• using R version 4.3.0 alpha (2023-03-31 r84137)
  • 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 ‘bbl/DESCRIPTION’ ... OK
  • this is package ‘bbl’ version ‘1.0.0’
  • 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 ‘bbl’ can be installed ... [14s/17s] OK
    See the install log for details.
  • used C++ compiler: ‘Apple clang version 13.0.0 (clang-1300.0.29.30)’
  • used SDK: ‘MacOSX11.3.sdk’
  • checking installed package size ... NOTE
      installed size is 6.4Mb
      sub-directories of 1Mb or more:
        extdata 2.3Mb
        libs 3.5Mb
  • 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 ... [0s/0s] OK
  • checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
  • checking whether the package can be unloaded cleanly ... [0s/0s] OK
  • checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
  • checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
  • checking loading without being on the library search path ... [0s/0s] 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 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 sizes of PDF files under ‘inst/doc’ ... OK
  • checking installed files from ‘inst/doc’ ... OK
  • checking files in ‘vignettes’ ... OK
  • checking examples ... [4s/5s] OK
  • checking for unstated dependencies in vignettes ... OK
  • checking package vignettes in ‘inst/doc’ ... OK
  • checking running R code from vignettes ... [96s/107s] OK
      ‘article.Rnw’ using ‘UTF-8’... [96s/107s] OK
  • checking re-building of vignette outputs ... [110s/121s] NOTE
    Error(s) in re-building vignettes:
    --- re-building ‘article.Rnw’ using Sweave
    Setting levels: control = No, case = Yes
    Loading required package: glmnet
    Loading required package: Matrix
    Loaded glmnet 4.1-7
    Setting levels: control = No, case = Yes
    Setting levels: control = No, case = Yes
    Loading required package: Biostrings
    Loading required package: BiocGenerics

    Attaching package: 'BiocGenerics'

    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, aperm,
        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

    Loading required package: S4Vectors
    Loading required package: stats4

    Attaching package: 'S4Vectors'

    The following objects are masked from 'package:Matrix':

        expand, unname

    The following objects are masked from 'package:base':

        I, expand.grid, unname

    Loading required package: IRanges
    Loading required package: XVector
    Loading required package: GenomeInfoDb

    Attaching package: 'Biostrings'

    The following object is masked from 'package:base':

        strsplit

    Error: processing vignette 'article.Rnw' failed with diagnostics:
    Running 'texi2dvi' on 'article.tex' failed.
    LaTeX errors:
    !pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
     ==> Fatal error occurred, no output PDF file produced!
    --- failed re-building 'article.Rnw'

    SUMMARY: processing the following file failed:
      'article.Rnw'

    Error: Vignette re-building failed.
    Execution halted
  • checking PDF version of manual ... [4s/4s] OK
  • DONE
    Status: 2 NOTEs
  • using check arguments '--no-clean-on-error '