1 && is.numeric(nsv) && is.vector(nsv)) {
            bn_promise <- nsv
        }
        else {
            bn_promise <- 1
        }
    }
    if (!is.null(rmPC)) {
        col_sel <- try(seq_len(colnum)[-rmPC], silent = TRUE)
        if (class(col_sel) == "try-error") 
            stop(errorm08)
        if (length(col_sel) == 0 | anyNA(col_sel)) 
            stop(errorm08)
        rm_promise <- seq_len(colnum)[-rmPC]
        store$PCA <- TRUE
        message(inform05)
    }
    if (!is.null(outlier)) {
        ol_promise <- try(match.arg(outlier, c("zscore", "esd")), 
            silent = TRUE)
        if (class(ol_promise) == "try-error") 
            stop(errorm09)
        store$outlier <- TRUE
        message(eval(inform06))
    }
    av_promise <- suppressMessages(reshape2::melt(data.frame(object)))
    colnames(av_promise) <- c("group", "y")
    anova_test <- anova(lm(y ~ group, data = av_promise))
    f_sample <- anova_test$`F value`[1]
    f_df <- anova_test$Df
    f_critical <- df(0.95, df1 = f_df[1], df2 = f_df[2])
    anova_passed <- (f_sample <= f_critical)
    out_history$F_critical <- round(f_critical, 2)
    out_history$F_sample <- round(f_sample, 2)
    out_history$F_anova <- anova_passed
    out_genes <- apply(object, 1, detectesd, alpha = 0.05, rmax = 4)
    outlier_det <- (100 * sum(out_genes, na.rm = TRUE))/nrow(object)
    out_history$outlier_detected <- round(outlier_det, 1)
    stats_fail <- all((outlier_det > 10) && !anova_passed)
    if (!exists("SVA", store) & !exists("PCA", store) & !exists("outlier", 
        store)) {
        out_sobject <- object
        sobject <- out_sobject
        stats_applied <- "none"
        if (stats_fail) 
            warning(warnim03)
    }
    else {
        stats_applied <- paste(ls(store), collapse = ",")
    }
    if (exists("SVA", store) & exists("PCA", store)) 
        warning(warnim04)
    if (exists("outlier", store)) {
        if (ol_promise == "esd") {
            sobject <- t(apply(object, 1, correctESD, alpha = 0.05, 
                rmax = 4))
        }
        if (ol_promise == "zscore") {
            sobject <- t(apply(object, 1, modZscore))
        }
        out_sobject <- sobject
    }
    else {
        sobject <- object
        out_sobject <- object
    }
    if (exists("PCA", store)) {
        pca_object <- prcomp(sobject, center = FALSE, scale. = FALSE)
        out_sobject <- pca_object$x[, rm_promise] %*% t(pca_object$rotation[, 
            rm_promise])
        sobject <- out_sobject
    }
    if (exists("SVA", store)) {
        exbatch <- as.factor(batchGroups)
        mod1 <- model.matrix(~exbatch)
        mod0 <- cbind(mod1[, 1])
        svse <- svaseq(sobject, mod1, mod0, n.sv = bn_promise)$sv
        out_sobject <- svaSolv(sobject, mod1, svse)
        sobject <- out_sobject
    }
    if (anyNA(sobject)) {
        cor_use <- "pairwise"
    }
    else {
        cor_use <- "everything"
    }
    if (is.vector(pc_promise) && is.logical(pc_promise)) {
        store$pc_index <- pc_promise
        out_assignment <- gN_promise[store$pc_index]
    }
    if (is.vector(pc_promise) && is.character(pc_promise)) {
        store$pc_index <- is.element(pc_promise, c("protein_coding", 
            "coding", "protein", "protein-coding", "protein coding"))
        out_assignment <- gN_promise[store$pc_index]
    }
    if (!exists("pc_index", store)) 
        stop(errorm10)
    if (length(which(store$pc_index)) < 5) 
        stop(errorm11)
    pc_matrix <- sobject[store$pc_index, ]
    nc_matrix <- sobject[!store$pc_index, ]
    message(eval(inform07))
    message(inform08)
    out_cormatrix <- try(callCor(corMethod, userFun, cor_use)(pc_matrix, 
        nc_matrix), silent = TRUE)
    if (class(out_cormatrix) == "try-error") 
        stop(errorm12)
    rownames(out_cormatrix) <- rownames(pc_matrix)
    colnames(out_cormatrix) <- rownames(nc_matrix)
    if (!all(is.finite(out_cormatrix))) {
        warning(warnim05)
        out_cormatrix[is.infinite(out_cormatrix) | is.na(out_cormatrix)] <- 0
    }
    out_ltlmatrix <- try(callCor(corMethod, userFun, cor_use)(nc_matrix, 
        nc_matrix), silent = TRUE)
    if (class(out_ltlmatrix) == "try-error") 
        stop(errorm13)
    rownames(out_ltlmatrix) <- rownames(nc_matrix)
    colnames(out_ltlmatrix) <- rownames(nc_matrix)
    if (!all(is.finite(out_ltlmatrix))) {
        out_ltlmatrix[is.infinite(out_ltlmatrix) | is.na(out_ltlmatrix)] <- 0
    }
    out_history$cor_max <- round(max(out_cormatrix, na.rm = TRUE), 
        2)
    out_history$corMethod <- corMethod
    out_history$cor_use <- cor_use
    out_history$pc_matrix <- pc_matrix
    out_history$nc_matrix <- nc_matrix
    out_history$stats_use <- stats_applied
    out_linc <- new("LINCmatrix")
    results(out_linc) <- list(statscorr = out_sobject)
    assignment(out_linc) <- out_assignment
    correlation(out_linc) <- list(cormatrix = out_cormatrix, 
        lnctolnc = out_ltlmatrix)
    express(out_linc) <- out_object
    history(out_linc) <- out_history
    out_linCenvir <- NULL
    out_linCenvir <- new.env(parent = emptyenv())
    out_linCenvir$linc <- out_linc
    linCenvir(out_linc) <- out_linCenvir
    return(out_linc)
}
<bytecode: 0x7f9936340650>
<environment: namespace:LINC>

