R-2.8.0 build process failed on configure on amd64 stage with the following error: configure: WARNING: I could not determine FPICFLAGS. configure: error: See the file doc/html/R-admin.html for more information. Full build.log is attached. Interesting that running configure from portage tempdir with the same options as for econf makes it to work further and finish successfully. So I suspect some unset/wrongly set environmental variable. ebuild environment is attached too. And this is my emerge --info: Portage 2.2_rc12 (default/linux/amd64/2008.0, gcc-4.3.2, glibc-2.8_p20080602-r0, 2.6.27-sheryl x86_64) ================================================================= System uname: Linux-2.6.27-sheryl-x86_64-Intel-R-_Celeron-R-_CPU_2.53GHz-with-glibc2.2.5 Timestamp of tree: Wed, 29 Oct 2008 16:19:01 +0000 ccache version 2.4 [enabled] app-shells/bash: 3.2_p39 dev-lang/python: 2.5.2-r8 dev-util/ccache: 2.4-r8 dev-util/cmake: 2.6.1 sys-apps/baselayout: 2.0.0 sys-apps/openrc: 0.3.0-r1 sys-apps/sandbox: 1.2.18.1-r3 sys-devel/autoconf: 2.13, 2.63 sys-devel/automake: 1.4_p6, 1.5, 1.8.5-r3, 1.9.6-r2, 1.10.1-r1 sys-devel/binutils: 2.18-r4 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.27-r2 ACCEPT_KEYWORDS="amd64 ~amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -funswitch-loops -fpredictive-commoning -fgcse-after-reload -ftree-vectorize -fomit-frame-pointer -pipe -fstack-protector -fdirectives-only" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /var/bind" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=nocona -O2 -funswitch-loops -fpredictive-commoning -fgcse-after-reload -ftree-vectorize -fomit-frame-pointer -pipe -fstack-protector -fdirectives-only" DISTDIR="/usr/portage/distfiles" FEATURES="ccache collision-protect distlocks parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch userpriv" FFLAGS="-march=nocona -O2 -funswitch-loops -fpredictive-commoning -fgcse-after-reload -ftree-vectorize -fomit-frame-pointer -pipe -fstack-protector -fdirectives-only" GENTOO_MIRRORS="ftp://ftp.chg.ru/pub/Linux/gentoo http://mirror.yandex.ru//gentoo-distfiles http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo" LANG="ru_RU.UTF-8" LC_ALL="" LDFLAGS="-Wl,-O1" LINGUAS="ru en" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage/layman/science /usr/local/portage/layman/sunrise /usr/local/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="aalib acl acpi adns amd64 apache2 bash-completion berkdb blas bluetooth bzip2 caps cdb cli clisp cracklib crypt cscope ctype cups curl curlwrappers cvs cxx cyrillic djvu doc eap-tls editor encode enscript examples exif expat fftw foomaticdb fortran ftp gdbm geoip gif ginac git gmp gnutls gpgme gpm gsl hardened hdf5 iconv idn imap iproute2 ipv6 isdnlog javascript jpeg jpeg2k keyscrub kpathsea lapack latex libcaca libwww lm_sensors logrotate lzo maildir mailwrapper mbox mhash midi mime mmap mmx mng mppe-mppc mudflap multilib mysql mysqli ncurses netcdf nls nntp nocd nptl nptlonly objc objc++ offensive openexr openmp otr pam pch pcntl pcre pdf perl png pop posix ppds pppd python raw readline recode reflection samba scanner session sharedmem slang slp smtp sockets socks5 sparse spell spl sse sse2 sse3 ssl subversion supernodal sysfs syslog szip tcpd threads tiff unicode usb vim-syntax wifi xattr xorg xpm yaz zlib" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="authz_host dir mime" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="ru en" USERLAND="GNU" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 170273 [details] Build log of R-2.8.0
Created attachment 170275 [details] Ebuild environment
I think gcc-4.3.2 plays a part here, because R configures fine on my gcc-4.1.2 amd64 system.
(In reply to comment #3) > I think gcc-4.3.2 plays a part here, because R configures fine on my gcc-4.1.2 > amd64 system. I don't think so. If it is gcc problem, then why in configures fine from command line? Moreover, if you'll take a look at R configure script, it will become obvious that it doesn't set $FPICFLAGS for some reason when invoked from ebuild scripts at my system. Why this variable is not set should be further investigated. Maybe I'll take a look tomorrow.
Please attach your /var/tmp/portage/dev-lang/R-2.8.0/work/R-2.8.0/config.log, and I'll attach one from a system where configure succeeds.
Created attachment 170290 [details] config.log for configure that succeeded (amd64, gcc-4.1.2)
Created attachment 170297 [details] config.log for failed configure
Well, the problem was here: configure:6210: checking whether we are using the GNU Fortran 77 compiler configure:6229: gfortran -c -march=nocona -O2 -funswitch-loops -fpredictive-commoning -fgcse-after-reload -ftree-vectorize -fomit-frame-point cc1: error: -fdirectives-only is incompatible with -traditional f951: warning: command line option "-fdirectives-only" is valid for C/C++/ObjC/ObjC++ but not for Fortran This leads to unset $G77 which leads itself to unset $FPICFLAGS. Whilst -fdirectives-only is both useless and harmless for gfortran, it triggers an incompatibility with -traditional. Currently I disabled this option in make.conf for FFLAGS, previously it was just FFLAGS=$CFLAGS. Perhaps, -fdirectives-only should be filtered out from FFLAGS for R package in ebuild.
(In reply to comment #8) > Currently I disabled this option in make.conf for FFLAGS, previously it was > just FFLAGS=$CFLAGS. Perhaps, -fdirectives-only should be filtered out from > FFLAGS for R package in ebuild. > Thank you very much for your bug report. Based on your findings it seems to me that the main problem is the fact that -fdirectives-only should not be in your FFLAGS in the first place and removing them from your make.conf was indeed the proper action in this case. That said, I'd personally rather not filter this flag in the build (it will probably break other fortran using using ebuilds as well). As far as I can tell, -fdirectives-only isn't even in gfortran's man page (for gcc-4.3.2). Please don't hesitate to re-open this bug if you feel that my assessment of the situation was incorrect. Best, Markus
