Bugzilla Bug 152379

The R Installation and Administration manual:
    http://cran.r-project.org/doc/manuals/R-admin.html
recommends setting -std=gnu99 in CFLAGS in /usr/lib/R/etc/Makeconf 
but the current ~x86 ebuild of dev-lang/R (for R 2.4.0) does not do so. This
causes compilation failures when installing certain R packages that depend on
C99. More details at
    http://www.laakshmi.com/aarre/wiki/index.php/Incident_2006-10-21.01
if you want them.



laakshmi portage # emerge --info
Portage 2.1.1 (default-linux/x86/2006.0, gcc-3.4.6, glibc-2.4-r3,
2.6.17-gentoo-r4 i686)
=================================================================
System uname: 2.6.17-gentoo-r4 i686 AMD Athlon(tm) processor
Gentoo Base System version 1.12.5
Last Sync: Wed, 11 Oct 2006 21:00:08 +0000
ccache version 2.3 [enabled]
app-admin/eselect-compiler: [Not Present]
dev-java/java-config: 1.2.11-r1
dev-lang/python:     2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     2.3
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.59-r7
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.13-r4
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r1
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-march=athlon-tbird -O3 -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.4/env /usr/kde/3.4/share/config
/usr/kde/3.4/shutdown /usr/kde/3.5/env /usr/kde/3.5/share/config
/usr/kde/3.5/shutdown /usr/lib/mozilla/defaults/pref /usr/share/X11/xkb
/usr/share/config /usr/share/texmf/dvipdfm/config/
/usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/
/usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/"
CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-march=athlon-tbird -O3 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig ccache distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="ftp://ftp.ussg.iu.edu/pub/linux/gentoo
http://distfiles.gentoo.org
http://www.ibiblio.org/pub/Linux/distributions/gentoo"
LINGUAS=""
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress
--force --whole-file --delete --delete-after --stats --timeout=180
--exclude='/distfiles' --exclude='/local' --exclude='/packages'"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="x86 X aac aim alsa apache2 apm arts bash-completion berkdb bitmap-fonts
blas bzip2 canna cdparanoia cdr cjk cli crypt cups curl dlloader dri dv eds
elibc_glibc emacs emacs-w3 emboss encode esd examples exif ffmpeg fftw flac
font foomaticdb fortran gd gdbm gif gnome gnuplot gpm graphviz gs gstreamer gtk
gtk2 imagemagick imap imlib input_devices_keyboard input_devices_mouse isdnlog
java javascript jbig jpeg jpeg2k kde kdeenablefinal kernel_linux lapack leim
libg++ libwww lm_sensors mad maildir mbox mikmod mmx motif mozilla mp3 mpeg msn
mule mysql mysqli ncurses nls nptl nptlonly offensive ofx ogg opengl oss pam
pcre pdf perl php plotutils png pppd python qt qt3 qt4 quicktime readline
reflection samba sasl sdl session spell spl ssl svg symlink tcltk tcpd tetex
tidy tiff truetype truetype-fonts type1-fonts udev unicode usb userland_GNU
video_cards_fbdev video_cards_nvidia video_cards_vesa vorbis win32codecs wmf
wxwindows xcomposite xemacs xml xmms xorg xscreensaver xv xvid yahoo zlib"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS,
PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

Hi  Aarre,

Thanks for pointing this out! I looked into this and it indeed looks
like we should append -std=gnu99 to CFLAGS. I've just changed
this in the ebuild for R-2.4.0.

Thanks,
Markus

Can we do -std=c99 instead, or does it actually use the gnu-specific
extensions?

(In reply to comment #2)
> Can we do -std=c99 instead, or does it actually use the gnu-specific
> extensions?
> 

Their docs state that ".. the C compiler should be IEC 600596, POSIX 1003.1 
and C99-compliant..". As far as I know, std=c99 will not cover POSIX compliance
but std=gnu99 will. I might be wrong though.

Thanks,
Markus

A little searching suggests you are right, but I couldn't actually find it
anywhere in official documentation.

I see that this is marked "RESOLVED FIXED" (thank you!) but FYI (or in case it
should come up again), the R Installation and Administration manual (downloaded
10/28/06 3:40am EDT):
    http://cran.r-project.org/doc/manuals/R-admin.html
which is "official documentation", states specifically and clearly that
-std=gnu99 as opposed to -std=c99 is required because of POSIX compliance:

"You need a means of compiling C and FORTRAN 77 (see Using FORTRAN). Some
add-on packages also need a C++ compiler. Your C compiler should be IEC 600596,
POSIX 1003.1 and C99-compliant if at all possible. R tries to choose suitable
flags for the C compilers it knows about, but you may have to set CFLAGS
suitably. For recent versions of gcc with glibc this means including -std=gnu99
in CFLAGS (-std=c99 excludes POSIX functionality)."

Oh, and keep in mind that this CFLAGS setting (in /usr/lib/R/etc/Makeconf) is
used *only* for compiling R add-on packages. It does not affect your
environment CFLAGS, so will not cause changes with compiling anything other
than R add-on packages.