Signatures:
        object   codingGenes
target  "matrix" "logical"  
defined "matrix" "ANY"      
 --- function search by body ---
S4 Method linc:LINC defined in namespace LINC with signature matrix#ANY 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:
      out_linCenvir$linc <- out_linc
      linCenvir(out_linc) <- out_linCenvir
      return(out_linc)
  }
  <bytecode: 0x7f85338a80e0>
  <environment: namespace:LINC>
  
  Signatures:
          object   codingGenes
  target  "matrix" "logical"  
  defined "matrix" "ANY"      
   --- function search by body ---
  S4 Method linc:LINC defined in namespace LINC with signature matrix#ANY 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/LINC.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘LINC’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Cppspear.cpp -o Cppspear.o
Cppspear.cpp:78:14: warning: unused variable 'qspear' [-Wunused-variable]
      double qspear;double nfraction;
             ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c LINC_init.c -o LINC_init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c docdd.cpp -o docdd.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c doesd.cpp -o doesd.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o LINC.so Cppspear.o LINC_init.o RcppExports.o docdd.o doesd.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-LINC/00new/LINC/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘history’ in package ‘LINC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LINC)

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("LINC")


This is LINC - Co-Expression Analysis of lincRNAs
 (Manuel Goepferich & Carl Herrmann)

Attaching package: 'LINC'

