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CHECK report for geecc on machv2

This page was generated on 2020-10-17 11:58:31 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE geecc PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 668/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geecc 1.22.0
Markus Boenn
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/geecc
Branch: RELEASE_3_11
Last Commit: df8fea0
Last Changed Date: 2020-04-27 14:43:04 -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: geecc
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:geecc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings geecc_1.22.0.tar.gz
StartedAt: 2020-10-17 01:22:17 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:23:43 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 85.6 seconds
RetCode: 1
Status:  ERROR 
CheckDir: geecc.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:geecc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings geecc_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/geecc.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 ‘geecc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geecc’ version ‘1.22.0’
* 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 ‘geecc’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'geecc' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/geecc.Rcheck/00install.out’ for details.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘geecc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geecc-package
> ### Title: Gene set enrichment for two or three categories
> ### Aliases: geecc-package geecc
> ### Keywords: package
> 
> ### ** Examples
> 
> ##
> ## a completely artificial example run
> ## through the routines of the package
> ##
> R <- 500
> #generate R random gene-ids
> ID <- sapply(1:R, function(r){paste( sample(LETTERS, 10), collapse="" ) } )
> ID <- unique(ID)
> 
> #assign artificial differentially expressed genes randomly
> category1 <- list( deg.smallFC=sample(ID, 100, rep=FALSE),
+ 	deg.hughFC=sample(ID, 100, rep=FALSE) )
> #assign artificial GO terms of genes randomly
> category2 <- list( go1=sample(ID, 50, replace=FALSE),
+ 	go2=sample(ID, 166, replace=FALSE),
+ 	go3=sample(ID, 74, replace=FALSE),
+ 	go4=sample(ID, 68, replace=FALSE) )
> #assign artificial sequence length of genes randomly
> LEN <- setNames(sample(seq(100, 1000, 100), length(ID), replace=TRUE), ID)
> category3 <- split( ID, f=factor(LEN, levels=seq(100, 1000, 100)) )
> CatList <- list(deg=category1, go=category2, len=category3)
> 
> ConCubFilter.obj <- new("concubfilter", names=names(CatList))
> ConCub.obj <- new("concub", categories=CatList)
Changed order of categories: deg,len,go
> ConCub.obj.2 <- runConCub( obj=ConCub.obj, filter=ConCubFilter.obj, nthreads=1 )
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
geecc
 --- call from context --- 
runConCub(obj = ConCub.obj, filter = ConCubFilter.obj, nthreads = 1)
 --- call from argument --- 
(length(nms_categories) != length(filter@names)) || (intersect(nms_categories, 
    filter@names) != nms_categories)
 --- R stacktrace ---
where 1: runConCub(obj = ConCub.obj, filter = ConCubFilter.obj, nthreads = 1)

