• 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 for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• 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
• checking whether the namespace can be loaded with stated dependencies ... OK
• 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
• 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
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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 '