Making all in caf make[2]: Entering directory `/var/tmp/portage/sci-biology/mira-3.0.3/work/mira-3.0.3/src/caf' i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.0.3\" -DPACKAGE_STRING=\"mira\ 3.0.3\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.0.3\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -DPUBLICQUIET -DAJ_Linux64 -O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb -I/usr/include -O2 -pthread -I/usr/include -MT caf.o -MD -MP -MF .deps/caf.Tpo -c -o caf.o caf.C In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.3/include/g++-v4/ext/hash_map:59, from ../stdinc/stlincludes.H:72, from ../mira/read.H:40, from caf.H:46, from caf.C:50: /usr/lib/gcc/i686-pc-linux-gnu/4.4.3/include/g++-v4/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. mv -f .deps/caf.Tpo .deps/caf.Po Flexing caf_flexer.flex.C caf_flexer.flex:172: warning, rule cannot be matched caf_flexer.flex:188: warning, rule cannot be matched i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.0.3\" -DPACKAGE_STRING=\"mira\ 3.0.3\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.0.3\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../ -DPUBLICQUIET -DAJ_Linux64 -O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb -I/usr/include -O2 -pthread -I/usr/include -MT caf_flexer.flex.o -MD -MP -MF .deps/caf_flexer.flex.Tpo -c -o caf_flexer.flex.o caf_flexer.flex.C caf_flexer.flex.C: In member function ‘int CAFFlexLexer::yyinput()’: caf_flexer.flex.C:2606: error: ‘EOF’ was not declared in this scope make[2]: *** [caf_flexer.flex.o] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.0.3/work/mira-3.0.3/src/caf' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-biology/mira-3.0.3/work/mira-3.0.3/src' make: *** [all-recursive] Error 1 * ERROR: sci-biology/mira-3.0.3 failed: * died running emake, base_src_make:make * * Call stack: * ebuild.sh, line 54: Called src_compile * environment, line 2942: Called base_src_compile * environment, line 416: Called base_src_make * environment, line 454: Called die * The specific snippet of code: * emake $@ || die "died running emake, $FUNCNAME:make"; * * If you need support, post the output of 'emerge --info =sci-biology/mira-3.0.3', * the complete build log and the output of 'emerge -pqv =sci-biology/mira-3.0.3'. * The complete build log is located at '/var/tmp/portage/sci-biology/mira-3.0.3/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/mira-3.0.3/temp/environment'. * S: '/var/tmp/portage/sci-biology/mira-3.0.3/work/mira-3.0.3' # emerge --info =sci-biology/mira-3.0.3 Portage 2.1.7.17 (default/linux/x86/10.0/desktop, gcc-4.4.3, glibc-2.11-r1, 2.6.33.1 i686) ================================================================= System Settings ================================================================= System uname: Linux-2.6.33.1-i686-Mobile_Intel-R-_Pentium-R-_4_-_M_CPU_1.80GHz-with-gentoo-2.0.1 Timestamp of tree: Mon, 22 Mar 2010 20:15:01 +0000 distcc 3.1 i686-pc-linux-gnu [disabled] app-shells/bash: 4.1_p2 dev-java/java-config: 1.3.7-r1, 2.1.10 dev-lang/python: 2.5.4-r4, 2.6.4-r1, 3.1.1-r1 dev-python/pycrypto: 2.1.0 dev-util/cmake: 2.8.0-r2 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.6.0-r1 sys-apps/sandbox: 2.2 sys-devel/autoconf: 2.13, 2.65 sys-devel/automake: 1.4_p6-r1, 1.5-r1, 1.6.3-r1, 1.7.9-r2, 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.19.1-r1 sys-devel/gcc: 3.3.6-r1, 4.2.4-r1, 4.3.4, 4.4.3 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.32 ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Nero-EULA-US skype-eula" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb /var/bind /var/lib/hsqldb /var/qmail/alias /var/qmail/control /var/vpopmail/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests distlocks fixpackages metadata-transfer news nostrip parallel-fetch protect-owned sandbox sfperms splitdebug strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://gentoo.mirror.web4u.cz" LDFLAGS="-Wl,-O1" LINGUAS="en cs cz" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" 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/sunrise /usr/local/portage/layman/x11 /usr/local/portage/layman/science /usr/local/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="32bit 7zip R X Xaw3d a52 aac aalib ace acl acpi alsa amr amrnb amrwb apache audacious audiofile bash-completion bcmath berkdb blas bluetooth boost branding bzip2 cairo caps cblas cddb cdparanoia cdr clamav cli colordiff compress consolekit cpio cracklib crypt cscope css ctype cups curl curlwrappers cxx dbi dbus dga dia directfb djbfft dri dts dv dvb dvd dvdr dvdread eds emacs emboss emf enblend encode enscript exif expat faad fam fame fat fbcon ffmpeg fftw firefox flac flash fortran fpx ftp gcj gd gdbm ggi gif gimp gimpprint glibc-compat20 glibc-omitfp glut gmp gnuplot gnutls gpgme gphoto2 gpm graphviz gs gsl gsm gstreamer gtk gtkhtml hal hdf hdf5 hp2xx i8x0 icc iconv icu id3 ieee1394 ifc imagemagick imlib inifile innodb ithreads jack java javascript jbig jce jikes jpeg jpeg2k kdtree kerberos lame lapack laptop lcms leim libcaca libedit libnotify libwww live lzo lzw mad maildir matroska mhash mikmod mime ming mjpeg mmap mmx mng mod_python modperl modplug modules motif mozilla moznoirc mp2 mp3 mp4 mpeg mpi mpi_njtree mpich2 mplayer mudflap mule musepack mxdatetime mysql mysqli ncurses netcdf netpbm network nls nntp nptl nptlonly nsplugin ntfs numeric ogg opengl openmp openssl pam pango pcmcia pcntl pcre pdf perl plotutils plugin png pnm postproc postscript ppds pppd procmail pymol python qt3support qt4 quicktime rar raw readline recode reflection reiserfs romio rpm samba sasl scanner scp seamonkey server session sftp sift slp smime sndfile soap sockets spell spl sqlite srt sse sse2 ssl startup-notification subtitles subversion svg svgz sysfs sysvipc t1lib tcl tcpd tetex theora threads thunar tidy tiff tk transcode truetype unicode urandom usb userlocales utils uuencode v4l v4l2 vcd vhook vim-syntax vim-with-x vorbis wifi win32codecs wmf wxwindows x264 x86 xanim xcf xfs xft xinerama xinetd xml xorg xpm xsl xslt xulrunner xv xvid xvmc yv12 zip zlib" ALSA_CARDS="intel-8x0m" 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="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config mem_cache mime mime_magic rewrite setenvif speling status unique_id userdir usertrack vhost_alias negotiation" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en cs cz" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="radeon vesa" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS # flex --version flex 2.5.35 #
Created attachment 225387 [details, diff] mira-3.0.3-flex.patch Upstream patch, works, please commit.
Such fix should go into source file, not a generated one.
As there's the best place seems to be right under '#include "caf_tokens.h"' in src/caf/caf_flexer.flex (and *perhaps* it should actually be <cstdio>).
Created attachment 225525 [details, diff] mira-3.0.3-flex.patch Patched to fix the source files instead. Tested by me, acknowledged by upstream to be in committed into cvs.
(In reply to comment #4) > Created an attachment (id=225525) [details] > mira-3.0.3-flex.patch > > Patched to fix the source files instead. Tested by me, acknowledged by upstream > to be in committed into cvs. > Forget this patch for 3.0.3 ebuild and go for 3.0.5 bugfix release instead.
Fixed with version bump
