• using R version 4.3.0 beta (2023-04-10 r84212)
  • using platform: aarch64-apple-darwin20 (64-bit)
  • R was compiled by
        Apple clang version 14.0.0 (clang-1400.0.29.202)
        GNU Fortran (GCC) 12.2.0
  • running under: macOS Big Sur 11.6.7
  • using session charset: UTF-8
  • checking for file ‘speaq/DESCRIPTION’ ... OK
  • this is package ‘speaq’ version ‘2.7.0’
  • package encoding: UTF-8
  • 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 executable files ... OK
  • checking for hidden files and directories ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking whether package ‘speaq’ can be installed ... [4s/5s] OK
    See the install log 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 ... [1s/1s] OK
  • checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
  • checking whether the package can be unloaded cleanly ... [1s/1s] OK
  • checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
  • checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
  • checking loading without being on the library search path ... [1s/1s] 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 ... [4s/4s] OK
  • checking Rd files ... [0s/0s] 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 ... [0s/0s] OK
  • checking LazyData ... OK
  • checking data for ASCII and uncompressed saves ... OK
  • checking installed files from ‘inst/doc’ ... OK
  • checking files in ‘vignettes’ ... OK
  • checking examples ... [1s/2s] ERROR
    Running examples in ‘speaq-Ex.R’ failed
    The error most likely occurred in:

    > ### Name: BWR
    > ### Title: BW ratio calculation
    > ### Aliases: BWR
    >
    > ### ** Examples
    >
    > res=makeSimulatedData();
    > X=res$data;
    > groupLabel=res$label;
    > peakList <- detectSpecPeaks(X,
    + nDivRange = c(128),
    + scales = seq(1, 16, 2),
    + baselineThresh = 50000,
    + SNR.Th = -1,
    + verbose=FALSE
    + );
    > resFindRef<- findRef(peakList);
    > refInd <- resFindRef$refInd;
    > maxShift = 50;
    > Y <- dohCluster(X,
    + peakList = peakList,
    + refInd = refInd,
    + maxShift = maxShift,
    + acceptLostPeak = TRUE, verbose=FALSE);
    Warning in min(peakList) :
      no non-missing arguments to min; returning Inf
    Warning in max(peakList) :
      no non-missing arguments to max; returning -Inf
    Error in startP:(minpeakList - 1) : result would be too long a vector
    Calls: dohCluster -> .withMaxShift -> hClustAlign
    Execution halted
  • checking for unstated dependencies in vignettes ... OK
  • checking package vignettes in ‘inst/doc’ ... OK
  • checking running R code from vignettes ... [0s/0s] NONE
      ‘classic_speaq_vignette.Rmd’ using ‘UTF-8’... [0s/0s] OK
      ‘speaq2_illustrations.Rmd’ using ‘UTF-8’... [0s/0s] OK
  • checking re-building of vignette outputs ... [9s/12s] ERROR
    Error(s) in re-building vignettes:
      ...
    --- re-building ‘classic_speaq_vignette.Rmd’ using rmarkdown
    Quitting from lines 111-120 (classic_speaq_vignette.Rmd)
    Error: processing vignette 'classic_speaq_vignette.Rmd' failed with diagnostics:
    result would be too long a vector
    --- failed re-building ‘classic_speaq_vignette.Rmd’

    --- re-building ‘speaq2_illustrations.Rmd’ using rmarkdown
    Quitting from lines 71-83 (speaq2_illustrations.Rmd)
    Error: processing vignette 'speaq2_illustrations.Rmd' failed with diagnostics:
    invalid 'times' argument
    --- failed re-building ‘speaq2_illustrations.Rmd’

    SUMMARY: processing the following files failed:
      ‘classic_speaq_vignette.Rmd’ ‘speaq2_illustrations.Rmd’

    Error: Vignette re-building failed.
    Execution halted
  • checking PDF version of manual ... [5s/6s] OK
  • DONE
    Status: 2 ERRORs
  • using check arguments '--no-clean-on-error '