• using R version 4.0.2 (2020-06-22)
  • using platform: x86_64-apple-darwin17.0 (64-bit)
  • using session charset: UTF-8
  • checking for file ‘RUVIIIC/DESCRIPTION’ ... OK
  • checking extension type ... Package
  • this is package ‘RUVIIIC’ version ‘1.0.17’
  • 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
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  • checking whether package ‘RUVIIIC’ can be installed ... [75s/76s] OK
  • checking installed package size ... NOTE
      installed size is 45.9Mb
      sub-directories of 1Mb or more:
        libs 45.3Mb
  • checking package 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
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  • checking whether the namespace can be unloaded cleanly ... OK
  • checking loading without being on the library search path ... 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
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  • checking for missing documentation entries ... OK
  • checking for code/documentation mismatches ... OK
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  • checking for unstated dependencies in examples ... OK
  • checking contents of ‘data’ directory ... OK
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  • checking line endings in C/C++/Fortran sources/headers ... OK
  • checking line endings in Makefiles ... OK
  • checking compilation flags in Makevars ... OK
  • checking for GNU extensions in Makefiles ... OK
  • checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
  • checking use of PKG_*FLAGS in Makefiles ... OK
  • checking compiled code ... OK
  • checking examples ... [2s/2s] ERROR
    Running examples in ‘RUVIIIC-Ex.R’ failed
    The error most likely occurred in:

    > ### Name: RUVIII_C
    > ### Title: RUV-III-C
    > ### Aliases: RUVIII_C
    >
    > ### ** Examples
    >
    > data(crossLab)
    > #Design matrix containing information about which runs are technical replicates of each other.
    > #In this case, random pairings of mass-spec runs analysing the same sample, at different sites.
    > #Note that we specify no intercept term!
    > M <- model.matrix(~ grouping - 1, data = peptideData)
    > #Get out the list of peptides, both HEK (control) and peptides of interest.
    > peptides <- setdiff(colnames(peptideData), c("filename", "site", "mixture", "Date", "grouping"))
    > #Reduce the data matrix to only the peptide data
    > onlyPeptideData <- data.matrix(peptideData[, peptides])
    > #All the human peptides are potential controls. That is, everything that's not an SIS peptides.
    > potentialControls <- setdiff(peptides, sisPeptides)
    > #But we want to use controls that are always found
    > potentialControlsAlwaysFound <- names(which(apply(onlyPeptideData[, potentialControls], 2,
    + function(x) sum(is.na(x))) == 0))
    > #Actually run correction
    > #Set number of threads for CRAN
    > RUVIIIC::omp_set_num_threads(2L)
    Error in RUVIIIC_omp_set_num_threads(num) :
      Not built with openmp suppport
    Calls: <Anonymous> -> RUVIIIC_omp_set_num_threads
    Execution halted
  • checking for unstated dependencies in ‘tests’ ... OK
  • checking tests ... [5s/5s] OK
      Running ‘testthat.R’ [5s/5s]
  • checking PDF version of manual ... OK
  • DONE
    Status: 1 ERROR, 1 NOTE
  • using check arguments '--no-clean-on-error '