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

    history

removed 4 zero variance genes from input
removed genes with duplicated names
linc: gene system(s) assumed:
ENTREZID
linc: Correlation function with 'everything' called
linc: Computation of correlation matrix started
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
LINC
 --- call from context --- 
linc(cor_test_mat, codingGenes = c(TRUE, FALSE, TRUE, TRUE, FALSE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, rep(FALSE, 
        7)))
 --- call from argument --- 
if (class(out_cormatrix) == "try-error") stop(errorm12)
 --- R stacktrace ---
where 1: linc(cor_test_mat, codingGenes = c(TRUE, FALSE, TRUE, TRUE, FALSE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, rep(FALSE, 
        7)))
where 2: linc(cor_test_mat, codingGenes = c(TRUE, FALSE, TRUE, TRUE, FALSE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, rep(FALSE, 
        7)))
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("LINC")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
Method Definition:

function (object, codingGenes = NULL, corMethod = "spearman", 
    batchGroups = NULL, nsv = 1, rmPC = NULL, outlier = NULL, 
    userFun = NULL, verbose = TRUE) 
{
    errorm00 <- paste("Assignment of protein-coding genes", "in 'codingGenes' is required")
    errorm01 <- paste("'codingGenes' must have the same", "length as 'nrow(object)'")
    errorm02 <- paste("'corMethod' needs to be 'pearson',", "'kendall' or 'spearman'")
    errorm03 <- "A numeric matrix is required as input"
    errorm04 <- "Size or content of matrix insufficient"
    errorm05 <- "Gene names as 'rownames(object)' required"
    errorm06 <- paste("'batchGroups' need to be of the", "same length as the columns")
    errorm07 <- paste("Not allowed to use the same name", "for every entry in 'batchGroups'")
    errorm08 <- paste("unable to use 'rmPC' as an index", "vector for the removal of pcs")
    errorm09 <- paste("'outlier' needs to be 'zscore',", "or 'esd'")
    errorm10 <- paste("'codingGenes' needs to be a gene", "annotation or a logical vector")
    errorm11 <- paste("Error in argument 'codingGenes',", "not enough protein-coding genes")
    errorm12 <- paste("unable to compute correlation matrix:", 
        "1. check input for infinite values / NAs", "2. check user-defined correlation function", 
        sep = "\n")
    errorm13 <- "computation of cor. matrix lnc vs lnc failed"
    warnim01 <- "Input 'object' contains infinite values"
    warnim02 <- "'linc' was unable to identify a gene system"
    warnim03 <- paste("single outliers and high sample variance were detected", 
        "by ESD and ANOVA; statistical correction is recommended", 
        sep = "\n")
    warnim04 <- paste("Subsequent use of sva and removal of", 
        "principle components is not intended")
    warnim05 <- paste("correlation matrix contains infinite", 
        "or missing values; converted to 0")
    inform01 <- quote(paste("linc: removed ", infrm, "rows contaning only infinite values"))
    inform02 <- quote(paste("removed", length(obvar[obvar == 
        0]), "zero variance genes from input"))
    inform22 <- "removed genes with duplicated names"
    inform03 <- "linc: gene system(s) assumed:"
    inform04 <- "linc: correction by sva was called"
    inform05 <- "linc: remove principle components"
    inform06 <- quote(paste("linc: The outlier method '", ol_promise, 
        "' was called"))
    inform07 <- quote(paste("linc: Correlation function", " with '", 
        cor_use, "' called", sep = ""))
    inform08 <- paste("linc: Computation of correlation", "matrix started")
    store <- new.env(parent = emptyenv())
    out_history <- new.env(parent = emptyenv())
    if (is.null(codingGenes)) 
        stop(errorm00)
    if (length(codingGenes) != nrow(object)) 
        stop(errorm01)
    pc_promise <- codingGenes
    if (class(verbose) != "logical") {
