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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LINC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings LINC_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/LINC.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/LINC/libs/i386/LINC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/LINC/libs/x64/LINC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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: 0x1a03a0c0>
<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

** running examples for arch 'x64' ... 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: 0x000000001a72ba98>
<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 tests for arch 'i386' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
      linCenvir(out_linc) <- out_linCenvir
      return(out_linc)
  }
  <bytecode: 0x19fa7118>
  <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
  
** running tests for arch 'x64' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
      linCenvir(out_linc) <- out_linCenvir
      return(out_linc)
  }
  <bytecode: 0x000000001a9fa2a8>
  <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: 4 ERRORs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/LINC.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/LINC_1.16.0.tar.gz && rm -rf LINC.buildbin-libdir && mkdir LINC.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LINC.buildbin-libdir LINC_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL LINC_1.16.0.zip && rm LINC_1.16.0.tar.gz LINC_1.16.0.zip
###
##############################################################################
##############################################################################


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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2518k  100 2518k    0     0  19.3M      0 --:--:-- --:--:-- --:--:-- 20.3M

install for i386

* installing *source* package 'LINC' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Cppspear.cpp -o Cppspear.o
Cppspear.cpp: In function 'Rcpp::NumericMatrix Cppspear(Rcpp::NumericMatrix, Rcpp::NumericMatrix)':
Cppspear.cpp:78:14: warning: unused variable 'qspear' [-Wunused-variable]
       double qspear;double nfraction;
              ^~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LINC_init.c -o LINC_init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c docdd.cpp -o docdd.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c doesd.cpp -o doesd.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o LINC.dll tmp.def Cppspear.o LINC_init.o RcppExports.o docdd.o doesd.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/LINC.buildbin-libdir/00LOCK-LINC/00new/LINC/libs/i386
** 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
  converting help for package 'LINC'
    finding HTML links ... done
    Arith-methods                           html  
    BRAIN_EXPR                              html  
    LINCbio-class                           html  
    LINCcluster-class                       html  
    LINCfeature-class                       html  
    LINCmatrix-class                        html  
    LINCsingle-class                        html  
    assignment-methods                      html  
    changeOrgDb                             html  
    clusterlinc-methods                     html  
    correlation-methods                     html  
    express-methods                         html  
    feature                                 html  
    getbio-methods                          html  
    getcoexpr                               html  
    getlinc-methods                         html  
    history-methods                         html  
    justlinc-methods                        html  
    linCenvir-methods                       html  
    linc-methods                            html  
    linctable-methods                       html  
    plotlinc-methods                        html  
    querycluster                            html  
    results-methods                         html  
    singlelinc-methods                      html  
** 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

install for x64

* installing *source* package 'LINC' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Cppspear.cpp -o Cppspear.o
Cppspear.cpp: In function 'Rcpp::NumericMatrix Cppspear(Rcpp::NumericMatrix, Rcpp::NumericMatrix)':
Cppspear.cpp:78:14: warning: unused variable 'qspear' [-Wunused-variable]
       double qspear;double nfraction;
              ^~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LINC_init.c -o LINC_init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c docdd.cpp -o docdd.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c doesd.cpp -o doesd.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o LINC.dll tmp.def Cppspear.o LINC_init.o RcppExports.o docdd.o doesd.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/LINC.buildbin-libdir/LINC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LINC' as LINC_1.16.0.zip
* DONE (LINC)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'LINC' successfully unpacked and MD5 sums checked