 --- value of length: 3 type: logical ---
[1] FALSE FALSE FALSE
 --- function from context --- 
function (obj, filter, nthreads = 2, subset = NULL, verbose = list(output.step = 0, 
    show.cat1 = FALSE, show.cat2 = FALSE, show.cat3 = FALSE)) 
{
    NCATS <- length(obj@categories)
    nms_categories <- names(obj@categories)
    if ((length(nms_categories) != length(filter@names)) || (intersect(nms_categories, 
        filter@names) != nms_categories)) {
        warning("Names from concubfilter-object (", paste0(nms_categories, 
            collapse = ","), ") and concub-object (", paste0(filter@names, 
            collapse = ","), ") do not match.")
        return(obj)
    }
    N <- length(obj@population)
    N_factor <- .getNumberOfFactorLevels(obj)
    items_factor <- .getItemsInEachCategory(obj)
    opt_factor <- .getOptOfCategory(obj)
    rng_factor <- vector("list", NCATS)
    sub_categories <- .getNamesOfEachCategory(obj)
    if (!is.null(subset)) {
        for (nm in names(subset)) {
            sub_categories[[nm]] <- intersect(subset[[nm]], sub_categories[[nm]])
        }
    }
    len_sub_categories <- sapply(sub_categories, length)
    ttt <- .getTypeOf_transformTable(form = obj@null.model, nms = nms_categories)
    do.strat <- FALSE
    if (NCATS == 3) {
        do.strat <- obj@options[[3]][["strat"]]
    }
    frm <- obj@null.model
    if (do.strat == TRUE & ttt[[1]] == "mi") {
        frm <- update(frm, as.formula(paste("~.-", names(obj@categories)[3])))
    }
    message(paste("Testing: counts ~ ", as.character(obj@null.model)[2], 
        " (", ttt[[1]], ")", sep = ""), sep = "")
    if (any(sapply(opt_factor, function(x) {
        return(x$grouping != "none")
    }))) {
        message(paste("Grouping: ", paste(names(opt_factor), 
            ":", sapply(opt_factor, function(x) {
                return(x$grouping)
            }), sep = "", collapse = ", "), sep = ""), sep = "")
    }
    RNG <- setNames(vector("list", NCATS), nms_categories)
    if (sum(sapply(opt_factor, function(x) {
        x[["grouping"]] != "none"
    })) > 1) {
        warning("Grouping-option for multiple categories. Results might be hard to interprete.")
    }
    for (g in nms_categories) {
        opt_grouping <- opt_factor[[g]][["grouping"]]
        opt_width <- opt_factor[[g]][["width"]]
        local_len <- len_sub_categories[g]
        local_rng <- sub_categories[[g]]
        RNG[[g]] <- setNames(vector("list", local_len), local_rng)
        for (g2 in 1:local_len) {
            term <- local_rng[g2]
            term2cum <- term
            if (opt_grouping == "none") {
                term2cum <- term
            }
            if (opt_grouping == "cumf") {
                if (g2 == local_len) {
                  next
                }
                term2cum <- local_rng[1:g2]
            }
            if (opt_grouping == "cumr") {
                if (g2 == 1) {
                  next
                }
                term2cum <- local_rng[g2:local_len]
            }
            if (opt_grouping == "sw") {
                l <- opt_width
                start <- max(c(1, g2 - l))
                stop <- min(c(g2 + l, local_len))
                term2cum <- local_rng[start:stop]
            }
            RNG[[g]][[term]] <- term2cum
        }
        if (opt_grouping == "cumf") {
            sub_categories[[g]] <- sub_categories[[g]][1:(local_len - 
                1)]
        }
        if (opt_grouping == "cumr") {
            sub_categories[[g]] <- sub_categories[[g]][2:local_len]
        }
    }
    Len_term3 <- c()
    if (NCATS == 3 && verbose$show.cat3) {
        L <- length(sub_categories[[3]])
        Len_term3 <- setNames(vector("list", L), sub_categories[[3]])
        for (l in 1:L) {
            x <- ifelse(l == 1, sub_categories[[3]][L], sub_categories[[3]][l - 
                1])
            Len_term3[[l]] <- paste(paste(rep("\b", times = nchar(x)), 
                collapse = ""), "\t", sub_categories[[3]][l], 
                collapse = "", sep = "")
        }
    }
    my_separator <- .my_separator()
