Hi, here is a an improved ebuild to cope with current structure of the source archive. Unfortunately the CXXFLAGS variable is somehow single-quoted by emerge, I do not know why. Because of that compilation fails. If I omit the CXXFLAGS setting the package compiles with plain -O3. The src_install() needs some fix so that the probconsRNA is found&installed. Personally I do not like binaries installed in /usr/lib/mafft/ but even currenmt ebuild does that/ The readme file mentions ENV variable which could be set if the binaries are placed in another location. Thanks for educating me. ;-)
from the src_install part ... [cut] sed "s:_LIBDIR:/usr/lib/mafft/lib/mafft:" mafft.tmpl > mafft sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-homologs.tmpl > mafft-homologs.rb cp mafft mafft-homologs.rb ../scripts chmod 755 ../scripts/* cp dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen score getlag dndpre dndpre2 setcore mafft.1 mafft-homologs.1 ../binaries chmod 755 ../binaries/* done. make PREFIX=/usr/lib/mafft CXX=i686-pc-linux-gnu-g++ 'CXXFLAGS=-O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb' make CPP=g++ CFLAGS1="-O3 " -C mxscarna_src make[1]: Entering directory `/var/tmp/portage/sci-biology/mafft-6.707/work/mafft-6.707-with-extensions/extensions/mxscarna_src' i686-pc-linux-gnu-g++ -O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb -c -o Main.o Main.cc Main.cc:8:24: error: SafeVector.h: No such file or directory Main.cc:9:27: error: MultiSequence.h: No such file or directory Main.cc:10:22: error: Defaults.h: No such file or directory Main.cc:11:23: error: ScoreType.h: No such file or directory Main.cc:12:32: error: ProbabilisticModel.h: No such file or directory Main.cc:13:30: error: EvolutionaryTree.h: No such file or directory Main.cc:14:26: error: SparseMatrix.h: No such file or directory [cut] # emerge --info Portage 2.1.6.13 (default/linux/x86/2008.0/desktop, gcc-4.3.3, glibc-2.10.1-r0, 2.6.29.3 i686) ================================================================= System uname: Linux-2.6.29.3-i686-Mobile_Intel-R-_Pentium-R-_4_-_M_CPU_1.80GHz-with-gentoo-2.0.1 Timestamp of tree: Mon, 13 Jul 2009 09:45:02 +0000 distcc 3.1 i686-pc-linux-gnu [disabled] app-shells/bash: 4.0_p24 dev-java/java-config: 1.3.7-r1, 2.1.8-r1 dev-lang/python: 2.5.4-r3, 2.6.2-r1 dev-python/pycrypto: 2.0.1-r8 dev-util/cmake: 2.6.4 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.4.3-r3 sys-apps/sandbox: 2.0 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11 sys-devel/binutils: 2.19.1-r1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.30 ACCEPT_KEYWORDS="x86 ~x86" 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 /var/bind /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 /etc/udev/rules.d" CXXFLAGS="-O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages metadata-transfer nostrip parallel-fetch protect-owned sandbox sfperms splitdebug strict 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/science /usr/local/portage/layman/sunrise /usr/local/portage/layman/java-overlay /usr/local/portage /usr/local/java-experimental /usr/local/portage/layman/java-overlay" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="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 cblas cddb cdparanoia cdr clamav cli colordiff compress 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 fam fame fat fbcon ffmpeg fftw firefox flac flash foomaticdb 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 isdnlog 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 midi mikmod mime ming mjpeg mmap mmx mng mod_python modperl modplug 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 pam pango pcmcia pcntl pcre pdf perl plotutils plugin png pnm postproc postscript ppds pppd procmail pymol python qt3 qt3support qt4 quicktime rar raw readline recode reflection reiserfs 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 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" 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
Created attachment 198705 [details] mafft-6.707.ebuild
Thanks for submitting your updated ebuild! Assigning to maintainers.
