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CHECK report for reb on merida1

This page was generated on 2021-05-06 12:36:21 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the reb package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1484/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
reb 1.68.0  (landing page)
Karl J. Dykema
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/reb
Branch: RELEASE_3_12
Last Commit: 25e1ca7
Last Changed Date: 2020-10-27 10:26:42 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: reb
Version: 1.68.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:reb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings reb_1.68.0.tar.gz
StartedAt: 2021-05-06 05:15:40 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:17:25 -0400 (Thu, 06 May 2021)
EllapsedTime: 104.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: reb.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:reb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings reb_1.68.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/reb.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘reb/DESCRIPTION’ ... OK
* this is package ‘reb’ version ‘1.68.0’
* 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 ‘reb’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'reb' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/reb.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Missing object imported by a ':::' call: ‘Biobase:::EXPRSET_DEPR_MSG’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.MAP2chromLoc: warning in mget(subnames, env = chrEnv, ifnotfound =
  NA): partial argument match of 'env' to 'envir'
rmAmbigMappings: warning in ls(env = get(package)): partial argument
  match of 'env' to 'envir'
.genMeanMatrix: no visible global function definition for ‘t.test’
buildChromCytoband: no visible global function definition for ‘new’
buildChromCytoband: no visible binding for global variable
  ‘Hs.cytoband’
buildChromCytoband: no visible binding for global variable
  ‘Rn.cytoband’
buildChromCytoband: no visible binding for global variable
  ‘Mm.cytoband’
buildChromMap: no visible global function definition for ‘new’
cgma: no visible binding for global variable ‘t.test’
cset2band: no visible global function definition for ‘aggregate’
fromRevIsh: no visible binding for global variable ‘vai.chr’
reb: no visible global function definition for ‘supsmu’
reb: no visible global function definition for ‘lowess’
reb: no visible global function definition for ‘approx’
regmap: no visible global function definition for ‘par’
regmap: no visible global function definition for ‘layout’
regmap: no visible global function definition for ‘image’
regmap: no visible global function definition for ‘axis’
smoothByRegion: no visible global function definition for ‘supsmu’
smoothByRegion: no visible global function definition for ‘lowess’
smoothByRegion: no visible global function definition for ‘approx’
summarizeByRegion: no visible binding for global variable ‘t.test’
tBinomTest: no visible global function definition for ‘binom.test’
writeGFF3: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  Hs.cytoband Mm.cytoband Rn.cytoband aggregate approx axis binom.test
  image layout lowess new par supsmu t.test vai.chr write.table
Consider adding
  importFrom("graphics", "axis", "image", "layout", "par")
  importFrom("methods", "new")
  importFrom("stats", "aggregate", "approx", "binom.test", "lowess",
             "supsmu", "t.test")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
File ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/reb/libs/reb.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘reb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cset2band
> ### Title: cset2band
> ### Aliases: cset2band
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
>    data(mcr.eset)
>    data(idiogramExample)
> 
> ## Create a vector with the index of normal samples
>    norms <- grep("MNC",colnames(mcr.eset@exprs))
> 
> ## Smooth the data using the default 'movbin' method,
> ## with the normal samples as reference and median centering
>    cset <- reb(mcr.eset@exprs,vai.chr,ref=norms,center=TRUE)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
reb
 --- call from context --- 
reb(mcr.eset@exprs, vai.chr, ref = norms, center = TRUE)
 --- call from argument --- 
is.null(chrom) || is.na(chrom)
 --- R stacktrace ---
where 1: reb(mcr.eset@exprs, vai.chr, ref = norms, center = TRUE)

 --- value of length: 24 type: logical ---
 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
 --- function from context --- 
function (eset, genome, chrom = "ALL", ref = NULL, center = FALSE, 
    aggrfun = absMax, method = c("movbin", "supsmu", "lowess", 
        "movt"), ...) 
{
    if (chrom == "ALL") {
        chrom <- names(attr(genome, "chromInfo"))
        if (is.null(chrom) || is.na(chrom)) 
            stop("chromLoc object does not contain any chromInfo\n")
    }
    else if (chrom == "arms") {
        chrom <- genome@chromLocs$armList
    }
    else if (chrom == "bands") {
        chrom <- genome@chromLocs$bandList
    }
    else if (chrom == "mb") {
        chrom <- genome@chromLocs$mbList
    }
    if (class(eset) == "exprSet") {
        exprs <- eset@exprs
        .Deprecated(msg = Biobase:::EXPRSET_DEPR_MSG)
    }
    else if (class(eset) == "ExpressionSet") 
        exprs <- assayData(eset)$exprs
    else exprs <- eset
    if (!is.null(ref)) {
        if (!is.numeric(ref)) 
            stop("column index's required")
    }
    method <- match.arg(method)
    if (!exists(method)) 
        stop(sQuote(method), " is not found")
    if (!is.null(ref)) {
        cat("Creating ratios...", "\n")
        ref_mean <- apply(exprs[, ref], 1, mean, na.rm = TRUE)
        exprs <- sweep(exprs, 1, ref_mean, "-")
    }
    if (center) 
        exprs <- scale(exprs, scale = F)
    temp.exprs <- matrix(ncol = ncol(exprs))
    for (chr in chrom) {
        uCG <- try(.usedChromExprs(exprs, genome, chr, aggrfun))
        if (inherits(uCG, "try-error") || is.null(uCG)) 
            next
        if (ncol(uCG$exprs) != ncol(exprs)) 
            next
        locs <- uCG$locs
        names(locs) <- uCG$simpleIDs
        gx <- uCG$exprs
        dix <- duplicated(locs)
        if (sum(dix) & is.null(aggrfun) & method != "movbin") {
            warning(sum(dix), " duplicate locations found...removing duplicates\n")
            gx <- gx[!dix, ]
            locs <- locs[!dix]
        }
        r.matrix <- matrix(NA, ncol = ncol(gx), nrow(gx))
        colnames(r.matrix) <- colnames(gx)
        rownames(r.matrix) <- names(locs)
        for (i in c(1:ncol(gx))) {
            nas <- is.finite(gx[, i])
            x <- locs[nas]
            y <- gx[nas, i]
            sm <- try(switch(method, movbin = try(movbin(y, ...)), 
                supsmu = try(supsmu(x, y, ...)$y), lowess = try(lowess(x, 
                  y, ...)$y), movt = try(movt(y, ...))), silent = FALSE)
            if (!inherits(sm, "try-error")) {
                aa <- try(approx(x, sm, xout = locs), silent = TRUE)
                if (!inherits(aa, "try-error")) {
                  r.matrix[, i] <- aa$y
                }
            }
        }
        temp.exprs <- rbind(temp.exprs, r.matrix)
    }
    temp.exprs <- temp.exprs[-1, ]
    return(temp.exprs)
}
<bytecode: 0x7fb949806740>
<environment: namespace:reb>
 --- function search by body ---
Function reb in namespace reb 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/reb.Rcheck/00check.log’
for details.


Installation output

reb.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘reb’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c movbin.c -o movbin.o
clang -mmacosx-version-min=10.13 -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 reb.so movbin.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-reb/00new/reb/libs
** R
** data
** 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 'reb' is deprecated and will be removed from Bioconductor
  version 3.13
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'reb' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (reb)

Tests output


Example timings

reb.Rcheck/reb-Ex.timings

nameusersystemelapsed
absMax0.0000.0000.001
buildChromCytoband0.0050.0040.010
buildChromMap0.0000.0000.001