    tmp0_nms1 <- c(t(outer(sub_categories[[1]], sub_categories[[2]], 
        paste, sep = my_separator)))
    if (NCATS == 3) {
        tmp0_nms1 <- c(t(outer(tmp0_nms1, sub_categories[[3]], 
            paste, sep = my_separator)))
    }
    tmp1 <- items_factor[[nms_categories[2]]]
    tmp2 <- RNG[[nms_categories[2]]]
    PreCalc__x_1_ <- setNames(vector("list", length(sub_categories[[nms_categories[2]]])), 
        names(sub_categories[[nms_categories[2]]]))
    for (t in as.integer(1:length(sub_categories[[nms_categories[2]]]))) {
        PreCalc__x_1_[[t]] <- unique(.special1(tmp1, tmp2, t))
    }
    PreCalc__x__1 <- PreCalc__x__2 <- list()
    if (NCATS == 3) {
        loc_nm3 <- nms_categories[3]
        tmp1 <- items_factor[[loc_nm3]]
        tmp2 <- RNG[[loc_nm3]]
        PreCalc__x__1 <- setNames(vector("list", length(sub_categories[[loc_nm3]])), 
            names(sub_categories[[loc_nm3]]))
        for (t in as.integer(1:length(sub_categories[[loc_nm3]]))) {
            PreCalc__x__1[[t]] <- unique(.special1(tmp1, tmp2, 
                t))
        }
    }
    ITER <- setNames(vector("list", length(tmp0_nms1)), tmp0_nms1)
    loc_nm1 <- nms_categories[1]
    for (g1 in 1:length(sub_categories[[loc_nm1]])) {
        term1 <- sub_categories[[loc_nm1]][g1]
        if (verbose$show.cat1) {
            cat(term1, sep = "")
        }
        notterm1 <- paste("not_", term1, sep = "")
        x1__ <- unique(unlist(items_factor[[loc_nm1]][RNG[[loc_nm1]][[term1]]], 
            use.names = FALSE))
        x2__ <- setdiffPresort(obj@population, x1__)
        RES_CAT2 <- list()
        loc_nm2 <- nms_categories[2]
        for (g2 in 1:length(sub_categories[[loc_nm2]])) {
            term2 <- sub_categories[[loc_nm2]][g2]
            if (verbose$show.cat2) {
                cat("\r\t", term2, "\t", sep = "")
            }
            x_1_ <- PreCalc__x_1_[[g2]]
            x_2_ <- setdiffPresort(obj@population, PreCalc__x_1_[[g2]])
            x1__Ix_1_ <- intersect(x1__, x_1_)
            x1__Ix_2_ <- intersectPresort(x_2_, x1__)
            x2__Ix_1_ <- intersectPresort(x2__, x_1_)
            x2__Ix_2_ <- setdiffPresort(obj@population, c(x1__Ix_1_, 
                x1__Ix_2_, x2__Ix_1_))
            RES_CAT3 <- list()
            if (NCATS == 2) {
                res <- list()
                subpop <- as.character((x1__Ix_1_))
                len_subpop <- length(subpop)
                CT <- array(c(len_subpop, vapply(list(x2__Ix_1_, 
                  x1__Ix_2_, x2__Ix_2_), length, FUN.VALUE = 123)), 
                  dim = c(2, 2), dimnames = list(factor1 = c(term1, 
                    notterm1), factor2 = c(term2, paste("not_", 
                    term2, sep = ""))))
                names(dimnames(CT)) <- nms_categories
                ExpectedValues <- hypergea::getExpectedValues(CT)
                if (!((skip.zeroobs(filter) && len_subpop == 
                  0) || (skip.min.obs(filter) >= len_subpop) || 
                  all(skip.min.group(filter) - c(length(x1__), 
                    length(x_1_)) > 0))) {
                  res <- .performTest_approx(frm, CT, CT, minExpectedValues = min(ExpectedValues), 
                    approx = obj@approx, nthreads, test.direction(filter))
                }
                res <- c(res, list(subpop = subpop))
                RES_CAT2[[term2]] <- res
            }
            if (NCATS == 3) {
                RES_CAT3 <- list()
                loc_nm3 <- nms_categories[3]
                for (g3 in 1:length(sub_categories[[loc_nm3]])) {
                  res <- list()
                  term3 <- sub_categories[[loc_nm3]][g3]
                  if (verbose$show.cat3) {
                    message(Len_term3[[term3]])
                  }
                  x__1 <- PreCalc__x__1[[g3]]
                  x__2 <- setdiffPresort(obj@population, PreCalc__x__1[[g3]])
                  subpop <- as.character(intersect(x1__Ix_1_, 
                    x__1))
                  len_subpop <- length(subpop)
                  CT <- array(NA, dim = c(2, 2, 2), dimnames = list(factor1 = c(term1, 
                    notterm1), factor2 = c(term2, paste("not_", 
