I updated world after syncing, then did a --depclean, after that followed it with revdep-rebuild, but R keeps on failing at the config stage (complete output of config.log is at http://pastebin.com/793302 for the next month)... checking how to get verbose linking output from gfortran... configure: WARNING: compilation failed checking for Fortran libraries of gfortran... checking how to get verbose linking output from i686-pc-linux-gnu-gcc... -v checking for C libraries of i686-pc-linux-gnu-gcc... -L/usr/lib/gcc/i686-pc-linux-gnu/4.1.1 -L/us/lib/gcc/i686-pc-linux-gnu/4.1.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gn/4.1.1/../../.. -lgcc_s checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... configure: error: cannot compile a simple Fortran proram See `config.log' for more details. !!! Please attach the following file when filing a report to bugs.gentoo.org: !!! /var/tmp/portage/R-2.3.1/work/R-2.3.1/config.log !!! ERROR: dev-lang/R-2.3.1 failed. Call stack: ebuild.sh, line 1546: Called dyn_compile ebuild.sh, line 937: Called src_compile R-2.3.1.ebuild, line 68: Called econf '--enable-nls' '--without-blas' '--without-lapack' '--wih-jpeglib' '--with-libpng' '--with-readline' '--with-x' '--enable-R-profiling' '--enable-R-shlib' --enable-linux-lfs' '--without-tcltk' ebuild.sh, line 540: Called die !!! econf failed !!! If you need support, post the topmost build error, and the call stack if relevant. gcc already had fortran support included, but I tried re-emerging anyway (and sourcing /etc/profile), but no go.
- Attach the config.log here, don't refer to pastebins. - Post emerge --info.
Apologies, here's emerge --info (was informed original posting was too long when I tried to include it). config.log is now attached. Gentoo Base System version 1.12.5 Portage 2.1.2_pre1 (default-linux/x86/2006.1/desktop, gcc-4.1.1, glibc-2.4-r3, 2.6.17-gentoo-r8 i686) ================================================================= System uname: 2.6.17-gentoo-r8 i686 Intel(R) Pentium(R) M processor 1200MHz Last Sync: Fri, 22 Sep 2006 23:50:01 +0000 distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] app-admin/eselect-compiler: [Not Present] dev-java/java-config: 1.3.3, 2.0.29 dev-lang/python: 2.3.5-r2, 2.4.3-r3 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: [Not Present] dev-util/confcache: [Not Present] sys-apps/sandbox: 1.2.18.1 sys-devel/autoconf: 2.13, 2.60 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: 2.17 sys-devel/gcc-config: 1.3.13-r3 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.17-r1 ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="" ARCH="x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-O3 -march=i686 -pipe" CHOST="i686-pc-linux-gnu" CLASSPATH="." CLEAN_DELAY="5" COLORFGBG="default;0" COLORTERM="rxvt" CONFIG_PROTECT="/etc /usr/share/X11/xkb" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/texmf/web2c" CVS_RSH="ssh" CXXFLAGS="-O3 -march=i686 -pipe" DBUS_SESSION_BUS_ADDRESS="unix:abstract=/tmp/dbus-5X9Ab56Xxg,guid=839817456d11bb150075a8d55ce83d00" DCCC_PATH="/usr/lib/distcc/bin" DESKTOP_SESSION="fluxbox" DISPLAY=":0.0" DISTCC_LOG="" DISTCC_VERBOSE="0" DISTDIR="/usr/portage/distfiles" EDITOR="/bin/nano" ELIBC="glibc" EMERGE_DEFAULT_OPTS="--ask --verbose" EMERGE_WARNING_DELAY="10" FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict" FETCHCOMMAND="/usr/bin/wget -t 5 -T 60 --passive-ftp -P ${DISTDIR} ${URI}" FLTK_DOCDIR="/usr/share/doc/fltk-1.1.7/html" GCC_SPECS="" GDK_USE_XFT="1" GDMSESSION="fluxbox" GDM_XSERVER_LOCATION="local" GENTOO_MIRRORS="ftp://ftp.swin.edu.au/gentoo " G_BROKEN_FILENAMES="1" G_FILENAME_ENCODING="UTF-8" HOME="/root" INFOPATH="/usr/share/info:/usr/share/binutils-data/i686-pc-linux-gnu/2.17/info:/usr/share/gcc-data/i686-pc-linux-gnu/3.4.6/info:/usr/share/gcc-data/i686-pc-linux-gnu/4.1.1/info:/usr/share/info/emacs-21" INPUT_DEVICES="keyboard mouse evdev" INSTALL_MASK="TODO.gz" JAVAC="/opt/sun-jdk-1.5.0.06/bin/javac" JAVA_HOME="/opt/sun-jdk-1.5.0.06" JDK_HOME="/opt/sun-jdk-1.5.0.06" KERNEL="linux" LESS="-R -M --shift 5" LESSOPEN="|lesspipe.sh %s" LINGUAS="en_GB" LOGNAME="root" LS_COLORS="no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.mng=01;35:*.pcx=01;35:*.yuv=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.pdf=00;32:*.ps=00;32:*.txt=00;32:*.patch=00;32:*.diff=00;32:*.log=00;32:*.tex=00;32:*.doc=00;32:*.flac=01;35:*.mp3=01;35:*.mpc=00;36:*.ogg=00;36:*.wav=00;36:*.mid=00;36:*.midi=00;36:*.au=00;36:*.flac=00;36:*.aac=00;36:*.ra=01;36:*.mka=01;36:" MAKEOPTS="-j2" MANPATH="/usr/local/share/man:/usr/share/man:/usr/share/binutils-data/i686-pc-linux-gnu/2.17/man:/usr/share/gcc-data/i686-pc-linux-gnu/3.4.6/man:/usr/share/gcc-data/i686-pc-linux-gnu/4.1.1/man::/opt/sun-jdk-1.4.2.10/man:/etc/java-config/system-vm/man/:/usr/qt/3/doc/man:/opt/sun-jdk-1.5.0.06/man" OPENGL_PROFILE="xorg-x11" PAGER="/usr/bin/less" PATH="/sbin:/bin:/usr/sbin:/usr/bin" PKGDIR="/usr/portage/packages" PKG_CONFIG_PATH="/usr/qt/3/lib/pkgconfig" PORTAGE_ARCHLIST="ppc s390 amd64 ppc64 x86-fbsd m68k arm sparc sh mips ia64 alpha ppc-macos hppa x86" PORTAGE_BINHOST_CHUNKSIZE="3000" PORTAGE_BIN_PATH="/usr/lib/portage/bin" PORTAGE_CALLER="emerge" PORTAGE_CONFIGROOT="/" PORTAGE_DEBUG="0" PORTAGE_DEPCACHEDIR="/var/cache/edb/dep" PORTAGE_ELOG_CLASSES="log warn error" PORTAGE_ELOG_MAILFROM="portage" PORTAGE_ELOG_MAILSUBJECT="[portage] ebuild log for ${PACKAGE} on ${HOST}" PORTAGE_ELOG_MAILURI="root" PORTAGE_GID="250" PORTAGE_INST_GID="0" PORTAGE_INST_UID="0" PORTAGE_PYM_PATH="/usr/lib/portage/pym" PORTAGE_RSYNC_EXTRA_OPTS="--exclude-from=/etc/portage/rsync_excludes" 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_RSYNC_RETRIES="3" PORTAGE_TMPDIR="/var/tmp" PORTAGE_WORKDIR_MODE="0700" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage /usr/portage/local/layman/musicbrainz" PRELINK_PATH="" PRELINK_PATH_MASK="/usr/lib/gstreamer-0.10:/usr/lib/gstreamer-0.8:/usr/lib/klibc" PS1="\[\033[01;31m\]\h\[\033[01;34m\] \W \$\[\033[00m\] " PWD="/home/neil/tmp" PYTHONPATH="/usr/lib/portage/pym" QMAKESPEC="linux-g++" QTDIR="/usr/qt/3" RESUMECOMMAND="/usr/bin/wget -c -t 5 -T 60 --passive-ftp -P ${DISTDIR} ${URI}" ROOT="/" ROOTPATH="/opt/bin:/usr/i686-pc-linux-gnu/gcc-bin/4.1.1:/opt/sun-jdk-1.4.2.10/bin:/opt/sun-jdk-1.4.2.10/jre/bin:/opt/sun-jdk-1.4.2.10/jre/javaws:/usr/qt/3/bin" RPMDIR="/usr/portage/rpm" SANE_CONFIG_DIR="/etc/sane.d" SGML_CATALOG_FILES="/etc/sgml/sgml-ent.cat:/etc/sgml/sgml-docbook.cat:/etc/sgml/sgml-docbook-4.1.cat:/etc/sgml/sgml-docbook-4.0.cat:/etc/sgml/dsssl-docbook-stylesheets.cat:/etc/sgml/sgml-docbook-3.0.cat:/etc/sgml/sgml-docbook-3.1.cat:/etc/sgml/xml-docbook-4.1.2.cat:/etc/sgml/xml-docbook-4.4.cat:/etc/sgml/sgml-lite.cat" SHELL="/bin/bash" SHLVL="3" SSH_AGENT_PID="1513" SSH_AUTH_SOCK="/tmp/ssh-eApBZf1494/agent.1494" STAGE1_USE="nptl nptlonly unicode" SYNC="rsync://rsync.au.gentoo.org/gentoo-portage" TERM="rxvt" TERMINFO="/usr/share/terminfo" USB_DEVFS_PATH="/dev/bus/usb" USE="x86 X alsa apache2 arts berkdb bitmap-fonts cairo cdr cli crypt cups dbus div4linux dlloader dri dvd dvdr eds elibc_glibc emacs emboss encode esd fam firefox fortran gdbm geoip gif glx gnome gpm gstreamer gtk gtk2 hal input_devices_evdev input_devices_keyboard input_devices_mouse ipod ipv6 isdnlog jpeg kernel_linux ldap libg++ linguas_en_GB mad mikmod mp3 mpeg ncurses nls nptl nptlonly ogg opengl oss pam pcre perl png ppds pppd python qt qt3 qt4 quicktime readline real reflection scanner sdl session spell spl ssl tcpd truetype truetype-fonts type1-fonts udev unicode usb userland_GNU video_cards_i810 vorbis win32codecs xml xorg xv zlib" USER="root" USERLAND="GNU" USERNAME="neil" USE_EXPAND="CROSSCOMPILE_OPTS DVB_CARDS ELIBC FCDSL_CARDS FOO2ZJS_DEVICES FRITZCAPI_CARDS INPUT_DEVICES KERNEL LINGUAS LIRC_DEVICES MISDN_CARDS USERLAND VIDEO_CARDS" USE_EXPAND_HIDDEN="CROSSCOMPILE_OPTS ELIBC KERNEL USERLAND" USE_ORDER="env:pkg:conf:defaults" VIDEO_CARDS="i810" WINDOWID="16777218" XARGS="xargs -r" XAUTHORITY="/root/.xauthcTdEcM" _="/usr/bin/emerge"
Created attachment 98081 [details] config.log from failed R emerge
Okay, I've managed to fix this, but don't think that things are really resolved since I'm not sure of the cause. Although its clear that the problem doesn't lie with R, but with gcc (and possibly upgrading gcc). It may be that I missed something out during a gcc upgrade (pretty sure I did everything in the upgrade guide), or that there is something wrong with the process of gcc upgrading. $ rm /usr/bin/g77 $ ln -s /usr/i686-pc-linux-gnu/gcc-bin/4.1.1/i686-pc-linux-gnu-g77 /usr/bin/g77 R then emerged no problem.
(In reply to comment #4) > $ rm /usr/bin/g77 > $ ln -s /usr/i686-pc-linux-gnu/gcc-bin/4.1.1/i686-pc-linux-gnu-g77 /usr/bin/g77 > > R then emerged no problem. > This is probably the "infamous" eselect-gcc4-gfortran bug. I am glad you were able to fix it and I'll close this bug as invalid since it is not really R's fault. Please feel free to re-open if there are any remaining issues. Thanks, Markus
