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Date:      Mon, 31 Jul 2017 16:38:07 +0000
From:      bugzilla-noreply@freebsd.org
To:        freebsd-ports-bugs@FreeBSD.org
Subject:   [Bug 221127] math/R: cannot install packages from CRAN
Message-ID:  <bug-221127-13@https.bugs.freebsd.org/bugzilla/>
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D221127

            Bug ID: 221127
           Summary: math/R: cannot install packages from CRAN
           Product: Ports & Packages
           Version: Latest
          Hardware: Any
                OS: Any
            Status: New
          Severity: Affects Only Me
          Priority: ---
         Component: Individual Port(s)
          Assignee: jrm@freebsd.org
          Reporter: rs.os@t-online.de
             Flags: maintainer-feedback?(jrm@freebsd.org)
          Assignee: jrm@freebsd.org

Hello,

recently I discovered an issue by installing a new package from CRAN:
`install.packages("roxygen2")` results in a segfault:

```
...
trying URL 'https://cran.r-project.org/src/contrib/brew_1.0-6.tar.gz'

 *** caught segfault ***
address 0x7fffdfdfe000, cause 'invalid permissions'

Traceback:
 1: download.file(url, destfile, method, mode =3D "wb", ...)
 2: doTryCatch(return(expr), name, parentenv, handler)
 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 4: tryCatchList(expr, classes, parentenv, handlers)
 5: tryCatch(expr, error =3D function(e) {    call <- conditionCall(e)    if
(!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))=20=
=20=20=20=20=20=20=20
    call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <-
paste("Error in", dcall, ": ")        LONG <- 75L        msg <-
conditionMessage(e)        sm <- strsplit(msg, "\n")[[1L]]        w <- 14L +
nchar(dcall, type =3D "w") + nchar(sm[1L], type =3D "w")        if (is.na(w=
))=20=20=20=20=20=20
      w <- 14L + nchar(dcall, type =3D "b") + nchar(sm[1L],                =
 type
=3D "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ") =
   }=20=20
 else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\=
n")=20
  .Internal(seterrmessage(msg[1L]))    if (!silent &&
identical(getOption("show.error.messages"),         TRUE)) {        cat(msg,
file =3D outFile)        .Internal(printDeferredWarnings())    }=20=20=20
invisible(structure(msg, class =3D "try-error", condition =3D e))})
 6: try(download.file(url, destfile, method, mode =3D "wb", ...))
 7: download.packages(pkgs, destdir =3D tmpd, available =3D available,=20=
=20=20=20
contriburl =3D contriburl, method =3D method, type =3D "source",     quiet =
=3D quiet,
...)
 8: install.packages("roxygen2")
```

I tried to install various packages from CRAN. Segfault occurs after
downloading a bunch of dependencies (there is not a certain dependency that
throws this error). I tried the R package from the quarterly branch as well=
 as
the package from the latest branch without any luck. Does this affect more
people? Are there any workarounds?

Best

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