CRAN Package Check Results for Package define

Last updated on 2020-05-29 06:48:24 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.8 10.03 84.07 94.10 OK
r-devel-linux-x86_64-debian-gcc 0.2.8 9.02 64.15 73.17 OK
r-devel-linux-x86_64-fedora-clang 0.2.8 123.94 OK
r-devel-linux-x86_64-fedora-gcc 0.2.8 111.18 OK
r-devel-windows-ix86+x86_64 0.2.8 32.00 160.00 192.00 OK
r-patched-linux-x86_64 0.2.8 10.62 81.24 91.86 OK
r-patched-solaris-x86 0.2.8 161.20 ERROR
r-release-linux-x86_64 0.2.8 10.86 82.24 93.10 OK
r-release-osx-x86_64 0.2.8 OK
r-release-windows-ix86+x86_64 0.2.8 22.00 143.00 165.00 OK
r-oldrel-osx-x86_64 0.2.8 OK
r-oldrel-windows-ix86+x86_64 0.2.8 23.00 98.00 121.00 OK

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/RtmpBAaaRx/working_dir/Rtmp.BairP/theoph.csv to /tmp/RtmpBAaaRx/working_dir/Rtmp.BairP/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
    (/tmp/RtmpBAaaRx/working_dir/Rtmp.BairP/out/minimal.tex
    LaTeX2e <2020-02-02> patch level 5
    L3 programming layer <2020-05-15>
    (/usr/local/texlive/2020/texmf-dist/tex/latex/base/article.cls
    Document Class: article 2019/12/20 v1.4l Standard LaTeX document class
    (/usr/local/texlive/2020/texmf-dist/tex/latex/base/size10.clo))
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    Package tocbibind Note: Using section or other style headings.
    
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    Package fixltx2e Warning: fixltx2e is not required with releases after 2015
    (fixltx2e) All fixes are now in the LaTeX kernel.
    (fixltx2e) See the latexrelease package for details.
    
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    No file minimal.aux.
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    [Loading MPS to PDF converter (version 2006.09.02).]
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    ty)) (/usr/local/texlive/2020/texmf-dist/tex/latex/fmtcount/fc-english.def)
    ! Missing $ inserted.
    <inserted text>
     $
    l.31 ...bf{/tmp/RtmpBAaaRx/working_dir/Rtmp.BairP}
     }
    ?
    ! Emergency stop.
    <inserted text>
     $
    l.31 ...bf{/tmp/RtmpBAaaRx/working_dir/Rtmp.BairP}
     }
    ! ==> Fatal error occurred, no output PDF file produced!
    Transcript written on /tmp/RtmpBAaaRx/working_dir/Rtmp.BairP/out/minimal.log.
    Error in as.pdf.document(z, stem = stem, dir = dir, ...) :
     could not make /tmp/RtmpBAaaRx/working_dir/Rtmp.BairP/out/minimal.pdf
    Calls: define -> define.character -> as.pdf -> as.pdf.document
    Execution halted
Flavor: r-patched-solaris-x86