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CHECK report for rHVDM on tokay2

This page was generated on 2019-04-09 11:55:37 -0400 (Tue, 09 Apr 2019).

Package 1349/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rHVDM 1.49.0
Martino Barenco
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/rHVDM
Branch: master
Last Commit: 7bce842
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: rHVDM
Version: 1.49.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rHVDM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rHVDM_1.49.0.tar.gz
StartedAt: 2019-04-09 05:23:56 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 05:24:59 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 63.4 seconds
RetCode: 1
Status:  ERROR  
CheckDir: rHVDM.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rHVDM.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rHVDM_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/rHVDM.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rHVDM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rHVDM' version '1.49.0'
* 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 'rHVDM' can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/rHVDM.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.bin.ut: no visible global function definition for 'quantile'
.binb.ut: no visible global function definition for 'quantile'
.geneoutput: no visible global function definition for 'png'
.geneoutput: no visible global function definition for 'par'
.geneoutput: no visible global function definition for 'plot'
.geneoutput: no visible global function definition for 'arrows'
.geneoutput: no visible global function definition for 'lines'
.geneoutput: no visible global function definition for 'dev.off'
.greport: no visible global function definition for 'runif'
.parameteroutput: no visible global function definition for 'png'
.parameteroutput: no visible global function definition for 'par'
.parameteroutput: no visible global function definition for 'arrows'
.parameteroutput: no visible global function definition for 'dev.off'
.parameteroutput: no visible global function definition for 'plot'
.parameteroutput: no visible global function definition for 'lines'
.parameteroutput: no visible global function definition for 'cov2cor'
.parameteroutputg: no visible global function definition for 'png'
.parameteroutputg: no visible global function definition for 'par'
.parameteroutputg: no visible global function definition for 'arrows'
.parameteroutputg: no visible global function definition for 'dev.off'
.parameteroutputg: no visible global function definition for 'cov2cor'
.parameteroutputg.nl: no visible global function definition for 'png'
.parameteroutputg.nl: no visible global function definition for 'par'
.parameteroutputg.nl: no visible global function definition for
  'arrows'
.parameteroutputg.nl: no visible global function definition for
  'dev.off'
.parameteroutputg.nl: no visible global function definition for
  'cov2cor'
.scoreoutput: no visible global function definition for 'qchisq'
.scoreoutput: no visible global function definition for 'png'
.scoreoutput: no visible global function definition for 'par'
.scoreoutput: no visible global function definition for 'plot'
.scoreoutput: no visible global function definition for 'dchisq'
.scoreoutput: no visible global function definition for 'points'
.scoreoutput: no visible global function definition for 'qnorm'
.scoreoutput: no visible global function definition for 'lines'
.scoreoutput: no visible global function definition for 'dev.off'
.scorout: no visible global function definition for 'pchisq'
.screenoutput: no visible global function definition for 'png'
.screenoutput: no visible global function definition for 'plot'
.screenoutput: no visible global function definition for 'lines'
.screenoutput: no visible global function definition for 'dev.off'
.sreport: no visible global function definition for 'runif'
.treport: no visible global function definition for 'runif'
Undefined global functions or variables:
  arrows cov2cor dchisq dev.off lines par pchisq plot png points qchisq
  qnorm quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "arrows", "lines", "par", "plot", "points")
  importFrom("stats", "cov2cor", "dchisq", "pchisq", "qchisq", "qnorm",
             "quantile", "runif")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'rHVDM-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimerrors
> ### Title: computes the standard deviation of the measurement error using
> ###   pre-calculated tables specific to the plattform or user-defined table
> ### Aliases: estimerrors
> ### Keywords: IO ts
> 
> ### ** Examples
> 
> data(HVDMexample)
> fiveGybis<-estimerrors(eset=fiveGyMAS5,plattid="affy_HGU133A",refchips=leastnoisychips)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
rHVDM
 --- call from context --- 
.computeinderrtable(X = X, errtable = errtable, refchips = refs)
 --- call from argument --- 
if (refchips == 0) {
    wei <- rep(0, m)
}
 --- R stacktrace ---
where 1: .computeinderrtable(X = X, errtable = errtable, refchips = refs)
where 2: .computerrs(eset = eset, errtable = errtable, refs = refchips)
where 3: estimerrors(eset = fiveGyMAS5, plattid = "affy_HGU133A", refchips = leastnoisychips)

 --- value of length: 3 type: logical ---
[1] FALSE FALSE FALSE
 --- function from context --- 
function (X, errtable, refchips) 
{
    N <- dim(X)[2]
    if (missing(refchips)) {
        refchips <- c(1:N)
    }
    m <- dim(errtable)[1]
    res <- matrix(rep(0, m * N), m, N)
    dimnames(res)[[2]] <- dimnames(X)[[2]]
    coeffmul <- rep(1/N, N)
    aver <- as.vector(X %*% coeffmul)
    difsq <- (X - aver)^2
    bnds <- c(-20, errtable[, 1])
    for (i in c(1:(m - 1))) {
        bnds[i + 1] <- errtable[i, 1]/2 + errtable[i + 1, 1]/2
    }
    bnds[m + 1] <- log(max(aver) + 1)
    if (refchips == 0) {
        wei <- rep(0, m)
    }
    for (i in c(1:m)) {
        keep <- ((log(aver) > bnds[i]) & (log(aver) <= bnds[i + 
            1]))
        ngenes <- sum(keep * 1)
        coe <- rep(1/ngenes, ngenes)
        res[i, ] <- as.vector(t(difsq[keep, ]) %*% coe)
        if (refchips == 0) {
            wei[i] <- ngenes
        }
    }
    if (refchips == 0) {
        refchips <- .retlessnoisy(X = res, weight = wei, N = 3)
        print(refchips)
    }
    nref <- length(refchips)
    coe <- rep(1/nref, nref)
    avrefchi <- res[, refchips] %*% coe
    ratio <- as.vector(errtable[, 2]/avrefchi)
    res <- cbind(errtable[, 1], res * ratio)
    dimnames(res)[[2]][1] <- "avg"
    res
}
<bytecode: 0x042e87b8>
<environment: namespace:rHVDM>
 --- function search by body ---
Function .computeinderrtable in namespace rHVDM has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1

