"memory not mapped" error during system() call

meik michalke meik.michalke at uni-duesseldorf.de
Sun May 6 14:16:25 UTC 2018


i'm trying to rebuild the binary packages for the repo with R 3.5 now, but 
RKWard seems to have a problem with running a system call.

let's say that "~/software/R/R-3.4.4/lib64/R" is a standalone installation of 
R 3.4.4 (i always have several of those to build binaries for multiple 
versions) and "~/package/roxyPackage" is the source code for roxyPackage.

when i call

 system("R_HOME=\"~/software/R/R-3.4.4/lib64/R\" ~/software/R/R-3.4.4/bin/R 
CMD build --no-manual --md5 ~/package/roxyPackage")

i get this error in RKWard:

* checking for file ‘~/package/roxyPackage/DESCRIPTION’ ... OK
* preparing ‘roxyPackage’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR

 *** caught segfault ***
address 0x68, cause 'memory not mapped'

 1: stri_locate_all_regex(string, pattern, omit_no_match = TRUE,     
opts_regex = opts)
 2: stringr::str_locate_all(input, inline.code)
 3: parse_inline(g, patterns)
 4: FUN(X[[i]], ...)
 5: 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$chunk.code)        params.src = 
if (group_pattern(chunk.begin)) {            
stringr::str_trim(gsub(chunk.begin, "\\1", g[1]))        }        else ""        
parse_block(g[-1], g[1], params.src)    }    else parse_inline(g, patterns)})
 6: split_file(lines = text)
 7: process_file(text, output)
 8: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet,     
encoding = encoding)
 9: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = 
10: vweave_rmarkdown(...)
11: engine$weave(file, quiet = quiet, encoding = enc)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: 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)})
16: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault

if i run the same code from a plain R session, it just works like it should:

* checking for file ‘~/package/roxyPackage/DESCRIPTION’ ... OK
* preparing ‘roxyPackage’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
Warnung: ‘inst/doc’ files
    ‘roxyPackage_vignette.Rmd’, ‘roxyPackage_vignette.html’,  
  ignored as vignettes have been rebuilt.
  Run R CMD build with --no-build-vignettes to prevent rebuilding.
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* adding MD5 file
* building ‘roxyPackage_0.06-2.tar.gz’

so i guess it's an issue with RKWard's R console, maybe?

viele grüße :: m.eik

  dipl. psych. meik michalke
  institut f"ur experimentelle psychologie
  abt. f"ur diagnostik und differentielle psychologie
  heinrich-heine-universit"at d-40204 d"usseldorf
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