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CHECK report for biosvd on tokay2

This page was generated on 2020-10-17 11:56:10 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE biosvd PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 183/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biosvd 2.24.0
Anneleen Daemen , Matthew Brauer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/biosvd
Branch: RELEASE_3_11
Last Commit: 4aa7204
Last Changed Date: 2020-04-27 14:38:03 -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: biosvd
Version: 2.24.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biosvd.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings biosvd_2.24.0.tar.gz
StartedAt: 2020-10-17 02:04:03 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:05:36 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 92.5 seconds
RetCode: 1
Status:  ERROR  
CheckDir: biosvd.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:biosvd.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings biosvd_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/biosvd.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 'biosvd/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'biosvd' version '2.24.0'
* 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 'biosvd' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'biosvd' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/biosvd.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
* 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
.checkColorMaps : <anonymous>: no visible global function definition
  for 'rainbow'
plot,Eigensystem-EigensystemPlotParam: no visible global function
  definition for 'pdf'
plot,Eigensystem-EigensystemPlotParam: no visible global function
  definition for 'dev.off'
plot,Eigensystem-EigensystemPlotParam: no visible global function
  definition for 'rainbow'
Undefined global functions or variables:
  dev.off pdf rainbow
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow")
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 'biosvd-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biosvd
> ### Title: Package for high-throughput data processing, outlier detection,
> ###   noise removal and dynamic modeling
> ### Aliases: biosvd biosvd-package
> ### Keywords: package
> 
> ### ** Examples
> 
> example( report )

report> ## Metabolomics starvation data obtained from http://genomics-pubs.princeton.edu/StarvationMetabolomics/Download.shtml
report> data(StarvationData)

report> ## Computes the eigensystem for the actual data
report> eigensystem <- compute(StarvationData)

report> ## Exclude the eigenfeatures representing steady-state intensity
report> eigensystem <- exclude(eigensystem)

report> ## Computes the eigensystem on the variance in the data after filtering out stead-state intensity
report> eigensystem <- compute(eigensystem, apply="variance")

report> ## No exclusion of eigenfeatures representing steady-scale variance
report> eigensystem <- exclude(eigensystem, excludeEigenfeatures=0)

report> ## Generate report for eigenfeatures 1 and 2
report> params <- new("EigensystemPlotParam")

report> if (.Platform$OS.type %in% "windows") path(params) <- getwd()

report> report(eigensystem, params)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
biosvd
 --- call from context --- 
report(eigensystem, params)
 --- call from argument --- 
class(featureMatrix(eigensystem)) != "NULL" && ncol(featureMatrix(eigensystem)) > 
    0
 --- R stacktrace ---
where 1: report(eigensystem, params)
where 2 at C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\Rtmp4Ecnes\Rex2f1c747a31f5#22: report(eigensystem, params)
where 3: eval(ei, envir)
where 4: eval(ei, envir)
where 5: withVisible(eval(ei, envir))
where 6: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix, 
    getOption("prompt")), continue.echo = paste0(prompt.prefix, 
    getOption("continue")), verbose = verbose, max.deparse.length = Inf, 
    encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
where 7: example(report)

 --- value of length: 2 type: logical ---
[1] TRUE TRUE
 --- function from context --- 
Method Definition:

function (x, y, ...) 
{
    eigensystem <- x
    params <- y
    polarAxes <- .checkEigenfeatureAxes(eigensystem, whichPolarAxes(params))
    polarplot.info <- cbind(rownames(matrix(eigensystem)), project(eigensystem, 
        polarAxes))
    colnames(polarplot.info) = c("Feature", paste("Coordinate to eigenfeature ", 
        polarAxes[2], sep = ""), paste("Coordinate to eigenfeature ", 
        polarAxes[1], sep = ""), "Radius", "Phase")
    if (class(featureMatrix(eigensystem)) != "NULL" && ncol(featureMatrix(eigensystem)) > 
        0) 
        polarplot.info <- cbind(polarplot.info, featureMatrix(eigensystem))
    write.table(polarplot.info, file = paste(prefix(params), 
        "report.eigenfeature", polarAxes[1], "vs", polarAxes[2], 
        "txt", sep = "."), row.names = FALSE)
}
<bytecode: 0x0c2f03b8>
<environment: namespace:biosvd>

