[R-pkg-devel] Compiled code checks raise a WARNING in Fedora 28

[Iñaki Úcar]

2018-05-23 17:40 GMT+02:00 Dirk Eddelbuettel <edd at debian.org>:
>
> On 23 May 2018 at 17:22, Iñaki Úcar wrote:
> | Hi,
> |
> | For other Fedora users that may be struggling with this too...
> |
> | Fedora 28 introduced new hardening flags for compiled code (see [1]).
> | Particularly, -D_GLIBCXX_ASSERTIONS is added to the default CXXFLAGS
> | (verify the output of 'R CMD config CXXFLAGS'), which enables range
> | checks for C++ arrays, vectors and strings. As a consequence, you may
> | see the following after running 'R CMD check' on your package with C++
> | code:
> |
> | checking compiled code ... WARNING
> | Found ‘abort’, possibly from ‘abort’ (C)
> | Found ‘printf’, possibly from ‘printf’ (C)
> |
> | I'm not sure whether this is a false positive or not. Anyway, a quick
> | workaround is to disable this flag by including -U_GLIBCXX_ASSERTIONS
> | in your local Makevars.
>
> AFAICT that has little do with Fedora, it is just R being picky. Writing R
> Extensions told you about abort() et al for years:
>
>   Under no circumstances should your compiled code ever call @code{abort}
>   or @code{exit}@footnote{or where supported the variants @code{_Exit} and
>   @code{_exit}.}: these terminate the user's @R{} process, quite possibly
>   including all his unsaved work.  One usage that could call @code{abort}
>   is the @code{assert} macro in C or C++ functions, which should never be
>   active in production code.  The normal way to ensure that is to define
>   the macro @code{NDEBUG}, and @command{R CMD INSTALL} does so as part of
>   the compilation flags.  If you wish to use @code{assert} during
>   development. you can include @code{-UNDEBUG} in @code{PKG_CPPFLAGS}.
>   Note that your own @file{src/Makefile} or makefiles in sub-directories
>   may also need to define @code{NDEBUG}.
>
> (Quoted from R-release's manual source)

Yes, I know. The thing is that, with -D_GLIBCXX_ASSERTIONS, I see

$ strings src/*.o | grep abort | sort | uniq
abort
__builtin_abort
__cxa_guard_abort

and without it, the first two lines go away. So it seems that those
assertions may result in a call to 'abort'. I don't know whether R is
right or not in its *pickiness* for this particular case.

Iñaki

>
> Also:
>
> edd at rob:~/deb/r-base$ ag "Found " src/library/tools/R/sotools.R
> 481:                 c(strwrap(gettextf("Found %s, possibly from %s",
> 702:              strwrap(paste("Found non-API calls to R:",
> 705:          } else paste("  Found non-API call to R:", sQuote(x))
> 716:              strwrap(paste("Found no calls to:",
> 719:          } else paste("  Found no call to:", sQuote(x))
> edd at rob:~/deb/r-base$
>
> I am kinda surprised you had not seen these before :)
>
> Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org