        verbose <- TRUE
    }
    else {
        if (!any(verbose)) 
            verbose <- FALSE
        if (any(verbose)) 
            verbose <- TRUE
    }
    if (!verbose) 
        message <- function(x) x
    cM_promise <- try(match.arg(corMethod, c("pearson", "kendall", 
        "spearman")), silent = TRUE)
    if (class(cM_promise) == "try-error") 
        stop(errorm02)
    if (!is.null(userFun)) 
        cor_Method <- "user-defined"
    if (!is.numeric(object)) 
        stop(errorm03)
    if (!all(is.finite(object))) {
        warning(warnim01)
        mobject <- object[apply(object, 1, function(x) {
            any(is.finite(x))
        }), ]
        pcobject <- object
        rownames(pcobject) <- pc_promise
        pcobject <- pcobject[apply(pcobject, 1, function(x) {
            any(is.finite(x))
        }), ]
        infrm <- nrow(object) - nrow(mobject)
        if (infrm != 0) {
            message(inform01)
            object <- mobject
            pc_promise <- rownames(pcobject)
        }
    }
    obvar <- apply(object, 1, var)
    if (is.element(0, obvar)) {
        object <- object[obvar != 0, ]
        pc_promise <- pc_promise[obvar != 0]
        message(eval(inform02))
    }
    if (any(duplicated(rownames(object)))) {
        pc_promise <- pc_promise[!duplicated(rownames(object))]
        object <- object[(!duplicated(rownames(object))), ]
        message(inform22)
    }
    out_object <- object
    object <- object[!is.na(rownames(object)), ]
    pc_promise <- pc_promise[!is.na(pc_promise)]
    if (!all(dim(object) > 5)) 
        stop(errorm04)
    colnum <- ncol(object)
    gN_promise <- rownames(object)
    if (is.null(gN_promise)) 
        stop(errorm05)
    gD_promise <- try(identifyGenes(gN_promise), silent = TRUE)
    if (class(gD_promise) == "try-error" | length(gD_promise) == 
        0) {
        warning(warnim02)
        out_history$gene_system <- NA
    }
    else {
        out_history$gene_system <- gD_promise
        message(inform03)
        sapply(gD_promise, function(x) message(x))
    }
    if (!is.null(batchGroups)) {
        if (length(batchGroups) != colnum) 
            stop(errorm06)
        if (1 == length(unique(batchGroups))) 
            stop(errorm07)
        store$SVA <- TRUE
        message(inform04)
        if (length(nsv) == 1 && is.numeric(nsv) && is.vector(nsv)) {
            bn_promise <- nsv
        }
        else {
            bn_promise <- 1
        }
    }
    if (!is.null(rmPC)) {
        col_sel <- try(seq_len(colnum)[-rmPC], silent = TRUE)
        if (class(col_sel) == "try-error") 
            stop(errorm08)
        if (length(col_sel) == 0 | anyNA(col_sel)) 
            stop(errorm08)
        rm_promise <- seq_len(colnum)[-rmPC]
        store$PCA <- TRUE
        message(inform05)
    }
    if (!is.null(outlier)) {
        ol_promise <- try(match.arg(outlier, c("zscore", "esd")), 
            silent = TRUE)
        if (class(ol_promise) == "try-error") 
            stop(errorm09)
        store$outlier <- TRUE
        message(eval(inform06))
    }
    av_promise <- suppressMessages(reshape2::melt(data.frame(object)))
    colnames(av_promise) <- c("group", "y")
    anova_test <- anova(lm(y ~ group, data = av_promise))
    f_sample <- anova_test$`F value`[1]
    f_df <- anova_test$Df
    f_critical <- df(0.95, df1 = f_df[1], df2 = f_df[2])
    anova_passed <- (f_sample <= f_critical)
    out_history$F_critical <- round(f_critical, 2)
    out_history$F_sample <- round(f_sample, 2)
    out_history$F_anova <- anova_passed
    out_genes <- apply(object, 1, detectesd, alpha = 0.05, rmax = 4)
    outlier_det <- (100 * sum(out_genes, na.rm = TRUE))/nrow(object)
    out_history$outlier_detected <- round(outlier_det, 1)
    stats_fail <- all((outlier_det > 10) && !anova_passed)
    if (!exists("SVA", store) & !exists("PCA", store) & !exists("outlier", 
        store)) {
        out_sobject <- object
