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[R-pkg-devel] Error in re-building vignettes

3 messages · Göran Broström, Dirk Eddelbuettel

Göran Broström
# 
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
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.

G?ran
On 2017-12-05 21:51, G?ran Brostr?m wrote:
Dirk Eddelbuettel
#
On 6 December 2017 at 11:40, G?ran Brostr?m wrote:
| 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.

Very much so, and R Core told us about it some time ago when the 'big recent
changes' (ALTREP etc) landed in R-devel.
 
| On its way to CRAN now.

Glad you have it squared away.

Dirk