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### Running command:
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###   chmod a+r vsn -R && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data vsn
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* checking for file 'vsn/DESCRIPTION' ... OK
* preparing 'vsn':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'A-vsn.Rmd' using rmarkdown
Loading required package: Biobase
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, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/nkid-scp-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/nkid-sdmean1-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/nkid-sdmean2-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/nkid-histM-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/lym-sdmean-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/lym-M-1.png" but not available.
Loading required package: affy
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hgu95av2cdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hgu95av2cdf'

The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/affy-1.png" but not available.

Attaching package: 'limma'

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

    plotMA

The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/limma-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/figstrata2-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/miss-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/ref-1.png" but not available.
Warning in xy.coords(x, y, xlabel, ylabel, log) :
  1 x value <= 0 omitted from logarithmic plot
Warning in xy.coords(x, y, xlabel, ylabel, log) :
  603 y values <= 0 omitted from logarithmic plot
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/nkid-calib4-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/nkid-calib5-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/vsnQ1-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/vsnQ2-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/shrink-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/figgraph-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/lymbox-1.png" but not available.
The magick package is required to crop "C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/Rtmp0isQWb/Rbuildc3c22a86acc/vsn/vignettes/A-vsn_files/figure-html/lymquscp-1.png" but not available.
--- finished re-building 'A-vsn.Rmd'

--- re-building 'C-likelihoodcomputations.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "C-likelihoodcomputations.tex" --max-iterations=20 -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/tex/latex" -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'C-likelihoodcomputations.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'C-likelihoodcomputations.pdf' for vignette with name 'C-likelihoodcomputations' and engine 'utils::Sweave'. The following files exist in working directory 'C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\Rtmp0isQWb\Rbuildc3c22a86acc\vsn\vignettes': 'A-vsn.R' (15275 bytes), 'A-vsn.Rmd' (49303 bytes), 'A-vsn.html' (1.24657e+06 bytes), 'C-likelihoodcomputations.Rnw' (10450 bytes), 'C-likelihoodcomputations.tex' (10955 bytes), 'D-convergence.Rnw' (462 bytes), 'vsn.bib' (4393 bytes)
--- failed re-building 'C-likelihoodcomputations.Rnw'

--- re-building 'D-convergence.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "D-convergence.tex" --max-iterations=20 -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/tex/latex" -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'D-convergence.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'D-convergence.pdf' for vignette with name 'D-convergence' and engine 'utils::Sweave'. The following files exist in working directory 'C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\Rtmp0isQWb\Rbuildc3c22a86acc\vsn\vignettes': 'A-vsn.R' (15275 bytes), 'A-vsn.Rmd' (49303 bytes), 'A-vsn.html' (1.24657e+06 bytes), 'C-likelihoodcomputations.R' (235 bytes), 'C-likelihoodcomputations.Rnw' (10450 bytes), 'C-likelihoodcomputations.tex' (10955 bytes), 'D-convergence.Rnw' (462 bytes), 'D-convergence.tex' (497 bytes), 'vsn.bib' (4393 bytes)
--- failed re-building 'D-convergence.Rnw'

SUMMARY: processing the following files failed:
  'C-likelihoodcomputations.Rnw' 'D-convergence.Rnw'

Error: Vignette re-building failed.
Execution halted