        sobject <- out_sobject
        stats_applied <- "none"
        if (stats_fail) 
            warning(warnim03)
    }
    else {
        stats_applied <- paste(ls(store), collapse = ",")
    }
    if (exists("SVA", store) & exists("PCA", store)) 
        warning(warnim04)
    if (exists("outlier", store)) {
        if (ol_promise == "esd") {
            sobject <- t(apply(object, 1, correctESD, alpha = 0.05, 
                rmax = 4))
        }
        if (ol_promise == "zscore") {
            sobject <- t(apply(object, 1, modZscore))
        }
        out_sobject <- sobject
    }
    else {
        sobject <- object
        out_sobject <- object
    }
    if (exists("PCA", store)) {
        pca_object <- prcomp(sobject, center = FALSE, scale. = FALSE)
        out_sobject <- pca_object$x[, rm_promise] %*% t(pca_object$rotation[, 
            rm_promise])
        sobject <- out_sobject
    }
    if (exists("SVA", store)) {
        exbatch <- as.factor(batchGroups)
        mod1 <- model.matrix(~exbatch)
        mod0 <- cbind(mod1[, 1])
        svse <- svaseq(sobject, mod1, mod0, n.sv = bn_promise)$sv
        out_sobject <- svaSolv(sobject, mod1, svse)
        sobject <- out_sobject
    }
    if (anyNA(sobject)) {
        cor_use <- "pairwise"
    }
    else {
        cor_use <- "everything"
    }
    if (is.vector(pc_promise) && is.logical(pc_promise)) {
        store$pc_index <- pc_promise
        out_assignment <- gN_promise[store$pc_index]
    }
    if (is.vector(pc_promise) && is.character(pc_promise)) {
        store$pc_index <- is.element(pc_promise, c("protein_coding", 
            "coding", "protein", "protein-coding", "protein coding"))
        out_assignment <- gN_promise[store$pc_index]
    }
    if (!exists("pc_index", store)) 
        stop(errorm10)
    if (length(which(store$pc_index)) < 5) 
        stop(errorm11)
    pc_matrix <- sobject[store$pc_index, ]
    nc_matrix <- sobject[!store$pc_index, ]
    message(eval(inform07))
    message(inform08)
    out_cormatrix <- try(callCor(corMethod, userFun, cor_use)(pc_matrix, 
        nc_matrix), silent = TRUE)
    if (class(out_cormatrix) == "try-error") 
        stop(errorm12)
    rownames(out_cormatrix) <- rownames(pc_matrix)
    colnames(out_cormatrix) <- rownames(nc_matrix)
    if (!all(is.finite(out_cormatrix))) {
        warning(warnim05)
        out_cormatrix[is.infinite(out_cormatrix) | is.na(out_cormatrix)] <- 0
    }
    out_ltlmatrix <- try(callCor(corMethod, userFun, cor_use)(nc_matrix, 
        nc_matrix), silent = TRUE)
    if (class(out_ltlmatrix) == "try-error") 
        stop(errorm13)
    rownames(out_ltlmatrix) <- rownames(nc_matrix)
    colnames(out_ltlmatrix) <- rownames(nc_matrix)
    if (!all(is.finite(out_ltlmatrix))) {
        out_ltlmatrix[is.infinite(out_ltlmatrix) | is.na(out_ltlmatrix)] <- 0
    }
    out_history$cor_max <- round(max(out_cormatrix, na.rm = TRUE), 
        2)
    out_history$corMethod <- corMethod
    out_history$cor_use <- cor_use
    out_history$pc_matrix <- pc_matrix
    out_history$nc_matrix <- nc_matrix
    out_history$stats_use <- stats_applied
    out_linc <- new("LINCmatrix")
    results(out_linc) <- list(statscorr = out_sobject)
    assignment(out_linc) <- out_assignment
    correlation(out_linc) <- list(cormatrix = out_cormatrix, 
        lnctolnc = out_ltlmatrix)
    express(out_linc) <- out_object
    history(out_linc) <- out_history
    out_linCenvir <- NULL
    out_linCenvir <- new.env(parent = emptyenv())
    out_linCenvir$linc <- out_linc
    linCenvir(out_linc) <- out_linCenvir
    return(out_linc)
}
<bytecode: 0x7f85338a80e0>
<environment: namespace:LINC>

Signatures:
        object   codingGenes
target  "matrix" "logical"  
defined "matrix" "ANY"      
 --- function search by body ---
S4 Method linc:LINC defined in namespace LINC with signature matrix#ANY has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1