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CHECK report for reb on tokay2

This page was generated on 2020-10-17 11:57:35 -0400 (Sat, 17 Oct 2020).

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 1449/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
reb 1.66.0
Karl J. Dykema
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/reb
Branch: RELEASE_3_11
Last Commit: 0c09abf
Last Changed Date: 2020-04-27 14:12:02 -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: reb
Version: 1.66.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:reb.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings reb_1.66.0.tar.gz
StartedAt: 2020-10-17 07:22:47 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:24:59 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 132.3 seconds
RetCode: 1
Status:  ERROR  
CheckDir: reb.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:reb.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings reb_1.66.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/reb.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 'reb/DESCRIPTION' ... OK
* this is package 'reb' version '1.66.0'
* 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 'reb' can be installed ... OK
* 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
* 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 ... 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 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/reb/libs/i386/reb.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/reb/libs/x64/reb.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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: 0x0c29c768>
<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

** running examples for arch 'x64' ... 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: 0x000000001724df30>
<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: 2 ERRORs, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/reb.Rcheck/00check.log'
for details.


Installation output

reb.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/reb_1.66.0.tar.gz && rm -rf reb.buildbin-libdir && mkdir reb.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=reb.buildbin-libdir reb_1.66.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL reb_1.66.0.zip && rm reb_1.66.0.tar.gz reb_1.66.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  489k  100  489k    0     0  6973k      0 --:--:-- --:--:-- --:--:-- 7775k

install for i386

* installing *source* package 'reb' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c movbin.c -o movbin.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o reb.dll tmp.def movbin.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/reb.buildbin-libdir/00LOCK-reb/00new/reb/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'reb'
    finding HTML links ... done
    Hs.arms                                 html  
    absMax                                  html  
    buildChromCytoband                      html  
    buildChromMap                           html  
    cset2band                               html  
    fromRevIsh                              html  
    isAbnormal                              html  
    mcr.eset                                html  
    movbin                                  html  
    movt                                    html  
    naMean                                  html  
    regmap                                  html  
    revish                                  html  
    rmAmbigMappings                         html  
    smoothByRegion                          html  
    summarizeByRegion                       html  
    tBinomTest                              html  
    writeGFF3                               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 'reb' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c movbin.c -o movbin.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o reb.dll tmp.def movbin.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/reb.buildbin-libdir/reb/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'reb' as reb_1.66.0.zip
* DONE (reb)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'reb' successfully unpacked and MD5 sums checked

Tests output


Example timings

reb.Rcheck/examples_i386/reb-Ex.timings

nameusersystemelapsed
absMax000
buildChromCytoband0.020.000.02
buildChromMap000

reb.Rcheck/examples_x64/reb-Ex.timings

nameusersystemelapsed
absMax000
buildChromCytoband000
buildChromMap000