Signatures:
        x             y                     
target  "Eigensystem" "EigensystemPlotParam"
defined "Eigensystem" "EigensystemPlotParam"
 --- function search by body ---
S4 Method report:biosvd defined in namespace biosvd with signature Eigensystem#EigensystemPlotParam has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biosvd
> ### Title: Package for high-throughput data processing, outlier detection,
> ###   noise removal and dynamic modeling
> ### Aliases: biosvd biosvd-package
> ### Keywords: package
> 
> ### ** Examples
> 
> example( report )

report> ## Metabolomics starvation data obtained from http://genomics-pubs.princeton.edu/StarvationMetabolomics/Download.shtml
report> data(StarvationData)

report> ## Computes the eigensystem for the actual data
report> eigensystem <- compute(StarvationData)

report> ## Exclude the eigenfeatures representing steady-state intensity
report> eigensystem <- exclude(eigensystem)

report> ## Computes the eigensystem on the variance in the data after filtering out stead-state intensity
report> eigensystem <- compute(eigensystem, apply="variance")

report> ## No exclusion of eigenfeatures representing steady-scale variance
report> eigensystem <- exclude(eigensystem, excludeEigenfeatures=0)

report> ## Generate report for eigenfeatures 1 and 2
report> params <- new("EigensystemPlotParam")

report> if (.Platform$OS.type %in% "windows") path(params) <- getwd()

report> report(eigensystem, params)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
biosvd
 --- call from context --- 
report(eigensystem, params)
 --- call from argument --- 
class(featureMatrix(eigensystem)) != "NULL" && ncol(featureMatrix(eigensystem)) > 
    0
 --- R stacktrace ---
where 1: report(eigensystem, params)
where 2 at C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpYdb1le\Rex283854f528b3#22: report(eigensystem, params)
where 3: eval(ei, envir)
where 4: eval(ei, envir)
where 5: withVisible(eval(ei, envir))
where 6: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix, 
    getOption("prompt")), continue.echo = paste0(prompt.prefix, 
    getOption("continue")), verbose = verbose, max.deparse.length = Inf, 
    encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
where 7: example(report)

 --- value of length: 2 type: logical ---
[1] TRUE TRUE
 --- function from context --- 
Method Definition:

function (x, y, ...) 
{
    eigensystem <- x
    params <- y
    polarAxes <- .checkEigenfeatureAxes(eigensystem, whichPolarAxes(params))
    polarplot.info <- cbind(rownames(matrix(eigensystem)), project(eigensystem, 
        polarAxes))
    colnames(polarplot.info) = c("Feature", paste("Coordinate to eigenfeature ", 
        polarAxes[2], sep = ""), paste("Coordinate to eigenfeature ", 
        polarAxes[1], sep = ""), "Radius", "Phase")
    if (class(featureMatrix(eigensystem)) != "NULL" && ncol(featureMatrix(eigensystem)) > 
        0) 
        polarplot.info <- cbind(polarplot.info, featureMatrix(eigensystem))
    write.table(polarplot.info, file = paste(prefix(params), 
        "report.eigenfeature", polarAxes[1], "vs", polarAxes[2], 
        "txt", sep = "."), row.names = FALSE)
}
<bytecode: 0x0000000011625a58>
<environment: namespace:biosvd>

Signatures:
        x             y                     
target  "Eigensystem" "EigensystemPlotParam"
defined "Eigensystem" "EigensystemPlotParam"
 --- function search by body ---
S4 Method report:biosvd defined in namespace biosvd with signature Eigensystem#EigensystemPlotParam 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, 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/biosvd.Rcheck/00check.log'
for details.


Installation output

biosvd.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/biosvd_2.24.0.tar.gz && rm -rf biosvd.buildbin-libdir && mkdir biosvd.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biosvd.buildbin-libdir biosvd_2.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL biosvd_2.24.0.zip && rm biosvd_2.24.0.tar.gz biosvd_2.24.0.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  523k  100  523k    0     0  5876k      0 --:--:-- --:--:-- --:--:-- 6386k

install for i386

* installing *source* package 'biosvd' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'biosvd'
    finding HTML links ... done
    Eigensystem-class                       html  
    EigensystemPlotParam-class              html  
    HeLaData                                html  
    StarvationData                          html  
    YeastData                               html  
    assayColorMap-set                       html  
    biosvd                                  html  
    compute-methods                         html  
    contrast-set                            html  
    exclude-methods                         html  
    featureColorMap-set                     html  
    figure-set                              html  
    filenames-set                           html  
    negativeValues-set                      html  
    palette-set                             html  
    path-set                                html  
    plot-methods                            html  
    plots-set                               html  
    prefix-set                              html  
    project-methods                         html  
    report-methods                          html  
    whichAssays-set                         html  
    whichEigenassays-set                    html  
    whichEigenfeatures-set                  html  
    whichFeatures-set                       html  
    whichPolarAxes-set                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'biosvd' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'biosvd' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'biosvd' ...
** testing if installed package can be loaded
Warning: Package 'biosvd' is deprecated and will be removed from Bioconductor
  version 3.12
* MD5 sums
packaged installation of 'biosvd' as biosvd_2.24.0.zip
* DONE (biosvd)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'biosvd' successfully unpacked and MD5 sums checked

Tests output


Example timings

biosvd.Rcheck/examples_i386/biosvd-Ex.timings

nameusersystemelapsed
Eigensystem-class0.000.010.01
EigensystemPlotParam-class0.020.000.02

biosvd.Rcheck/examples_x64/biosvd-Ex.timings

nameusersystemelapsed
Eigensystem-class0.000.020.01
EigensystemPlotParam-class0.000.010.02