• using R version 4.1.2 (2021-11-01)
• using platform: x86_64-apple-darwin17.0 (64-bit)
• using session charset: UTF-8
• checking for file ‘lfc/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘lfc’ version ‘0.2.2’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Package suggested but not available for checking: ‘airway’
• 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 ‘lfc’ can be installed ... [2s/2s] OK
• 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 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 ... [2s/2s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [0s/0s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [0s/0s] NONE
    ‘lfc_vignette.Rmd’ using ‘UTF-8’... [0s/0s] OK
• checking re-building of vignette outputs ... [8s/8s] WARNING
  Error(s) in re-building vignettes:
  --- re-building ‘lfc_vignette.Rmd’ using rmarkdown
  Loading required package: S4Vectors
  Loading required package: stats4
  Loading required package: BiocGenerics
  Loading required package: parallel
  
  Attaching package: 'BiocGenerics'
  
  The following objects are masked from 'package:parallel':
  
      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
      clusterExport, clusterMap, parApply, parCapply, parLapply,
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  The following objects are masked from 'package:stats':
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from 'package:base':
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
      tapply, union, unique, unsplit, which.max, which.min
  
  
  Attaching package: 'S4Vectors'
  
  The following objects are masked from 'package:base':
  
      I, expand.grid, unname
  
  Loading required package: IRanges
  Loading required package: GenomicRanges
  Loading required package: GenomeInfoDb
  Loading required package: SummarizedExperiment
  Loading required package: MatrixGenerics
  Loading required package: matrixStats
  
  Attaching package: 'MatrixGenerics'
  
  The following objects are masked from 'package:matrixStats':
  
      colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
      colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
      colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
      colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
      colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
      colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
      colWeightedMeans, colWeightedMedians, colWeightedSds,
      colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
      rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
      rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
      rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
      rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
      rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
      rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
      rowWeightedSds, rowWeightedVars
  
  Loading required package: Biobase
  Welcome to Bioconductor
  
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  
  Attaching package: 'Biobase'
  
  The following object is masked from 'package:MatrixGenerics':
  
      rowMedians
  
  The following objects are masked from 'package:matrixStats':
  
      anyMissing, rowMedians
  
  
  Attaching package: 'lfc'
  
  The following object is masked from 'package:DESeq2':
  
      results
  
  Quitting from lines 35-44 (lfc_vignette.Rmd)
  Error: processing vignette 'lfc_vignette.Rmd' failed with diagnostics:
  there is no package called 'airway'
  --- failed re-building ‘lfc_vignette.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘lfc_vignette.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted
  
• checking PDF version of manual ... OK
• DONE
  Status: 1 WARNING, 1 NOTE
• using check arguments '--no-clean-on-error '