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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:biosvd.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings biosvd_2.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/biosvd.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 ‘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 for sufficient/correct file permissions ... 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 ‘/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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 /tmp/Rtmp8Er8Xj/Rexdf74203a8c47#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: 0x7f806201e360>
<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: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/biosvd.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL biosvd
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘biosvd’ ...
** using staged installation
** 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 '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
* DONE (biosvd)