CRAN Package Check Results for Package define

Last updated on 2020-06-18 07:50:12 CEST.

Check Details

Version: 0.2.8
Check: examples
Result: ERROR
    Running examples in ‘define-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: define
    > ### Title: Define objects per FDA guidance.
    > ### Aliases: define define.character
    >
    > ### ** Examples
    >
    > library(spec) # read and write data specifications
    > library(latexpdf) # make dummy logo for pdf
    > library(encode) # encode factor levels for spec file
    >
    > dir <- tempdir() # a place to experiment
    > dir <- gsub('\\\\','/',dir) # clean up windows path
    > outdir <- file.path(dir,'out') # where to put the define archive
    > csv <- file.path(dir,'theoph.csv') # path to data
    > script <- file.path(dir,'theoph.R') # path to script making data
    > spec <- file.path(dir,'theoph.spec') # path to data specification
    >
    > # make dummy logo
    > ## Not run:
    > ##D as.pdf('{\\huge \\em Pharma, Inc.}',wide = 50, long = 8,stem = 'logo', dir = dir)
    > ## End(Not run)
    > # browseURL(system.file(package = 'define', 'logo.pdf')) # cached
    > logo <- system.file(package = 'define', 'logo.pdf') # path to dummy logo
    >
    > # make data more interesting
    > Theoph$renal <- 0
    >
    > # create script
    > code <- "write.csv(x = Theoph,file = csv,row.names = FALSE,quote = FALSE)"
    > writeLines(code,script)
    >
    > # 'run' the script
    > eval(parse(text = code))
    >
    > # make data specification
    > s <- specification(Theoph)
    > renalcat <- c(
    + 'GFR >= 90 mL/min/1.73m^2',
    + '60 <= GFR < 90 mL/min/1.73m^2',
    + '45 <= GFR < 60 mL/min/1.73m^2',
    + '30 <= GFR < 45 mL/min/1.73m^2',
    + 'GFR < 30 mL/min/1.73m^2'
    + )
    > codes <- encode(0:4, renalcat)
    > codes
    [1] "||0|GFR >= 90 mL/min/1.73m^2||1|60 <= GFR < 90 mL/min/1.73m^2||2|45 <= GFR < 60 mL/min/1.73m^2||3|30 <= GFR < 45 mL/min/1.73m^2||4|GFR < 30 mL/min/1.73m^2||"
    > s$guide[s$column == 'renal'] <- codes
    >
    > write.spec(s,spec)
    >
    > file.exists(csv)
    [1] TRUE
    > file.exists(spec)
    [1] TRUE
    > define(c(theoph = csv),stem = 'minimal',dir = outdir, clean=FALSE)
    exporting /tmp/Rtmp1kaiov/working_dir/RtmpqwaO9g/theoph.csv to /tmp/Rtmp1kaiov/working_dir/RtmpqwaO9g/out/./theoph.xpt
    This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex)
     restricted \write18 enabled.
    entering extended mode
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    ! Missing $ inserted.
    <inserted text>
     $
    l.31 ...bf{/tmp/Rtmp1kaiov/working_dir/RtmpqwaO9g}
     }
    ?
    ! Emergency stop.
    <inserted text>
     $
    l.31 ...bf{/tmp/Rtmp1kaiov/working_dir/RtmpqwaO9g}
     }
    ! ==> Fatal error occurred, no output PDF file produced!
    Transcript written on /tmp/Rtmp1kaiov/working_dir/RtmpqwaO9g/out/minimal.log.
    Error in as.pdf.document(z, stem = stem, dir = dir, ...) :
     could not make /tmp/Rtmp1kaiov/working_dir/RtmpqwaO9g/out/minimal.pdf
    Calls: define -> define.character -> as.pdf -> as.pdf.document
    Execution halted
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