[R-pkg-devel] Error in re-building vignettes (SOLVED)

[Göran Broström]

Hi again,

today I INSTALLED R-devel (2017-12-05 r73849) and updated all packages

 > update.packages(checkBuilt = TRUE)

and rebuilt eha_2.5.1 and now all checks passed! Maybe the update of 
packages was necessary.

On its way to CRAN now.

Göran

On 2017-12-05 21:51, Göran Broström wrote:
> Hi,
> 
> I am checking my eha package with R-3.4.3:
> 
> goran at M6800:~/R$ R CMD check --as-cran eha_2.5.1.tar.gz
> 
> which results in
> 
> * DONE
> 
> Status: OK
> 
> Fine, but with R-devel (2017-12-04 r73829)
> 
> goran at M6800:~/R$ ~/src/R-devel/bin/R CMD check --as-cran eha_2.5.1.tar.gz
> 
> .........
> 
> * checking re-building of vignette outputs ... WARNING
> Error in re-building vignettes:
>    ...
> 
>   *** caught segfault ***
> address 0x1, cause 'memory not mapped'
> 
> Traceback:
>   1: .Call(C_stri_locate_all_regex, str, pattern, omit_no_match, 
> opts_regex)
>   2: stri_locate_all_regex(string, pattern, omit_no_match = TRUE, 
> opts_regex = opts)
>   3: stringr::str_locate_all(input, inline.code)
>   4: parse_inline(g, patterns)
>   5: FUN(X[[i]], ...)
>   6: lapply(groups, function(g) {    block = grepl(chunk.begin, g[1]) if 
> (!set.preamble && !parent_mode()) {        return(if (block) "" else 
> g)    }    if (block) {        n = length(g)        if (n >= 2 && 
> grepl(chunk.end, g[n]))             g = g[-n]        g = strip_block(g, 
> patterns$chunk.code)        params.src = if (group_pattern(chunk.begin)) 
> {            stringr::str_trim(gsub(chunk.begin, "\\1", g[1]))        } 
>        else ""        parse_block(g[-1], g[1], params.src)    }    else 
> parse_inline(g, patterns)})
>   7: split_file(lines = text)
>   8: process_file(text, output)
>   9: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, 
>     encoding = encoding)
> 10: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = 
> globalenv())
> 11: vweave_rmarkdown(...)
> 12: engine$weave(file, quiet = quiet, encoding = enc)
> 13: doTryCatch(return(expr), name, parentenv, handler)
> 14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 15: tryCatchList(expr, classes, parentenv, handlers)
> 16: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc) 
> setwd(startdir)    find_vignette_product(name, by = "weave", engine = 
> engine)}, error = function(e) {    stop(gettextf("processing vignette 
> '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)), 
> domain = NA, call. = FALSE)})
> 17: buildVignettes(dir = "/home/goran/R/eha.Rcheck/vign_test/eha")
> An irrecoverable exception occurred. R is aborting now ...
> Segmentation fault (core dumped)
> 
> * checking PDF version of manual ... OK
> * DONE
> 
> Status: 1 WARNING, 2 NOTEs
> 
> So, can I send this version of eha to CRAN?
> 
> Göran Broström
> 
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