** running examples for arch 'x64' ... ERROR
Running examples in 'rHVDM-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimerrors
> ### Title: computes the standard deviation of the measurement error using
> ###   pre-calculated tables specific to the plattform or user-defined table
> ### Aliases: estimerrors
> ### Keywords: IO ts
> 
> ### ** Examples
> 
> data(HVDMexample)
> fiveGybis<-estimerrors(eset=fiveGyMAS5,plattid="affy_HGU133A",refchips=leastnoisychips)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
rHVDM
 --- call from context --- 
.computeinderrtable(X = X, errtable = errtable, refchips = refs)
 --- call from argument --- 
if (refchips == 0) {
    wei <- rep(0, m)
}
 --- R stacktrace ---
where 1: .computeinderrtable(X = X, errtable = errtable, refchips = refs)
where 2: .computerrs(eset = eset, errtable = errtable, refs = refchips)
where 3: estimerrors(eset = fiveGyMAS5, plattid = "affy_HGU133A", refchips = leastnoisychips)

 --- value of length: 3 type: logical ---
[1] FALSE FALSE FALSE
 --- function from context --- 
function (X, errtable, refchips) 
{
    N <- dim(X)[2]
    if (missing(refchips)) {
        refchips <- c(1:N)
    }
    m <- dim(errtable)[1]
    res <- matrix(rep(0, m * N), m, N)
    dimnames(res)[[2]] <- dimnames(X)[[2]]
    coeffmul <- rep(1/N, N)
    aver <- as.vector(X %*% coeffmul)
    difsq <- (X - aver)^2
    bnds <- c(-20, errtable[, 1])
    for (i in c(1:(m - 1))) {
        bnds[i + 1] <- errtable[i, 1]/2 + errtable[i + 1, 1]/2
    }
    bnds[m + 1] <- log(max(aver) + 1)
    if (refchips == 0) {
        wei <- rep(0, m)
    }
    for (i in c(1:m)) {
        keep <- ((log(aver) > bnds[i]) & (log(aver) <= bnds[i + 
            1]))
        ngenes <- sum(keep * 1)
        coe <- rep(1/ngenes, ngenes)
        res[i, ] <- as.vector(t(difsq[keep, ]) %*% coe)
        if (refchips == 0) {
            wei[i] <- ngenes
        }
    }
    if (refchips == 0) {
        refchips <- .retlessnoisy(X = res, weight = wei, N = 3)
        print(refchips)
    }
    nref <- length(refchips)
    coe <- rep(1/nref, nref)
    avrefchi <- res[, refchips] %*% coe
    ratio <- as.vector(errtable[, 2]/avrefchi)
    res <- cbind(errtable[, 1], res * ratio)
    dimnames(res)[[2]][1] <- "avg"
    res
}
<bytecode: 0x00000000087fb140>
<environment: namespace:rHVDM>
 --- function search by body ---
Function .computeinderrtable in namespace rHVDM has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1

* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/rHVDM.Rcheck/00check.log'
for details.

Installation output

rHVDM.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/rHVDM_1.49.0.tar.gz && rm -rf rHVDM.buildbin-libdir && mkdir rHVDM.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rHVDM.buildbin-libdir rHVDM_1.49.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL rHVDM_1.49.0.zip && rm rHVDM_1.49.0.tar.gz rHVDM_1.49.0.zip
###
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  % 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 5228k  100 5228k    0     0  6530k      0 --:--:-- --:--:-- --:--:-- 6584k

install for i386

* installing *source* package 'rHVDM' ...
** R
** data
** byte-compile and prepare package for lazy loading
Note: break used in wrong context: no loop is visible 
** help
*** installing help indices
  converting help for package 'rHVDM'
    finding HTML links ... done
    HVDMcheck                               html  
    HVDMreport                              html  
    estimerrors                             html  
    fitgene                                 html  
    fitgene.lin                             html  
    fitgene.nl                              html  
    fiveGyMAS5                              html  
    genestoscreen                           html  
    leastnoisychips                         html  
    p53traingenes                           html  
    rHVDMplattforms                         html  
    screening                               html  
    screening.nl                            html  
    training                                html  
    training.nl                             html  
    twodosesMAS5                            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 'rHVDM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rHVDM' as rHVDM_1.49.0.zip
* DONE (rHVDM)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'rHVDM' successfully unpacked and MD5 sums checked

Tests output

Example timings

rHVDM.Rcheck/examples_i386/rHVDM-Ex.timings

nameusersystemelapsed
HVDMcheck0.330.030.36
HVDMreport0.690.030.72

rHVDM.Rcheck/examples_x64/rHVDM-Ex.timings

nameusersystemelapsed
HVDMcheck0.250.030.28
HVDMreport0.720.010.74