                    term2, sep = "")), factor3 = c(term3, paste("not_", 
                    term3, sep = ""))))
                  names(dimnames(CT)) <- nms_categories
                  res <- list(estimate = 1, p.value = 1, subpop = subpop)
                  if (skip.zeroobs(filter) && len_subpop == 0 || 
                    skip.min.obs(filter) >= len_subpop) {
                    RES_CAT3[[term3]] <- res
                    next
                  }
                  group.len <- sapply(list(x1__, x_1_, x__1), 
                    length)
                  if (any(skip.min.group(filter) >= group.len)) {
                    RES_CAT3[[term3]] <- res
                    next
                  }
                  CT <- .getContingencyCube(CT, x1__Ix_1_, x2__Ix_2_, 
                    x1__Ix_2_, x2__Ix_1_, x__1, x__2)
                  ExpectedValues <- getExpectedValues(CT)
                  if (ttt[[1]] %in% c("mi")) {
                    res <- .performTest_approx(frm, CT, CT, minExpectedValues = min(ExpectedValues), 
                      approx = obj@approx, nthreads = nthreads, 
                      test.direction(filter))
                  }
                  else {
                    if (ttt[[1]] %in% c("sp.1", "sp.2", "sp.3")) {
                      CT_t <- .transformTable(CT, x = ttt)
                      ExpectedValues_t <- getExpectedValues(CT_t)
                      res <- .performTest_approx(frm, CT, CT_t, 
                        minExpectedValues = min(ExpectedValues_t), 
                        approx = obj@approx, nthreads = nthreads, 
                        test.direction(filter))
                    }
                    else {
                      res <- .performTest(frm, CT)
                    }
                  }
                  RES_CAT3[[term3]] <- c(res, list(subpop = subpop))
                }
                tmp_nms3 <- names(RES_CAT3)
                RES_CAT2[paste(term2, tmp_nms3, sep = my_separator)] <- RES_CAT3[tmp_nms3]
            }
            if (verbose[["output.step"]] > 0 && ((g2%%verbose[["output.step"]] == 
                0) || (g2 == length(rng_factor[[2]])))) {
                if (verbose$show.cat2) {
                  cat("\n\tpassed: second category (", nms_categories[2], 
                    "), variable ", term2, " (", g2, ")", sep = "")
                }
                if (verbose$show.cat2) {
                  cat("\n")
                }
            }
        }
        tmp_nms2 <- names(RES_CAT2)
        ITER[paste(term1, tmp_nms2, sep = my_separator)] <- RES_CAT2[tmp_nms2]
        if (verbose$show.cat1) {
            cat("\n")
        }
        if (g1%%10 == 0) {
            gc()
        }
    }
    cat("\n")
    obj@test.result <- ITER
    return(obj)
}
<bytecode: 0x7fe00ff56348>
<environment: namespace:geecc>
 --- function search by body ---
Function runConCub in namespace geecc has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical
* 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: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/geecc.Rcheck/00check.log’
for details.


Installation output

geecc.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘geecc’ ...
** 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 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 rcpp_hello_world.cpp -o rcpp_hello_world.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 specialists.cpp -o specialists.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 geecc.so RcppExports.o rcpp_hello_world.o specialists.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-geecc/00new/geecc/libs
** R
** data
** 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
Warning: Package 'geecc' is deprecated and will be removed from Bioconductor
  version 3.12
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'geecc' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (geecc)

Tests output


Example timings

geecc.Rcheck/geecc-Ex.timings

nameusersystemelapsed
GO2list36.098 1.31537.455
concub-class0.0010.0000.001
concubfilter-class0.0010.0000.003
filterConCub0.0000.0000.001