Message-ID: <7dfae793-52ab-0402-23d0-12e9876d992e@umu.se>
Date: 2017-12-06T10:40:28Z
From: Göran Broström
Subject: [R-pkg-devel] Error in re-building vignettes (SOLVED)
In-Reply-To: <62ad5860-9572-cc2b-ec3d-4e783622108a@umu.se>
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.
G?ran
On 2017-12-05 21:51, G?ran Brostr?m 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?
>
> G?ran Brostr?m
>
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