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

Dirk Eddelbuettel edd @ending from debi@n@org
Wed May 23 17:40:09 CEST 2018

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)


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 :)


http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

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