Created attachment 198943 [details] mafft-6.707.ebuild Cleaned up ebuild. Come on Martin, you know how to write good ebuilds :) The extensions compile crashes, and I don't have time to debug it right now, so if someone can fix it it would be awesome. <snip> make -j8 -C extensions PREFIX=/usr/lib64/mafft CXX=x86_64-pc-linux-gnu-g++ 'CXXFLAGS=-march=native -O2 -pipe' make: Entering directory `/var/tmp/portage/sci-biology/mafft-6.707/work/mafft-6.707-with-extensions/extensions' make CPP=g++ CFLAGS1="-O3 " -C mxscarna_src make[1]: Entering directory `/var/tmp/portage/sci-biology/mafft-6.707/work/mafft-6.707-with-extensions/extensions/mxscarna_src' x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -c -o Main.o Main.cc x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -c -o McCaskill.o McCaskill.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -c -o vienna/energy_param.o vienna/energy_param.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -c -o seq2scs.o seq2scs.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -c -o Globaldp.o Globaldp.cpp x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -c -o postProcessings.o postProcessings.cpp Main.cc:8:24: error: SafeVector.h: No such file or directory Main.cc:9:27: error: MultiSequence.h: No such file or directory Main.cc:10:22: error: Defaults.h: No such file or directory Main.cc:11:23: error: ScoreType.h: No such file or directory Main.cc:12:32: error: ProbabilisticModel.h: No such file or directory Main.cc:13:30: error: EvolutionaryTree.h: No such file or directory Main.cc:14:26: error: SparseMatrix.h: No such file or directory seq2scs.cpp:8:24: error: SafeVector.h: No such file or directory seq2scs.cpp:10:22: error: Sequence.h: No such file or directory seq2scs.cpp:11:27: error: MultiSequence.h: No such file or directory In file included from seq2scs.cpp:12: BPPMatrix.hpp:12:26: error: SparseMatrix.h: No such file or directory x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -c -o AlifoldMEA.o AlifoldMEA.cpp In file included from BPPMatrix.hpp:13, from Main.cc:15: McCaskill.hpp:14:29: error: energy_param.hpp: No such file or directory In file included from Main.cc:17: Globaldp.hpp:18:22: error: Sequence.h: No such file or directory In file included from BPPMatrix.hpp:13, from seq2scs.cpp:12: McCaskill.hpp:14:29: error: energy_param.hpp: No such file or directory In file included from McCaskill.cpp:2: McCaskill.hpp:14:29: error: energy_param.hpp: No such file or directory In file included from Globaldp.cpp:1: Globaldp.hpp:17:27: error: MultiSequence.h: No such file or directory <snip>
I know why there are the problems. The Makefiles force CC=gcc and CFLAGS in them contain include paths to headers, set -DNDEBG -DVERSION and many others. I have emailed upstream on this.
Created attachment 199524 [details] mafft-6.707.ebuild This should be working as upstream fixed the two Makefiles. For unknown reason, emerge misquotes for me the CFLAGS, why? >>> Compiling source in /var/tmp/portage/sci-biology/mafft-6.707/work/mafft-6.707-with-extensions ... make -C core PREFIX=/usr/lib/mafft CC=i686-pc-linux-gnu-gcc 'CFLAGS=-O2 -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb'
Created attachment 199526 [details] Makefile1
Created attachment 199528 [details] Makefile2
No, the last ebuild has still some flaw, Andrey?, please ... >>> Completed installing mafft-6.707 into /var/tmp/portage/sci-biology/mafft-6.707/image/ ecompressdir: bzip2 -9 /usr/lib/mafft/man * QA Notice: // installed in ${D}/${D} * QA Notice: //usr installed in ${D}/${D} * QA Notice: //usr/lib installed in ${D}/${D} * QA Notice: //usr/lib/mafft installed in ${D}/${D} * * ERROR: sci-biology/mafft-6.707 failed. * Call stack: * misc-functions.sh, line 729: Called install_qa_check * misc-functions.sh, line 281: Called die * The specific snippet of code: * die "Aborting due to QA concerns: ${INSTALLTOD} files installed in ${D}/${D}" * The die message: * Aborting due to QA concerns: 4 files installed in /var/tmp/portage/sci-biology/mafft-6.707/image///var/tmp/portage/sci-biology/mafft-6.707/image/
Created attachment 200249 [details] Makefile1
Created attachment 200250 [details] Makefile2
The Makefiles are now fixed to respect CC, CXX, CFLAGS and CXXFLAGS. and will be in an upcoming upstream release. The ebuild src_install() step is still somehow wrong (QA issue), Andrey, would you please have a look into this? Quoting from my communication with Kazutaka Katoh: <quote> Indeed, in the new makefile, "-finline-limit=20000" is overridden if user specifies CXXFLAGS. The best threshold to make functions inline probably depends on CPU type and version of compiler. So I think it is better not to force this for a user who wants to specify CFLAGS. The '-DNDEBUG -DNumInsertStates=1 -DVERSION="2.0"' flags are always necessary. As for your second mail, the executables are installed into /usr/local/lib/mafft/, instead of into /usr/local/bin/. These executables are called by the mafft script, but not directly used by users. The main program, mafft (a shell script), is installed into /usr/local/bin/. </quote> I am not certain whether we want to keep executables in /usr/lib/mafft/ on Gentoo, though.
Created attachment 201591 [details] mafft-6.709.ebuild Upstream released a fix version 6.709. The ebuild now is finally working and has clean output. It can go into the testing tree.
Already higher version in the tree
