Multiple platform build/check report for BioC 3.9 - BUILD report for glmSparseNet on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data glmSparseNet
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* checking for file ‘glmSparseNet/DESCRIPTION’ ... OK
* preparing ‘glmSparseNet’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘example_brca_logistic.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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:dplyr':

    combine, intersect, setdiff, union

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, colMeans, colSums, 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, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    first, rename

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    collapse, desc, slice

Loading required package: GenomeInfoDb
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

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

    count

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

Registered S3 method overwritten by 'rvest':
  method            from
  read_xml.response xml2
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: glmnet
Loading required package: foreach
Loaded glmnet 2.0-16

Warning in has_utility("convert", "ImageMagick") :
  ImageMagick not installed or not in PATH
--- finished re-building ‘example_brca_logistic.Rmd’

--- re-building ‘example_brca_protein-protein-interactions_survival.Rmd’ using rmarkdown
Loading required package: grid
Warning in has_utility("convert", "ImageMagick") :
  ImageMagick not installed or not in PATH
Warning: NAs introduced by coercion
Warning in gsub("˜m", msg, message, fixed = TRUE) :
  argument 'replacement' has length > 1 and only the first element will be used
--- finished re-building ‘example_brca_protein-protein-interactions_survival.Rmd’

--- re-building ‘example_brca_survival.Rmd’ using rmarkdown
Warning: NAs introduced by coercion
Warning in has_utility("convert", "ImageMagick") :
  ImageMagick not installed or not in PATH
--- finished re-building ‘example_brca_survival.Rmd’

--- re-building ‘example_prad_survival.Rmd’ using rmarkdown
Warning in has_utility("convert", "ImageMagick") :
  ImageMagick not installed or not in PATH
--- finished re-building ‘example_prad_survival.Rmd’

--- re-building ‘example_skcm_survival.Rmd’ using rmarkdown
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(days_to_last_followup, days_to_death, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in has_utility("convert", "ImageMagick") :
  ImageMagick not installed or not in PATH
Quitting from lines 161-162 (example_skcm_survival.Rmd) 
Error: processing vignette 'example_skcm_survival.Rmd' failed with diagnostics:
object 'variable' not found
--- failed re-building ‘example_skcm_survival.Rmd’

SUMMARY: processing the following file failed:
  ‘example_skcm_survival.Rmd’

Error: Vignette re-building failed.
Execution halted
BUILD report for glmSparseNet on celaya2

Summary

Command output
